Catalogue of Molecular Biology Programs Release 6.1 23 Jul 1999 All thanks are in the file biocatal.thanks. ===================================================================== AC BC00121 NAME AMPAC with Graphical User Interface DOMAIN Molecular modelling and graphics DESCRIPTION Semiempirical Quantum mechanical methods DESCRIPTION Input_Format: MOPAC, AMPAC, cartesian DESCRIPTION Output_Format: MOPAC, AMPAC DESCRIPTION Molecular_Model: wire, ball_and_stick DESCRIPTION Output_Type: display, AUTHOR Andy Holder RT - ADDRESS President, Semichem / Prof., U. of Missouri-KC ADDRESS Tel: (913)268-3271 ADDRESS Fax: (913)268-3445 CONTACT aholder@vax1.umkc.edu SITE - SITE-CONTACT - OS Unix, VMS OS IBM RS/6000, SGI, VAX, DECStation, Alpha AXP, Convex, Cray, HP LANGUAGE Graphic_Library: X11 VOLUME - REQUIRES - COMMENTS - AC BC00122 NAME ATOMTV DOMAIN Molecular modelling and graphics DESCRIPTION atomic trajectories DESCRIPTION Input_Format: cartesian coordinates DESCRIPTION Molecular_Model: shaded spheres DESCRIPTION Output_Type: display, sgi rgb images, rayshade scene description AUTHOR Rudy Ziegler RT - ADDRESS University of Toronto Instructional and Research Computing CONTACT rudy@utirc.utoronto.ca SITE ftp anonymous ftp.utirc.utoronto.ca SITE Directory /pub/atomtv SITE-CONTACT - OS Irix OS SGI (tested on Indigo^2 Extreme and 4D70GT, should run on others) LANGUAGE Graphic_Library: GL VOLUME - REQUIRES - COMMENTS - AC BC00123 NAME BABEL DOMAIN Molecular modelling and graphics DESCRIPTION file conversion DESCRIPTION Input_Format: Mopac Cartesian Mopac Internal Mopac Output DESCRIPTION Input_Format: CSD GSTAT CSD CSSR Free Form Fractional DESCRIPTION Input_Format: Macromodel MM2 Output PDB DESCRIPTION Input_Format: Alchemy XYZ Mac Molecule DESCRIPTION Input_Format: Chem3D MicroWorld Ball and Stick DESCRIPTION Input_Format: MOLIN DESCRIPTION Output_Format: Mopac Cartesian Mopac Internal Gaussian Input DESCRIPTION Output_Format: IDATM Macromodel Mac Molecule DESCRIPTION Output_Format: MM2 Input MM2 Ouput PDB file DESCRIPTION Output_Format: Report of interatiomic distances,angles,and torsions DESCRIPTION Output_Format: Alchemy XYZ Ball and Stick DESCRIPTION Output_Format: Chem3D MicroWorld AUTHOR Pat Walters RA Shah A.V., Walters W.P., Shah R., Dolata D.P.; RT "Babel a Tool for Converting Between Molecular RT Data Formats"; RL Computerized Chemical Data Standards :Databases,Data Interchange, RL and Information Systems, RL ASTM Philadelphia (1994), STP 1214, RL R. Lysakowski and C. E. Gragg, Eds. ADDRESS Dept. of Chemistry University of Arizona CONTACT babel@mercury.aichem.arizona.edu SITE ftp anonymous joplin.biosci.arizona.edu SITE Directory /pub/Babel SITE-CONTACT - OS Unix (AIX, Ultrix, Sun-OS, Convex, SGI, Cray, Linux), MS-DOS OS Macs running at least System 7.0 LANGUAGE - VOLUME - REQUIRES - COMMENTS - AC BC00124 NAME FLEX DOMAIN Molecular modelling and graphics DESCRIPTION Flex is a simple,. portable molecular graphics program DESCRIPTION that interactively displays 3D ball-and-stick models DESCRIPTION on workstations runn the X-window system. AUTHOR - RT - ADDRESS The Computational Center for Macromolecular Structure (CCMS) ADDRESS USA CONTACT ccms-request@sdsc.edu (listserver) CONTACT ccms-help@sdsc.edu (human) SITE WWW server at URL http://www.sdsc.edu/1/Parts_Collabs/CCMS SITE-CONTACT - OS Unix LANGUAGE - VOLUME - AC BC00125 NAME GCI DOMAIN Molecular modelling and graphics DESCRIPTION A network server for interactive 3D graphics AUTHOR Tuparev G., Vriend, G. and Sander C. RA Tuparev G., Vriend G., Sander C.; RT "GCI - A network server for interactive 3d graphics."; RL J. Mol. Graphics 10:12-16(1992). RX SeqAnalRef; TUPG9201. ADDRESS European Molecular Biology Laboratory ADDRESS Meyerhofstrasse 1, 69117 Heidelberg, Germany CONTACT vriend@embl-heidelberg.de SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix UNIX software are stored SITE as archive (tar) files compressed (.Z). SITE-CONTACT nethelp@ebi.ac.uk OS Unix LANGUAGE C VOLUME - AC BC00126 NAME INTERCHEM DOMAIN Molecular modelling and graphics DESCRIPTION simple_molecule, drug, crystal, protein, nucleic acid, inorganic DESCRIPTION Input_Format: PDB, CSD, XYZ, MOPAC, Gamess-UK, Interchem, DESCRIPTION Input_Format: Sybyl, Insight, MDL-mol DESCRIPTION Input_Format: Structure_building, Protein_Sequence DESCRIPTION Output_Format: PDB, CSD, XYZ, MOPAC, Gamess-UK, Interchem, Sybyl, Insight DESCRIPTION Molecular_Model: wire, stick, stick_and_ball, CPK, ribbon, alpha_trace, DESCRIPTION Molecular_Model: Red_Green_Stereo_options DESCRIPTION Output_Type: display, SGI-rgb AUTHOR Peter Bladon RL QCPE_Bulletin 13:1(1993). ADDRESS University_of_Strathclyde, Glasgow, Scotland, G66 4HX ADDRESS Tel: +44-41-776-1718 ADDRESS Fax: +44-41-776-1718 CONTACT cbas25@vaxa.strathclyde.ac.uk SITE - SITE-CONTACT - OS Unix (Irix 4.0.x) OS SGI-4D20/25/35, SGI-Indigo, SGI-Indigo-2, SGI-Indy LANGUAGE Graphic_Library: GL VOLUME - REQUIRES - COMMENTS - AC BC00127 NAME Insight II DOMAIN Molecular modelling and graphics DESCRIPTION Simple_Molecule, Drug, Crystal, Polymer, Protein, Inorganic, DESCRIPTION Biopolymer,Molecular Mechanics, Semi Empirical Quantum Mechanics, DESCRIPTION ab initio Quantum Mechanics DESCRIPTION Molecular Dynamics, Model Building, Crystallography, Solvation, DESCRIPTION NMR Analysis & Refinement, Sample Characterization, Powder Diffraction, DESCRIPTION Single Crystal Diffraction, Fiber Diffraction, DESCRIPTION 29Si NMR, EXAFS Simulation, DESCRIPTION Rietveld Refinement, Model Building, IR Simulation DESCRIPTION Crystallite Morphology, Born Model Calculation, Reaction Kinetics DESCRIPTION 2d-3d Database Conversion, Small Molecule Analysis, DESCRIPTION Structure Activity Relationships DESCRIPTION Protein Homology Modelling, Receptor Site Analysis, Open Interface DESCRIPTION Molecular_Model: wire, stick, stick_and_ball, CPK, ribbon, DESCRIPTION Molecular_Model: alpha_trace, generalized polyhedra DESCRIPTION Input_Format: PDB, CSD, XYZ, MOPAC, BIOSYM, MDL, SYBIL MOL2, USER DEFINED DESCRIPTION Output_Format: PDB, CSD, XYZ, MOPAC, SYBIL MOL2, MDL, USER DEFINED DESCRIPTION Output_Type: display, PostScript, HPGL, PICT, Encapsulated PostScript AUTHOR Clive Freeman RT - ADDRESS BIOSYM's Catalysis and Sorption Project ADDRESS Tel: +1-619-458-9990 (international number of the headquarters) ADDRESS Fax: +1-619-458-0136 CONTACT clive@biosym.com SITE - SITE-CONTACT - OS Unix OS IBM RS/6000, SGI LANGUAGE Graphic_Library: GL, X11 VOLUME - REQUIRES - COMMENTS - AC BC00128 NAME MODELLER DOMAIN Molecular modelling and graphics DESCRIPTION Modeller is most frequently used for homology or comparative DESCRIPTION modeling of protein three dimensional structure: the user provides DESCRIPTION an alignment of a sequence to be modeled with known related DESCRIPTION structures and MODELLER will automatically calculate a DESCRIPTION full-atom model. More generally, MODELLER models protein 3D DESCRIPTION structure by satisfaction of spatial restraints. In principle, DESCRIPTION the restraints can be derived from a number of different sources. DESCRIPTION These include homologous structures (comparative modeling), DESCRIPTION NMR experiments (NMR refinement), rules of secondary structure DESCRIPTION packing (combinatorial modeling), cross-linking experiments, DESCRIPTION fluorescence spectroscopy, image reconstruction in electron DESCRIPTION microscopy, site-directed mutagenesis, intuition, residue-residue DESCRIPTION atom-atom potentials of mean force, etc. DESCRIPTION The output of MODELLER is a 3D structure of a protein that satisfies DESCRIPTION these restraints as well as possible. The optimization is carried DESCRIPTION out by the variable target function procedure employing methods of DESCRIPTION conjugate gradients and molecular dynamics with simulated annealing. DESCRIPTION The program includes a 100-page manual. AUTHOR Andrej Sali RA Sali A., Blundell T.L.; RT "Comparative protein modelling by satisfaction of spatial restraints."; RL J. Mol. Biol. 234:779-815(1993). RX Medline; 94076350. RX SeqAnalRef; SALA9301. ADDRESS Box 270, The Rockefeller University,1230 York Avenue, ADDRESS New York, NY 10021, USA. ADDRESS Tel: +1 (212) 327 7550. Fax: +1 (212) 327 7540 CONTACT sali@rockvax.rockefeller.edu SITE ftp anonymous guitar.rockefeller.edu SITE Directory /pub/modeller SITE-CONTACT - SITE ftp anonymous ftp.icgeb.trieste.it SITE Directory /pub/modeller SITE-CONTACT - OS Unix LANGUAGE FORTRAN VOLUME - REQUIRES An encryption key to unpack the distribution file COMMENTS Print and sign the licence form (academic-license.ps) and mail or COMMENTS fax it to Andrej Sali. You will then receive the encryption key COMMENTS (MODELLER_KEY) with which you will be able to unpack the COMMENTS encrypted distribution file. AC BC00129 NAME MOIL-View DOMAIN Molecular modelling and graphics DESCRIPTION Protein, user_definable_parameters DESCRIPTION Input_Format: PDB,CRD DESCRIPTION Molecular_Model: wire, sphere, ribbon, any_combination DESCRIPTION Output_Type: display, Postscript AUTHOR Carlos Simmerling RT - ADDRESS University_of_IL_at_Chicago ADDRESS Tel: 1-312-996-4737 ADDRESS Fax: 1-312-996-0431 CONTACT carlos@pap.chem.uic.edu SITE ftp anonymous sheep0.chem.uic.edu SITE Directory /dist SITE-CONTACT - OS Unix OS IBM RS/6000, SGI LANGUAGE Graphic_Library: GL VOLUME - REQUIRES - COMMENTS - AC BC00130 NAME MOLEKEL DOMAIN Molecular modelling and graphics DESCRIPTION Organic, inorganic, organometallic, protein, visualization DESCRIPTION of computational results (orbitals, density, mep, dynamics) DESCRIPTION Input_Format: PDB, Gaussian-, DeMon-, ExtHuc-, Charmm-, DESCRIPTION and other output files DESCRIPTION Output_Format: PDB and surface description files DESCRIPTION Molecular_Model: wire, stick, stick_and_ball, CPK, surfaces DESCRIPTION Output_Type: display, SGI-rasterfile AUTHOR Dr. Peter F. Fluekiger RA Fluekiger P.F.; RL CrossCuts 2:4(1993). RL (Newsletter of the Swiss Scientific Computing Center) ADDRESS Swiss Scientific Computing Center ADDRESS Tel: +41-91-50 82 05 ADDRESS Fax: +41-91-50 67 11 CONTACT Dr. Peter F. Fluekiger CONTACT flukiger@cscs.ch SITE ftp anonymous pobox.cscs.ch SITE Directory /pub/CSCS/graphics/molekel SITE-CONTACT - OS Unix OS SGI-workstation (from Indy to RE2) LANGUAGE Graphic_Library: GL VOLUME - REQUIRES - COMMENTS - AC BC00131 NAME MOLVIEWER DOMAIN Molecular modelling and graphics DESCRIPTION MolViewer is a program designed to display 3D views of molecules DESCRIPTION and allow you to play around with them interactively. A lot of DESCRIPTION the features center on protein chemistry, but the program is DESCRIPTION still quite useful for other molecules as well AUTHOR Steve Ludtke RT - ADDRESS - CONTACT Steve Ludtke: steve@ion.rice.edu SITE ftp anonymous ion.rice.edu (128.42.70.6) SITE Directory /pub SITE-CONTACT Steve Ludtke: steve@ion.rice.edu OS run only under NeXTStep 3.0. LANGUAGE - VOLUME - AC BC00132 NAME MSP DOMAIN Molecular modelling and graphics DESCRIPTION "MSP" (Molecular Surface Package) can be licensed (Academic DESCRIPTION pricing). The package will render vertices, edges, and triangles DESCRIPTION of a molecular surface polyhedron; pixel map of RGB values for a DESCRIPTION rendered surface and model; calculate contact, reentrant, molecular, DESCRIPTION and accessible area of each atom;and list cavities:centroid, volume, DESCRIPTION area, and bordering atoms. It has lots of other capabilities as well. AUTHOR Dr. Michael Connolly RA Connolly M.L.; RT "The molecular-surface package."; RL J. Mol. Graphics 11:139-141(1993). ADDRESS Tel: (1) (415) 346-3505 ADDRESS FAX: (1) (415) 922-0149 CONTACT connolly@netcom.com SITE - SITE-CONTACT - OS - LANGUAGE C VOLUME - REQUIRES - AC BC00133 NAME MacroModel DOMAIN Molecular modelling and graphics DESCRIPTION simple_molecule, drug, protein, polynucleotide DESCRIPTION Input_Format: macromodel, PDB DESCRIPTION Output_Format: PDB, macromodel DESCRIPTION Molecular_Model: wire, stick_and_ball, polytube, CPK, alpha_trace DESCRIPTION Output_Type: display, PostScript AUTHOR F. Mohamadi et al. RA Mohamadi F., Richards N.G.J., Guida W.C., Liskamp R., Lipton M., RA Caufield C., Chang G., Hendrickson T., Still W.C.; RT "Macromodel - an integrated software system for modeling organic RT and bioorganic molecules using molecular mechanics."; RL J. Comput. Chem. 11:440(1990). ADDRESS Columbia University ADDRESS Tel: (212) 854-8665 ADDRESS Fax: (212) 854-5429 or 678-9039 CONTACT Ms. Joan Q. Horgan CONTACT technical: mmod@still3.chem.columbia.edu; CONTACT ordering: sl1joan@still3.chem.columbia.edu SITE - SITE-CONTACT - OS Unix (IRIX, AIX) OS IBM RS/6000, SGI, (Cray, Convex for back-end) LANGUAGE X/Motif (local or remote); GL (local); DGL (remote, SGI only) VOLUME - REQUIRES - COMMENTS - AC BC00134 NAME MidasPlus DOMAIN Molecular modelling and graphics DESCRIPTION Molecular Interactive Display and Simulation DESCRIPTION proteins, nucleic acids, drugs DESCRIPTION Input_Format: PDB DESCRIPTION Output_Format: PDB DESCRIPTION Molecular_Model: wire, stick, stick_and_ball, CPK, ribbon DESCRIPTION Output_Type: display, PostScript, SGI "Image File" AUTHOR T.E. Ferrin, C.C. Huang, L.E. Jarvis and R. Langridge RA Ferrin T.E., Huang C.C., Jarvis L.E., Langridge R.; RT "The MIDAS display system"; RL J. Mol. Graph. 6(1):13-27(1988). RA Huang C.C., Pettersen E.F., Klein T.E, Ferrin T.E., Langridge R.; RT "Conic: A fast renderer for space-filling molecules with shadows."; RT J. Mol. Graph. 9(4):230-236(1991). RX Medline; 92126623. RA Ferrin T.E., CouchG.S., Huang C.C., Pettersen E.F., Langridge R.; RT "An Affordable Approach to Interactive Desktop Molecular Modeling"; RL J. Mol. Graph. 9(1):27-32,37-38(1991). ADDRESS Computer Graphics Laboratory ADDRESS University of California, San Francisco ADDRESS Tel: +1-415-476-5128 ADDRESS Fax: +1-415-476-0866 CONTACT midasplus@cgl.ucsf.edu SITE - SITE-CONTACT - OS Unix OS SGI (all models), DECstation 5000, DEC Alpha, NeXTstation LANGUAGE Graphic_Library: GL, OpenGL, or NextStep VOLUME - REQUIRES - COMMENTS - AC BC00135 NAME NAMOT DOMAIN Molecular modelling and graphics DESCRIPTION NAMOT(Nucleic Acid MOdeling Tool) is a tool DESCRIPTION developed at Los Alamos National Laboratory for the structural DESCRIPTION manipulation of single or double stranded, RNA or DNA. NAMOT DESCRIPTION uses a set of reduced co-ordinates to describe base/unit, sugar DESCRIPTION and phosphate geometry. Detailed description of these parameters DESCRIPTION can be found in the references listed at the bottom of this DESCRIPTION announcement. Namot features an X11 graphics interface for DESCRIPTION display of the molecule while modifications are being carried DESCRIPTION out. Both Motif and XView toolkit versions exist, which should DESCRIPTION allow namot to be easily ported to most unix machines. DESCRIPTION Namot features: DESCRIPTION Input: PDB,Amber, or parameters DESCRIPTION Output: Amber, PDB, or parameters, encapsulated postscript. DESCRIPTION General:Can be used to manipulate ss or ds RNA or DNA via DESCRIPTION reduced parameters. Which have intuitive meaning, DESCRIPTION and allow easy manipulation of the base/unit DESCRIPTION without bond breakage. Auto-adjusts:O3'-P-O5' to allow the DESCRIPTION phosphate to cross varying gaps. Monitors distances:A simple DESCRIPTION point and click, connects two atoms with a dashed line and DESCRIPTION displays the distances wheneverthe structure is changed. DESCRIPTION Generation of structures:Generates the parameters for A,B,& Z. DESCRIPTION RNA/DNA, ss or ds DESCRIPTION Can be used as a starting place. DESCRIPTION Label BP: Displays the unit number on the right side of the DESCRIPTION screen at the same level as the C3' DESCRIPTION Online help: There is an extensive online help system. DESCRIPTION Rotations: Easily accessible rotational controls. AUTHOR Gene Carter,esc@transposon.lanl.gov AUTHOR Chang-Shung Tung, cst@transposon.lanl.gov RA Tung C.-S., Soumpasis D.M., Hummer G.; RT "An extension of the rigorous base-unit oriented RT description of nucleic acid structures." RL J. Biomol. Struct. and Dyn. 11(6):1327-1344(1994). RX Medline; 95032895. RA Garcia A.E., Krumhansl J.A.; RT "Agreement between single crystal X-ray and molecular mechanical RT sugar ring conformations. "; RL J. Biomol. Struct. and Dyn. 5(3):513-537(1987). RX Medline; 90148413. RA Tung C-S, Soumpasis D. M., Jovin, T. M.; RT "Computation of Biomolecular Structures: Achievements, RT Problems,and Perspectives"; RL eds, Springer-Verlag, NY (1993). RA Tung C.-S., Carter E.S. II; RT "Nucleic acid modeling tool (NAMOT): an interactive graphic tool RT for modeling nucleic acid structures."; RL Comput. Appl. Biosci. 10:427-433(1994). RX SeqAnalRef; TUNC9401. ADDRESS Los Alamos National Laboratory CONTACT namot@transposon.lanl.gov. SITE ftp anonymous namot.lanl.gov SITE Directory /pub/namot SITE-CONTACT - SITE WWW Server at URL http://namot.lanl.gov/ OS SunOS (5.2,4.1.3),OSF1,AIX,IRIX LANGUAGE C, X11 (Motif and Xview versions) VOLUME - REQUIRES - COMMENTS Copyright, 1994, The Regents of the University of California. COMMENTS This software was produced under U.S. Government contract(W-7405-ENG-36) COMMENTS by Los Alamos National Laboratory, which is operated by the University COMMENTS of California for the U.S. Department of Energy. The U.S Government COMMENTS is licensed to use, reproduce, and distribute this software. Permission COMMENTS is granted to the public to copy and use this software without charge, COMMENTS provided that this Notice and any statement of authorship are reproduced COMMENTS on all copies. Neither the Government nor the University makes any COMMENTS warranty, express or implied, or assumes any liability or responsibility COMMENTS for the use of this software. AC BC00138 NAME PROMOD DOMAIN Molecular modelling and graphics DESCRIPTION 3D modeling software AUTHOR Peitsch Manuel RT - ADDRESS Glaxo Institute for Molecular Biology SA ADDRESS Ch. Aulx 14, 1228 Plan les Ouates, Switzerland CONTACT mcp13936@ggr.co.uk SITE ftp anonymous expasy.hcuge.ch SITE Directory /pub/ProMod SITE-CONTACT Amos Bairoch: bairoch@cmu.unige.ch OS Unix LANGUAGE - VOLUME - AC BC00139 NAME PROPHET DOMAIN Molecular modelling and graphics DESCRIPTION NIH Prophet System Bioresearch Tools DESCRIPTION is a Unix-based workstation software package DESCRIPTION that gives researchers a wide range of DESCRIPTION computing capabilities. AUTHOR The Prophet Distribution Group RA Rindone W.P.; RT "PROPHET, A national computing resource for life RT science research."; RL Nucleic Acids Res. 14:21-24(1986). RX Medline; 86120299. RX SeqAnalRef; RINW8601. RA Hollister C.; RT "PROPHET - a national computing resource for life RT science research."; RL Nucleic Acids Res. 16:1873-1875(1988). RX Medline; 88176427. RX SeqAnalRef; HOLI8801. ADDRESS BBN Systems & Technologies ADDRESS 10 Moulton Street, M/S 6/2A ADDRESS Cambridge, MA 02138. USA CONTACT prophet-info@bbn.com or prophet-help@bbn.com CONTACT Hotline: +1 (617) 873-2669 SITE ftp anonymous www-prophet.bbn.com SITE Directory /pub/prophet_distribution SITE WWW Server at URL http://www-prophet.bbn.com/ OS Unix: Sun-4/SPARCstation, running SunOS or Solaris OS DECStations (Ultrix), DECAlpha (OSF1), SGI (IRIX) LANGUAGE C VOLUME - COMMENTS The FTP anonymous seems to be only available for COMMENTS users in the US. COMMENTS Sequence analysis tools will be added in June 1995 AC BC00140 NAME PSSHOW DOMAIN Molecular modelling and graphics DESCRIPTION General molecular graphics DESCRIPTION Input_Format: PDB, CSD, Amber, MAACS, MOPAC, DGEOM, Gaussian, MOL2, Zmat, ... DESCRIPTION Output_Format: PDB, Amber, MAACS, MOPAC, DGEOM, Gaussian, MOL2, ... DESCRIPTION Molecular_Model: wire, stick, stick_and_ball, CPK, ribbon, alpha_trace DESCRIPTION Output_Type: display, PostScript AUTHOR Eric Swanson RT - ADDRESS Tel: +1-206-783-7253 CONTACT swanson@proteus.bioeng.washington.edu SITE - SITE-CONTACT - OS Unix (IRIX 3.x, 4.x),SGI IRIS, Indigo LANGUAGE Graphic_Library: SGI GL VOLUME - REQUIRES - COMMENTS - AC BC00141 NAME QUANTA DOMAIN Molecular modelling and graphics DESCRIPTION QUANTA is a large program with many functionalities including DESCRIPTION interactive graphics,CHARMm, X-PLOR and MODELLER. DESCRIPTION It is a commercial product. DESCRIPTION simple_molecule, drug, crystal, polymer, protein, inorganic, ... DESCRIPTION Small molecule, drug design, protein, polysaccharide," DESCRIPTION nucleic acid, crystallography, NMR structure determination DESCRIPTION Input_Format / Output_Format: PDB, XPLOR, FDAT, CCDB, MDL, DESCRIPTION Molecular_Model: Wire, stick,ball & stick, CPK, ribbon, alpha-carbon DESCRIPTION Molecular_Model: mixed (all of the above in a single picture), Ray Trace DESCRIPTION Output_Type: display Postscript, HPGL AUTHOR - RT - ADDRESS Ms. Jo Ellen Collins at Molecular Simulations Inc, ADDRESS 16 new England Executive Park, Burlington, MA 01803-5297, USA ADDRESS Tel: (1) (617) 2299800 Fax: (1) (617) 2299899 CONTACT Cathy Terwedow; Marketing Manager CONTACT support@msi.com SITE - SITE-CONTACT - OS Unix OS IBM RS/6000, SGI Indigo, All SGI's; DEC; HP7xx; IBM RS/6000 LANGUAGE Graphic_Library: GL VOLUME - REQUIRES - COMMENTS - AC BC00142 NAME RASMOL DOMAIN Molecular modelling and graphics DESCRIPTION RasMol is an X Window System tool intended for the visualisation DESCRIPTION of proteins and nucleic acids. It reads Brookhaven Protein DESCRIPTION Databank (PDB) files and interactively renders them in a variety DESCRIPTION of formats on either an 8bit or 24/32bit colour display DESCRIPTION Molecular_Model: wire, stick, stick_and_ball, CPK, ribbon, DESCRIPTION alpha_trace) hydrogen bonding and disulphide bridges (stick & wire) DESCRIPTION Input and Output Format: PDB, Alchemy DESCRIPTION Output_Type: display, PostScript, GIF, Sun Rasterfile, PPM, BMP AUTHOR Sayle R. RT - ADDRESS Department of Computer Science University of Edinburgh ADDRESS Edinburgh EH9 3JZ, UK. ADDRESS Tel: +44-31-650-5163 , Fax: +44-31-667-7209 CONTACT Sayle R. ros@dcs.ed.ac.uk SITE ftp anonymous ftp.dcs.ed.ac.uk [129.215.160.5] SITE Directory /pub/rasmol (Unix, MAC and DOS versions) SITE_CONTACT rasmol@dcs.ed.ac.uk SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix UNIX software are stored SITE as archive (tar) files compressed (.Z). SITE ftp anonymous kekule.osc.edu SITE Directory /pub/chemistry/software/MAC/ SITE ftp anonymous ftp.cict.fr SITE Directory /pub/mac/sci/Rasmol.sea.hqx SITE-CONTACT nethelp@ebi.ac.uk OS sun3, sun4, sun386i,hp9000, sequent, DEC alpha, IBM RS/6000,SGI, Macintosh LANGUAGE C X Window VOLUME - REQUIRES UNIX and VMS versions require an 8bit, 24bit or 32bit X Window frame REQUIRES buffer (X11R4 or later) AC BC00143 NAME Raster3D DOMAIN Molecular modelling and graphics DESCRIPTION Raster3D is a set of tools for generating high quality raster DESCRIPTION images of proteins or other molecules. The core program renders DESCRIPTION spheres, triangles, and cylinders with specular highlighting, DESCRIPTION Phong shading,and shadowing using an efficient Z-buffer algorithm DESCRIPTION Ancillary programs process atomic coordinates from Brookhaven PDB DESCRIPTION files into rendering descriptions for pictures composed of ribbons, DESCRIPTION space-filling atoms, bonds, ball+stick, etc. Raster3D can also be DESCRIPTION used to render pictures composed in Per Kraulis MOLSCRIPT program DESCRIPTION in glorious 3D with highlights, shadowing, etc. (NB:you will need DESCRIPTION MOLSCRIPT V1.4 to get the full benefit of this). Output is to DESCRIPTION pixel image files with 24 bits of color information per pixel. AUTHOR originally written by David J. Bacon and Wayne F. Anderson; AUTHOR extensions, revisions, modifications, ancillary programs by AUTHOR Mark Israel, Stephen Samuel, Michael Murphy, Albert Berghuis, AUTHOR and Ethan A Merritt RA Bacon D. J., Anderson W.F.; RT "A Fast Algorithm for Rendering Space-Filling Molecule Pictures"; RL J. Mol. Graph. 6:219-220(1998). RA Bacon D. J., Anderson W.F.; RT "A Fast Algorithm for Rendering Space-Filling Molecule Pictures"; RL Paper presented at the Seventh Annual Meeting of the Molecular RL Graphics Society, San Francisco, 10-12 August 1988. RA Merritt E.A., Murphy M.E.P.; RT "Raster3D Version 2.0, a Program for Photorealistic RT Molecular Graphics"; RL Acta Cryst. 50:869-873(1994). ADDRESS Ethan A Merritt ADDRESS Dept of Biological Structure SM-20 ADDRESS University of Washington, Seattle WA 98195, USA CONTACT merritt@u.washington.edu SITE ftp anonymous ftp.bmsc.washington.edu SITE Directory /pub/raster3d SITE-CONTACT - SITE WWW Server at URL http://www.bmsc.washington.edu/raster3d/raster3d.html OS Unix LANGUAGE FORTRAN, C VOLUME - REQUIRES - COMMENTS Raster3d is freely available but unsupported. COMMENTS The current version is 2.02, last updated on 28 November 1994. COMMENTS The programs have been tested on DEC, SGI, IBM, ESV, and SUN COMMENTS unix workstations. The code does not depend in any way on COMMENTS graphics hardware, so it should be portable to other machines COMMENTS as well. AC BC00144 NAME Ribbons DOMAIN Molecular graphics and crystallography DESCRIPTION Ribbons software interactively displays molecular models, analyzes DESCRIPTION crystallographic results, and creates publication quality images. DESCRIPTION The `ribbon drawing' popularized by Richardson is featured. DESCRIPTION Space-filling and ball-and-stick representations, dot and DESCRIPTION triangular surfaces, density map contours, and text are supported. DESCRIPTION Extensive help is on-line in HTML format. DESCRIPTION Input_Format: PDB DESCRIPTION Output_Format: RGB images DESCRIPTION Molecular_Model: stick, ball_and_stick, CPK, ribbons DESCRIPTION Output_Type: SGI *.rgb format images (can convert to many others). DESCRIPTION Output_Type: VRML(1.0) *.iv and VRML(2.0) *.wrl format AUTHOR Mike Carson RA Carson M.; RT "Ribbons"; RL Methods in Enzymology. 277:493-505(1997). RA Carson M.; RT "Ribbons 2.0"; RL J. Appl. Cryst. 24:958-961(1991). RX SeqAnalRef; CARM9101. RA Carson M., Bugg C.E.; RT "Algorithm for ribbon models of proteins."; RL J. Mol. Graph. 4:121-122(1986). RX SeqAnalRef; CARM8601. ADDRESS UAB Center for Macrolmolecular Crystallography ADDRESS Tel: +1-205-934-1983 ADDRESS Fax: +1-205-934-0480 CONTACT carson@cmc.uab.edu SITE http://www.cmc.uab.edu/ribbons SITE-CONTACT - OS Unix OS SGI, DEC, IBM, ESV LANGUAGE Graphic_Library: OpenGL, GL, PEX VOLUME - REQUIRES - COMMENTS - AC BC00145 NAME SCARECROW DOMAIN Molecular modelling and graphics DESCRIPTION Analysis of Molecular Dynamics trajectories and molecular display DESCRIPTION Input_Format: Coord - PDB, CHARMM, DISCOVER, AMBER, YASP, MUMOD, GROMOS, DESCRIPTION Input_Format: HyperChem, MOPAC, GAMESS-output, free format DESCRIPTION Input_Format: MD trajectory - CHARMM, DISCOVER, AMBER, YASP, MUMOD, GROMOS, DESCRIPTION Input_Format: HyperChem DESCRIPTION Output_Format: Coord - Free, CHARMM, Ball&Stick, PDB DESCRIPTION Output_Format: Data - Ascii DESCRIPTION Output_Format: Graphics - PostScript DESCRIPTION Molecular_Model: Stick, ball & stick, CPK, surfaces, mono/stereo DESCRIPTION Output_Type: Display, PostScript AUTHOR Leif Laaksonen RT J. Molecular Graphics 10 (1992) 33 ADDRESS Center for Scientific Computing ADDRESS Tel: +358-0-4572378 ADDRESS Fax: +358-0-4572302 CONTACT Leif.Laaksonen@csc.fi SITE - SITE-CONTACT - OS Unix, IRIX OS SGI LANGUAGE Graphic_Library: GL VOLUME - REQUIRES - COMMENTS - AC BC00146 NAME SCHAKAL DOMAIN Molecular modelling and graphics DESCRIPTION molecules, crystal sections + surfaces DESCRIPTION "realistic" shading incl. highlights + shadows DESCRIPTION (depth dependent) lightness + pseudo-transparency DESCRIPTION automatic labelling of atoms, broken bonds DESCRIPTION Input_Format: atom names + coordinates, (symmetry), SHELX DESCRIPTION Output_Format: atom names + coordinates DESCRIPTION Molecular_Model: wire, ball_and_stick, CPK DESCRIPTION Output_Type: 8 bit (256 colours) display, HPGL, HP L.Jet III AUTHOR Dr. E. Keller RA Keller E.; RT "Some computer drawings of molecular and solid-state structures"; RL J. Appl. Crystallogr. 22:19(1989). ADDRESS Kristallogr. Inst. der Universitaet ADDRESS Hebelstr. 25, D-79104 Freiburg, Germany ADDRESS Tel: +49-761-203-6438 ADDRESS Fax: +49-761-203-6434 CONTACT KELL@sun1.ruf.uni-freiburg.de SITE - SITE-CONTACT - OS DOS PC, IBM RS/6000, SGI IRIS + Indigo OS DECstation, (VAXstation) OS MSDOS, UNIX LANGUAGE C VOLUME - REQUIRES Graphic_Library: GL, X11 COMMENTS - AC BC00147 NAME SHAPE DOMAIN Molecular modelling and graphics DESCRIPTION SHAPE is a package for analysis of molecular surfaces. DESCRIPTION It includes programs for determining whether a point is in a DESCRIPTION groove or crevice in a surface, and for determining the largest DESCRIPTION sphere that can fit at a location. DESCRIPTION You should sign a license agreement AUTHOR L. A. Kuhn, M. A. Siani, M. E. Pique, C. L. Fisher, AUTHOR E. D. Getzoff, and J. A. Tainer. RA Kuhn L.A., Siani M.A., Pique M.E., Fisher C.L., RA Getzoff E.D., Tainer J.A.; RT "The Interdependence of Surface Topography and Bound RT Water Molecules Revealed by Surface Accessibility RT and Fractal Density Measures."; RL J. Mol. Biol. 228:13-22(1992). ADDRESS Computational Center for Macromolecular Structures ADDRESS San Diego Supercomputer Center, P.O. Box 85608, ADDRESS San Diego, CA, 92138-5608, USA CONTACT ccms-help@sdsc.edu (human) CONTACT ccms-request@sdsc.edu (listserv) SITE WWW Server at URL http://www.sdsc.edu/1/Parts_Collabs/CCMS SITE-CONTACT ccms-help@sdsc.edu OS Sun4, DEC/ULTRIX,SGI LANGUAGE - VOLUME - AC BC00148 NAME SciAn DOMAIN Molecular modelling and graphics DESCRIPTION Input_Format: XYZ, Gaussian AUTHOR Eric Pepke RT - ADDRESS Florida State University CONTACT Eric Pepke SITE - SITE-CONTACT - OS Unix LANGUAGE - VOLUME - REQUIRES - COMMENTS - AC BC00149 NAME Squid DOMAIN Molecular modelling and graphics DESCRIPTION simple_molecule, drug, polymer, protein, inorganic, DNA, XY-plot DESCRIPTION XYZ-plot, Data-processing, Crystallographic Analysis, MD analysis DESCRIPTION Cluster analysis, DESCRIPTION Input_Format: PDB, KARPLUS, GROMOS, AMBER, General Ascii files DESCRIPTION Output_Format: PDB, KARPLUS, MD-trajectory, General Ascii files DESCRIPTION Molecular_Model: wire, stick, stick_and_ball, CPK, ribbon, DESCRIPTION Molecular_Model: alpha_trace, colour, stereo, vectors, labels DESCRIPTION Output_Type: display, PostScript, HPGL, Xfig, (plot84), user AUTHOR Tom Oldfield RA Oldfield T. RT "SQUID - A program for the analysis and display of data from RT crystallography and molecular-dynamics."; RL J. Mol. Graph. 10:247-252(1992). ADDRESS (Private) Molecular Simulations Inc., ADDRESS (Private) 16 New England Executive Park ADDRESS (Private) Burlington, MA 01803-5297 , USA. ADDRESS (Private) Tel 617 229 9800 ADDRESS (Private) Fax 617 229 9899 ADDRESS Tel: (Academic) ++904 432599 CONTACT (Academic) oldfield@yorvic.york.ac.uk SITE ftp anonymous yorvic.york.ac.uk SITE Directory /guestfpt SITE-CONTACT - OS Unix, Windows, VMS OS IBM RS/6000, SGI Indigo, VAX (Old), Convex, Sun, Aliant,... LANGUAGE Graphic_Library: GL, X11, tektronix, vt100, user VOLUME - REQUIRES - COMMENTS - AC BC00151 NAME UniChem DOMAIN Molecular modelling and graphics DESCRIPTION simple_molecule, polymer, inorganic, ... DESCRIPTION Input_Format:UniChem,Cambridge,PDB,XYZ,MDLMolfile,Insight carfile DESCRIPTION Output_Format:UniChem,Cambridge,PDB,XYZ,MDL Molfile,Insight carfile DESCRIPTION Molecular_Model: wire, stick, ball_and_stick, CPK, van der Waals DESCRIPTION Output_Type: display, print as PostScript, PBM, PICT, GIF, TIFF AUTHOR Thomas Raeuchle RT Cray Publications APG-5500, APG-5505 ADDRESS Cray Research, Inc. ADDRESS Tel: 1-800-284-2729 x 33646 ADDRESS Fax: 1-612-683-3699 CONTACT raeuchle@gravity.cray.com SITE - SITE-CONTACT - OS UNICOS/IRIX/UNIX OS Cray EL, X-MP, Y-MP, C90 / SGI (All Workstations) OS X-Window System Workstations LANGUAGE Graphic_Library: GL, DGL, X11, Motif VOLUME - REQUIRES - COMMENTS - AC BC00152 NAME VADAR DOMAIN Molecular modelling and graphics DESCRIPTION Molecular Modeller AUTHOR - RT - ADDRESS VADAR c/o PENCE ADDRESS 7-13 HMRC ADDRESS University of Alberta, Edmonton, AB T6G 2S2, Canada ADDRESS Fax: (1) 403 492-1473 CONTACT vadar@procyon.biochem.ualberta.ca SITE ftp anonymous canopus.biochem.ualberta.ca SITE Directory /pub/ SITE-CONTACT - OS Unix (SUN and SGI) LANGUAGE - VOLUME - REQUIRES - AC BC00153 NAME XMol DOMAIN Molecular modelling and graphics DESCRIPTION simple_molecule, drug, crystal, polymer, protein, inorganic, ... DESCRIPTION Input_Format: XYZ, Mopac, Gaussian92, CHEMLAB-II, Molsim, Alchemy, PDB DESCRIPTION Output_Format: XYZ, Mopac, Gaussian92, CHEMLAB-II, Molsim, Alchemy, PDB DESCRIPTION Molecular_Model: ball_and_stick, stick, CPK, ribbon, alpha_trace DESCRIPTION Output_Type: display, PostScript AUTHOR David C. Doherty RT - ADDRESS Minnesota Supercomputer Center, Inc. ADDRESS Tel: +1-(612)337-3402 ADDRESS Fax: +1-(612)337-3400 CONTACT xmol@msc.edu SITE ftp anonymous ftp.msc.edu SITE Directory /pub/xmol SITE-CONTACT - OS IBM RS/6000, SGI Iris/4D, DecStation, Sun3, Sparcstation OS Irix, Ultrix, AIX, SunOS LANGUAGE Graphic_Library: X11/Motif VOLUME - REQUIRES - COMMENTS - AC BC00187 NAME WHAT-IF DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Alignment Search software DOMAIN Molecular modelling and graphics DOMAIN Database and analysis DOMAIN Searching databases DESCRIPTION WHAT IF is an extensive protein DESCRIPTION modeling, protein structure analysis, DESCRIPTION database handler, molecular graphics package.It is DESCRIPTION available for all Silicon Graphics machines (from the DESCRIPTION Indigo all the way up to the 8 processor VGX machine). DESCRIPTION WHAT IF is also supported for the Bruker NMR spectrometer DESCRIPTION computers, DEC-alpha,-OSF SUN and for IBM-Pc (clones) DESCRIPTION running LINUX or DOS. The Pc version is distributed by a DESCRIPTION third party, but fully supported by us. A do-it-yourself DESCRIPTION version exists for IBM RS6000 machines. If really needed, DESCRIPTION WHAT IF can be made available for all Evans and Sutherland DESCRIPTION machines, but this will be an unsupported version. Contact DESCRIPTION me for special arrangements for such machines. The DESCRIPTION program costs $5000,-. Non-profit organisations pay DESCRIPTION $250,-. The program comes WITH source code (300.000 lines DESCRIPTION FORTRAN 77), WITH databases, and WITH extensive DESCRIPTION documentation (600 page writeup). There are no monthly DESCRIPTION fees. There are no strings attached to using WHAT IF. DESCRIPTION However, (re-)distribution is not allowed. There is NO DESCRIPTION service desk, and no guarantees are given. At present DESCRIPTION there are 240 installed sites world wide. A lisence is DESCRIPTION site-wide, and covers an unlimited number of workstations. DESCRIPTION Updates are send upon request and will cost $250,- to DESCRIPTION everybody. An update can be obtained as often as possible, DESCRIPTION and comes again with all data, writeup, etc. AUTHOR Gert Vriend RA Vriend G.; RT "WHAT IF: a molecular modelling and drug design program."; RL J. Mol. Graph. 8:52-56(1990). RX SeqAnalRef; VRIG9002. ADDRESS Gert Vriend ADDRESS EMBL, Meyerhofstrasse 1 ADDRESS D-69117 Heidelberg, Germany CONTACT vriend@EMBL-Heidelberg.DE SITE WWW Server at URL http://www.sander.embl-heidelberg.de/whatif/ OS UNIX, MSDOS LANGUAGE FORTRAN, C VOLUME Between 15-300MB (or up to 3GB) REQUIRES X windows or GL graphics for UNIX. COMMENTS We have seen WHAT IF working on: COMMENTS DEC ULTRIX, DEC ALPHA, PC Linux, PC DOS, SGI IRIX, IBM AIX, COMMENTS SUN SUNoS, SUN SOLARIS COMMENTS The original distribution can not be done via FTP, but source COMMENTS code updates can be done over FTP. Updates via FTP are free of COMMENTS costs. AC BC00194 NAME PDBview DOMAIN Protein structure analysis DOMAIN Molecular modelling and graphics DESCRIPTION A viewer and render of PDB entries AUTHOR W. Chang, I.N. Shindyalov, C. Puu and P.E. Bourne RA Chang W., Shindyalov I.N., Puu C., Bourne P.E.; RT "Design and application of PDBlib, a C++ RT macromolecular class library."; RL Comput. Appl. Biosci. 10(6):575-586(1994). RX SeqAnalRef; CHAW9401. ADDRESS Department of Biochemistry and Molecular Biophysics / ADDRESS Columbia University / USA ADDRESS Tel: +1-212-305-3657, Fax: +1-212-305-7379 CONTACT Phil Bourne: system@cuhhca.hhmi.columbia.edu SITE ftp anonymous cuhhca.hhmi.columbia.edu SITE Directory /pub/programs/PDB/PDBlib SITE-CONTACT - OS Unix LANGUAGE C (X11, Motif) VOLUME - REQUIRES PDBlib AC BC00347 NAME SETOR DOMAIN Molecular modelling and graphics DESCRIPTION SETOR is a program for displaying macromolecules and is DESCRIPTION available to non-profit users for a small nominal fee. DESCRIPTION It allows the display of various kinds of solid models DESCRIPTION ("ropes", "secondary structure a la Jane Richardson", DESCRIPTION "stick", "CPK") and a wide range of colouring methods DESCRIPTION (including changing the background). It can display DESCRIPTION Connolly surfaces and electron density maps (with varying DESCRIPTION line widths if you so desire). It has a complete range of DESCRIPTION captioning and labelling possibilities. It can have multiple DESCRIPTION light sources (including coloured lights) and one can vary DESCRIPTION the degree of smoothness of the model and have DESCRIPTION antialiasing of your final image. Finally it can save DESCRIPTION output direct to an RGB file (including automatic cropping DESCRIPTION to the 2/3 ratio of 35mm slide film). AUTHOR Stephen Evans RA Evans S.; RT - RL J. Mol. Graph. 11:134-138(1993). ADDRESS Macromolecular Structure Group, ADDRESS Biotechnology Research Institute ADDRESS c/o Institute for Biological Sciences ADDRESS National Research Council ADDRESS Building M-54, Montreal Road ADDRESS Ottawa, Ontario, CANADA K1A 0R6 CONTACT elmo@nrcbsa.bio.nrc.ca SITE - SITE-CONTACT - OS SGI LANGUAGE - VOLUME - REQUIRES - Submitted by AC BC00368 NAME PRO-EXPLORE DOMAIN Molecular modelling and graphics DOMAIN Alignment editing and display DOMAIN Pattern Identification DESCRIPTION PRO-EXPLORE is a graphical protein modelling package. It DESCRIPTION provides tools for multi-sequence editing and alignment, DESCRIPTION sequence analysis, database investigation, and 3D modelling. AUTHOR - RT - ADDRESS OXFORD MOLECULAR, THE OXFORD SCIENCE PARK, OXFORD, OX4 4GA UK CONTACT Paul DAVIE , tel: +44 1865 784600 SITE - SITE-CONTACT - OS All Silicon Graphics (IRIX 4.0) LANGUAGE - VOLUME - REQUIRES PRO-EXPLORE package COMMENTS Silicon Graphics : gl_s run time library COMMENTS 24 bit planes for colour or RGB dithering COMMENTS 24 bit planes for Z-buffering COMMENTS ESV Graphics : PEX 2.0 COMMENTS Commercial software AC BC00386 NAME FoldIt DOMAIN Molecular modelling and graphics DESCRIPTION FoldIt (light)' is a molecular modelling DESCRIPTION program to visualize and manipulate proteins. 'FoldIt DESCRIPTION (light)' is an interactive program with a user friendly DESCRIPTION interface. The goal of this program was to build an DESCRIPTION integrated environment in which statistical analysis as DESCRIPTION well 3D observations could be realized on PDB files without DESCRIPTION having to transfer files or swap machines. Our major DESCRIPTION underlying research project is still to try to improve the DESCRIPTION folding prediction methods (hence the name 'FoldIt'). This DESCRIPTION is also the sole desactivated feature in this released DESCRIPTION version (hence the adjective '(light)'). DESCRIPTION 'FoldIt (light)' is intented to provide the possibility to DESCRIPTION analyze proteins up to 1600 residues in size, to visualize DESCRIPTION and manipulate them interactively. It can directly read any DESCRIPTION protein coordinate text file from the Brookhaven Protein DESCRIPTION Data Bank (PDB) (Bernstein et al., 1977) including DESCRIPTION hetero-atoms and water molecules. 'FoldIt (light)' has two DESCRIPTION main windows: a color image window to display the protein DESCRIPTION structure and a text window to record the result of all DESCRIPTION operations requested by the user. DESCRIPTION The protein structure can be manipulated easily in real DESCRIPTION time with the mouse, zoomed or observed in stereo. DESCRIPTION Structure movement can also occur stepwise for a more DESCRIPTION precise control. Animations can be created. Steric DESCRIPTION conflicts, disulfide bonds, hydrogen and ionic interactions DESCRIPTION can be located and displayed in the protein structure. DESCRIPTION These interactions are also reported in the text window. DESCRIPTION Atoms and residues can be tagged individually (or globally) DESCRIPTION and structural information can then be extracted. DESCRIPTION Portions of a structure can be read into memory or DESCRIPTION displayed. Two structures can be read at the same time in DESCRIPTION memory and can be overlapped automatically. The second DESCRIPTION structure can be manipulated independently of the first. DESCRIPTION Bonds can be rotated and atomic parameters can be changed. DESCRIPTION The sequential folding of a protein can be simulated. It DESCRIPTION is possible to create a protein de novo from the menu or by DESCRIPTION entering the sequence from the keyboard. Structures can DESCRIPTION then be manipulated locally or forced into helices. The DESCRIPTION application can process structures in the batch mode to DESCRIPTION extract a number of structural features: Ramachandran DESCRIPTION plots, SS-bond plots, H-bond plots. Statistics on atomic DESCRIPTION parameters are displayed as histograms. The content of DESCRIPTION image and text windows as well as histograms can be saved DESCRIPTION to disk. AUTHOR Jean-Claude JESIOR RT - ADDRESS Infodis/TIMC (URA D1618), Institut Albert Bonniot, ADDRESS Faculte de Medecine , 38706 La Tronche Cedex (France) ADDRESS tel: +33 76 54 94 91 fax: +33 76 54 95 49 CONTACT jean-claude.jesior@imag.fr SITE ftp anonymous ftp.imag.fr SITE Directory /pub/TIMC SITE-CONTACT - SITE WWW Server at URL ftp://ftp.imag.fr/pub/TIMC/FoldIt.html OS MacOS system 7.0 or higher (68030 CPU, 68040 CPU) and PowerMac LANGUAGE Symantec Think Pascal VOLUME - REQUIRES 675 KB of memory and 3.3 KB of additional memory for each REQUIRES read residue: this means that 660 KB of extra REQUIRES RAM are necessary to read a typical 200-residue protein COMMENTS You'll find two versions of the application: COMMENTS -Download the 'FoldIt (light)' version if COMMENTS you have a machine equipped with a 68030 CPU (+68881/82 COMMENTS coprocessor) or with a 68040 CPU (not a 68LC040!) COMMENTS -Download the 'FoldIt (light) no FPU' version otherwise COMMENTS (e.g. on a PowerMac FoldIt will come soon in a native COMMENTS PowerMac version). AC BC00403 NAME KINEMAGE DOMAIN Molecular modelling and graphics DESCRIPTION Kinemages are "kinetic protein images" that accompany DESCRIPTION many of the articles published in Protein Science. The DESCRIPTION files with extension *.kin are ascii files that are DESCRIPTION read by the program MAGE to produce kinemages. Kinemages DESCRIPTION are produced from Brookhaven PDB formatted files using DESCRIPTION the program PREKIN. AUTHOR Charles W. Sokolik RT - ADDRESS Department of Chemistry ADDRESS Denison University ADDRESS Granville, Ohio 43023, USA CONTACT sokolik@cc.denison.edu SITE ftp anonymous ftp.uci.edu SITE Directory /protein/Kinemage SITE-CONTACT - SITE WWW Server at URL ftp://ftp.uci.edu/protein/Kinemage/ OS MacOS, MS-DOS LANGUAGE - VOLUME - REQUIRES - AC BC00404 NAME HINT (3-D hydrophobic/hydrophilic) DOMAIN Protein structure analysis DOMAIN Molecular modelling and graphics DESCRIPTION HINT provides empirical modelling tools that are integrated DESCRIPTION into Sybyl, InsightII, or Chem-X. HINT calculated not only DESCRIPTION two-dimentional log P values, but also 3-D hydropathy fields DESCRIPTION based on atomistic approximations of charge and hydro- DESCRIPTION phobicity. These tools are valuable for use with PROTEIN DESCRIPTION STRUCTURE ANALYSIS (crystallography or homology), DOCKING, DESCRIPTION LOG P ANALYSIS, QSAR (integrated tools for ComFA and DOCK), DESCRIPTION and 3-D mapping of molecular hydrophobicity. Free DEMO! AUTHOR Drs. Glen Kellogg and Donald Abraham RA Kellogg G.E. et al; RL Med. Chem. Res. 1:444-453(1992). RA Kellogg G.E., Abraham D.J.; RT "KEY, LOCK, and LOCKSMITH - complementary hydropathic map RT predictions of drug structure from a known receptor RT structure from known drugs."; RL J. Mol. Graph. 10:212-217(1992). RX Medline; 93119963. RA Meng E.C., Kuntz I.D., Abraham D.J., Kellogg G.E.; RT "Evaluating docked complexes with the HINT exponential function RT and empirical atomic hydrophobicities."; RL J. Comput. Aided Mol. Des. 8:299-306(1994). RA Waller C.L.; RT "A 3-dimensional technique for the calculation of octanol RT water partition-coefficients."; RL Quant. Struct.-Act. Relat. 13:172-176(1994). RA White S.P., Birch P., Kumar R.; RT "Interactions at the Alpha-1-Beta-1 interface in hemoglobin - RT A single amino-acid change affects dimer ratio in transgenic RT mice expressing human hemoglobin."; RL Hemoglobin 18:413-426(1994). RX Medline; 95229428. ADDRESS Dr. David N. Haney ADDRESS 12010 Medoc Ln., San Diego, CA 92131-1417, USA ADDRESS tel: +1 619-566-1127 fax: +1 610-586-1481 CONTACT haney@netcom.com SITE WWW Server at URL http://www.i2020.net/edusoft/hint.html OS IRIX 4.0.5, 5.X LANGUAGE - VOLUME - REQUIRES SGI, Modelling software license, HINT license COMMENTS Works with Sybyl 6.0.4 or later, InsightII 2.35 or later, or COMMENTS Chem-X 1/94 or later. License for one of these modelling COMMENTS packages is required as well as license for HINT. A free COMMENTS DEMO is available. AC BC00406 NAME NAMD DOMAIN Molecular modelling and graphics DESCRIPTION NAMD is a molecular dynamics program designed to provide DESCRIPTION high performance simulations for large biological molecular DESCRIPTION systems. CHARMM-19 and CHARMM-22 force fields DESCRIPTION and X-PLOR PSF and DCD file formats are supported. DESCRIPTION NAMD uses spatial decomposition coupled with a DESCRIPTION multithreaded, message-driven design to provide a DESCRIPTION scalable, efficient parallel framework. It also DESCRIPTION incorporates the Distributed Parallel Multipole Tree DESCRIPTION Algorithm (DPMTA) developed by the Scientific Computing DESCRIPTION group at Duke University, which allows full electrostatic DESCRIPTION force evaluation in O(N) time. NAMD attains DESCRIPTION modularity by using an object-oriented design DESCRIPTION and implementation in C++. As part of the MDScope DESCRIPTION system, NAMD is connected via the communication system DESCRIPTION MDComm to the molecular graphics program VMD (also DESCRIPTION developed by the Theoretical Biophysics group) to provide DESCRIPTION such an interactive system where researchers can view and DESCRIPTION interact with a running simulation. AUTHOR The Theoretical Biophysics Group at the Beckman Institute, AUTHOR University of Illinois at Urbana-Champaign RT - ADDRESS Theoretical Biophysics, University of Illinois, ADDRESS 3117 Beckman Institute, 405 North Matthews, ADDRESS Urbana, IL 61801, USA CONTACT brunner@ks.uiuc.edu SITE ftp anonymous ftp.ks.uiuc.edu SITE Directory /pub/mdscope/namd SITE-CONTACT namd@ks.uiuc.edu SITE WWW Server at URL http://www.ks.uiuc.edu/Research/vmd OS Unix LANGUAGE C++ VOLUME - REQUIRES - COMMENTS NAMD should run on any parallel platform with a C++ compiler and PVM COMMENTS version 3.3.6 or later. Tested Makefiles are included for clusters COMMENTS of HP, SGI, and IBM workstations, Cray T3D, and Convex Exemplar. COMMENTS Precompiled binaries are provided for HP and SGI workstations. AC BC00407 NAME NAOMI DOMAIN Molecular modelling and graphics DOMAIN Protein structure analysis DESCRIPTION NAOMI is a computer program aimed at both specialist DESCRIPTION and non-specialist researchers who make use of DESCRIPTION three-dimensional structures of proteins in their DESCRIPTION work. The general features offered by the program DESCRIPTION make it it a useful addition to programs such as DESCRIPTION X-PLOR for performing structure-function related DESCRIPTION computations on protein structures. In addition, a DESCRIPTION number of specific types of calculation are offered DESCRIPTION which are of interest to groups of people. DESCRIPTION NAOMI provides interfaces to the graphics programs DESCRIPTION MOLSCRIPT, INSIGHT II and QUANTA, as well as its own DESCRIPTION graphical output, to allow efficient visualizations of DESCRIPTION the results of calculations and analyses. It is DESCRIPTION operated by an intuitive command language, coupled DESCRIPTION with interactive documentation, that allows the user DESCRIPTION to perform manipulations of and calculations on DESCRIPTION three-dimensional structures of proteins in a DESCRIPTION time-efficient manner AUTHOR Simon M. Brocklehurst RT - ADDRESS Oxford Centre for Molecular Sciences, ADDRESS Department of Biochemistry, ADDRESS University of Oxford, Oxford, UK CONTACT smb@bioch.ox.ac.uk SITE ftp anonymous nmrz.ocms.ox.ac.uk SITE Directory /pub/smb/naomi/ SITE-CONTACT smb@bioch.ox.ac.uk SITE WWW Server at URL http://www.ocms.ox.ac.uk/~smb/Software/N_details/naomi.html OS Silicon Graphics workstations LANGUAGE ANSI C, PostScript VOLUME 1 MB disk space REQUIRES At least 32 MB RAM COMMENTS NAOMI is Copyright Simon M. Brocklehurst 1992-1995. AC BC00411 NAME VMD DOMAIN Molecular modelling and graphics DESCRIPTION VMD is designed for interactive display, animation, manipulation DESCRIPTION and analysis of proteins, nucleic acids, lipid membranes and DESCRIPTION and other biological molecules. The software supports OpenGL and DESCRIPTION SGI GL with stereo displays, the CAVE and input formats for many DESCRIPTION popular renderers including VRML, POV-Ray and Raster3D. DESCRIPTION VMD can directly read Protein Data Bank(PDB) files, DESCRIPTION X-PLOR PSF/DCD files and Amber CRD files or use Babel to DESCRIPTION convert from other file formats. The wide variety of methods for DESCRIPTION rendering and coloring molecules offered by VMD includes VdW, DESCRIPTION licorice, cartoon and surface models. Animation information can DESCRIPTION can come from a trajectory file or via a connection to a running DESCRIPTION molecular dynamics program. The VMD scripting language is based DESCRIPTION on Tcl/Tk and may be used to query for molecular information, DESCRIPTION perform analysis and to display the results interactively, DESCRIPTION yielding a powerful base for implementing new methods in DESCRIPTION structure visualization and analysis. To further development, DESCRIPTION the complete C++ source code is freely available along with DESCRIPTION documentation for using and modifying the program. AUTHOR The Theoretical Biophysics group at the Beckman Institute, AUTHOR University of Illinois at Urbana-Champaign RT - ADDRESS Theoretical Biophysics, University of Illinois ADDRESS 3117 Beckman Institute, 405 North Matthews ADDRESS Urbana, IL 61801, USA CONTACT vmd@ks.uiuc.edu SITE ftp anonymous ftp.ks.uiuc.edu SITE Directory /pub/mdscope/vmd SITE-CONTACT - SITE WWW Server at URL http://www.ks.uiuc.edu/Research/vmd/ OS IRIX 5.x, 6.x; HP-UX 9, 10; Linux, Solaris LANGUAGE C++ VOLUME - REQUIRES - COMMENTS Several versions of the distribution are available, one COMMENTS including the complete VMD source code, and others which just COMMENTS include a precompiled VMD executable for the given OS. AC BC00424 NAME XmMol DOMAIN Molecular modelling and graphics DESCRIPTION Designed to provide both interactive molecular DESCRIPTION visualization and easy interface with external DESCRIPTION applications under any X11/Motif platform. DESCRIPTION Provides wireframe and spline representations DESCRIPTION and includes part of the FORME package. DESCRIPTION A communication protocol allows XmMol to be used DESCRIPTION as a visualization tool for external programs DESCRIPTION (minimizers for example). AUTHOR Tuffery P. RA Tuffery P.; RT "XmMol: An X11 and motif program for RT macromolecular visualization and modelling."; RL J. Mol. Graph. 13:67-72 (1995). RX Medline; 95315109. RX SeqAnalRef; TUFP9501. ADDRESS Centre de Bioinformatique, Universite Paris 7, ADDRESS tour 53-1er etage, 2 place Jussieu ADDRESS 75251 Paris Cedex 05, FRANCE CONTACT tuffery@urbb.jussieu.fr SITE ftp anonymous duc.urbb.jussieu.fr (134.157.50.33) SITE Directory /README.XmMol SITE-CONTACT tuffery@urbb.jussieu.fr OS UNIX (HP, SGI, IBM RS6000, SUN,Dec alpha, Linux PCs.) LANGUAGE C VOLUME - REQUIRES X11/Motif COMMENTS This software is available free of charge COMMENTS for academic, teaching and non-commercial purposes. COMMENTS However, it requires a special password to be issued before COMMENTS you can download the software. To get it, please complete COMMENTS the academic agreement form below and return it (mail, not COMMENTS email or fax). On receipt, details on how to load the COMMENTS software will be sent to you. Get the file README.XmMol AC BC00433 NAME TURBO FRODO DOMAIN Crystallography DOMAIN Molecular modelling and graphics DESCRIPTION Turbo Frodo is a general purpose molecular modelling DESCRIPTION environnement aimed at people with the need to model de DESCRIPTION novo macromolecules, polypeptides as well as nucleic acids, DESCRIPTION to build such macromolecules from experimental 3-D data DESCRIPTION obtained from X-ray crystallography and NMr, to display the DESCRIPTION resulting models using various representations including DESCRIPTION Van der Waals and Connolly's molecular dot surfaces as well DESCRIPTION as spline surfaces. Compact views include CPK, icosahedra DESCRIPTION and ball -and- stick representations styles, alone or in DESCRIPTION combination. With Turbo Frodo, you can color your DESCRIPTION molecules according to different criteria, either DESCRIPTION objectively or subjectively, to compare them with existing DESCRIPTION structures and to evaluate their geometry. Turbo Frodo is DESCRIPTION also aimed at ligand fitting and protein stacking. You can DESCRIPTION interactively mutate a protein or chemically modify it, and DESCRIPTION evaluate the resulting conformational changes. Secondary DESCRIPTION structure calculation and their representation can be DESCRIPTION performed automatically. AUTHOR Alain Roussel PhD. headed by Christian Cambillau PhD. RA Roussel,A., and Cambillau, C.; RL Silicon Graphics Directory, Silicon Graphics Mountain View, CA,USA (1991) ADDRESS AFMB- Marseille France ADDRESS Tel: +33-91 11 77 98 - Fax: +33-91 61 25 67 CONTACT turbo@lccmb.cnrs-mrs.fr SITE - SITE-CONTACT - OS Sgi Unix LANGUAGE C VOLUME - REQUIRES Licence COMMENTS Turbo Frodo represents the new generation of graphics COMMENTS software because it has fast graphics and easy-to-learn COMMENTS pull down menus and dials. Plot files can be generated as COMMENTS Postcript files, which can be plotted on any postcript COMMENTS laser printer, such as for example the one of your COMMENTS Macintosh. COMMENTS Constant upgrading and maintenance ( 2 releases per year) COMMENTS are available. COMMENTS Turbo -X is a new extension of Turbo Frodo using X- motifs COMMENTS on Silicon Graphics Library , Hewlett Packard or on COMMENTS X-terminals ( Colour or black and white). It has most of COMMENTS the facilities found in the original program. COMMENTS For Nationals laboratories and academic research groups COMMENTS interim version of Turbo-X computer COMMENTS software is being made available as a B -site as is it developed. AC BC00456 NAME ICM (Internal Coordinate Mechanics) DOMAIN Molecular modelling and graphics DESCRIPTION ICM is a program for biomolecular structure DESCRIPTION prediction, peptide folding, homology modeling, molecular DESCRIPTION association (docking), molecular graphics and structure DESCRIPTION analysis. DESCRIPTION Applications: modeling by homology, peptide structure DESCRIPTION predictions, protein-protein docking, ligand docking, domain DESCRIPTION movements. DESCRIPTION Shell: 15 objects types including vectors, matrices, molecular DESCRIPTION selections, maps and shell-structures; full arithmetics with the DESCRIPTION objects; loops, conditions, functions, macros. DESCRIPTION Energy: ECEPP/2, surface energy, entropy, grid energy. DESCRIPTION Electrostatics: MIMEL, fast boundary element Poisson DESCRIPTION electrostatics DESCRIPTION Global optimization: Probability Biased Monte Carlo DESCRIPTION minimization, loop sampling, pseudo Brownian Monte Carlo for DESCRIPTION docking. DESCRIPTION Sequence analysis: multiple sequence alignment, secondary DESCRIPTION structure prediction DESCRIPTION Graphics: wire, CPK, ball&stick, ribbon, accessible surface, DESCRIPTION analytical molecular surface, general solid 3D objects, density DESCRIPTION maps, countours, molecular movies. DESCRIPTION Graphics output: Wavefront (.obj), vectorized postscript for DESCRIPTION molecular images, compressed tiff. DESCRIPTION Structure analysis: surface and volume calculations, secondary DESCRIPTION structure assignment, structure superposition DESCRIPTION Searches: fragment searches, spatial similarity searches DESCRIPTION Mathematics: statistics, principal component analysis, 2D and DESCRIPTION 3D plots AUTHOR originally written by Ruben Abagyan AUTHOR rewritten and extended by Ruben Abagyan, Maxim Totrov, Sergei Batalov AUTHOR and the Biosoft group. ADDRESS FAX: (1) (908) 321-4180 RA Abagyan R.A., Totrov M.M., Kuznetsov D.A.; RT "ICM: a new method for structure modeling and design: RT Applications to docking and structure prediction from RT the distorted native conformation."; RL J. Comp. Chem. 15:488-506(1994). RA Abagyan R.A., Totrov M.M.; RT "Biased Probability Monte Carlo Conformational Searches and RT Electrostatic Calculations for Peptides and Proteins."; RL J. Mol. Biol. 235:983-1002(1994). RX Medline; 94118365. RA Totrov M.M., Abagyan R.A.; RT "Detailed ab initio prediction of lysozyme-antibody RT complex with 1.6A accuracy."; RL Nature Structural Biology 1:259-263(1994). RA Totrov M.M., Abagyan R.A.; RT "Efficient parallelization of the energy, surface and RT derivative calculations for internal coordinate mechanics."; RL J. Comp. Chem. 15:1105-1112 (1994). RA Cardozo T., Totrov M., Abagyan R.; RT "Homology modeling by the ICM method"; RL Proteins 23:403-414 RA Totrov M.M., Abagyan R.A.; RT "The Contour-Buildup Algorithm to Calculate the Analytical RT Molecular Surface." RL J. Struct. Biol. 115:1-6(1996). CONTACT info@molsoft.com SITE WWW Server at URL http://www.molsoft.com/ OS Unix, SGI workstation, DEC alpha, Windows NT, Windows 95 LANGUAGE C; Graphic_Library: OpenGL AC BC00459 NAME QTree DOMAIN Molecular modelling and graphics DESCRIPTION A program for generating CPK, ball & stick and DESCRIPTION worms images of proteins using the quad tree algorithm. AUTHOR Andrew C.R. Martin RT - ADDRESS SciTech Software, ADDRESS 23 Stag Leys, ADDRESS Ashtead, ADDRESS Surrey. KT21 2TD, UK ADDRESS Now at: ADDRESS BSM Unit, Dept. Biochem. & Mol. Biol., ADDRESS University College London, ADDRESS Gower Street, ADDRESS London WC1E 6BT CONTACT martin@biochem.ucl.ac.uk SITE WWW Server at URL http://www.biochem.ucl.ac.uk/~martin/text/QTree.readme OS unix, VMS, AmigaDOS, any? LANGUAGE C VOLUME - REQUIRES - AC BC00465 NAME Swiss-PdbViewer DOMAIN Molecular modelling and graphics DESCRIPTION Swiss-PdbViewer is a Macintosh application that can display DESCRIPTION PDB files. Several proteins can be analyzed at the same time DESCRIPTION and can be "piled-up" in 3D space by picking 3 corresponding DESCRIPTION reference atoms of the structures to align. RMS differences DESCRIPTION can then be calculated on selected amino acids of the aligned DESCRIPTION proteins using alpha carbon atoms, backbone atoms, sidechain DESCRIPTION atoms or all atoms. The comparison of active sites and other DESCRIPTION relevant regions is therefore very easy. Swiss-PdbViewer can DESCRIPTION also measure distances, angles, torsions angles between atoms DESCRIPTION as well as add/remove amino acids to/from the view with simple DESCRIPTION mouse clicks thanks to the intuitive graphic and menu driven DESCRIPTION interface. A Control Panel regroups all of the most frequently DESCRIPTION used display facilities so that display/undisplay of individual DESCRIPTION amino acids sidechain, van der Waals dots surface, color, atom DESCRIPTION types and names (according to [1]), are accessible with a single DESCRIPTION click. H-bonds can be estimated for the whole molecule even if the DESCRIPTION PDB file does not provide explicit H atoms, and it is possible to DESCRIPTION mutate amino acids sidechains by browsing a rotamer library [2]. DESCRIPTION The best rotamer is automatically suggested. DESCRIPTION Furthermore, during the mutation process, H-bonds and steric DESCRIPTION hindrances are automatically estimated and displayed in real DESCRIPTION time, facilitating the best rotamer choice. Views can be DESCRIPTION exported as Pdb files, Picts files, or Pov [3] scenes DESCRIPTION descriptions. The short-term purpose is to develop a DESCRIPTION multi-platform (MAC, PC, UNIX) modeling package that will DESCRIPTION allow multiple sequence alignements as well as directly DESCRIPTION submit modeling requests to the SWISS-model server [4]. AUTHOR Nicolas Guex, Manuel Peitsch RA [1] Weiner S.J., Kollman P.A., Case D.A., Singh U.C., RA Ghio C., Alagona G., Profeta S.,Weiner P.K. (1984). RA [2] Ponder J.W. et al.; RL J. Mol. Biol. 215:403-410(1987) RA [4] Peitsch M. C.; RT "Protein modelling by e-mail. From amino acid sequence to protein RT structure: a free one-hour service."; RL Bio/Technology 13:658-660(1995). RX SeqAnalRef; PEIM9502. ADDRESS Glaxo Institute for Molecular Biology ADDRESS ch. des Aulx 14, ADDRESS 1228 Plan-les-Outes, Geneva, Switzerland CONTACT ng45767@ggr.co.uk SITE ftp anonymous expasy.hcuge.ch SITE Directory /pub/PDBViewers/Prot3Dviewer SITE-CONTACT ng45767@ggr.co.uk SITE WWW Server at URL http://expasy.hcuge.ch/swissmod/SWISS-MODEL.html OS Macintosh LANGUAGE - VOLUME - REQUIRES - COMMENTS There are version for Macintosh with FPU and for PowerMac. COMMENTS Suscribe to the Swiss-Flash electronic bulletin to be kept COMMENTS informed of new releases (http://expasy.hcuge.ch/www/swiss-flash.html) COMMENTS [3] Pov is a popular multi-platform free Ray-tracer that COMMENTS can be retrieved by anonymous FTP from: ftp://ftp.povray.org/pub/povray AC BC00466 NAME PdbAlign - PdbDist - DistAlign DOMAIN Molecular modelling and graphics DESCRIPTION Given a GCG multiple sequence alignment file (a GCG MSF file), DESCRIPTION which a includes a sequence of known structure, the program DESCRIPTION pdbalign maps the sequence variability onto the known structure. DESCRIPTION The central premise is of course, that for a closely related DESCRIPTION family of proteins (sequence ID > 40%) the 3-D structures will DESCRIPTION not be significantly different. DESCRIPTION usage: pdbalign [options] [] DESCRIPTION options: -entropy -zvelebil -conservation -pairwise DESCRIPTION where the -zvelebil option refers to the measure of variability DESCRIPTION used in M.Zvelebil, G.J.Barton, W.R.Taylor, M.J.E.Sternberg, DESCRIPTION "Pediction of Protein Secondary Structure and Active Sites using DESCRIPTION the Alignment of Homologous Proteins",J.Mol.Biol, (1987), 195, DESCRIPTION p.957-961. Color by temperature (eg in RasMol) can be used to DESCRIPTION display the output. DESCRIPTION The usage for pdbdist is DESCRIPTION usage: pdbdist [-ligand ] [outfile] DESCRIPTION without the -ligand option (default) HETATM records are used, DESCRIPTION where the definition of ligand is that used by RasMol (ie the DESCRIPTION set of non solvent HETATMs). A given residue can be used as the DESCRIPTION ligand eg. -ligand THR36. pdbdist calculates the distance from DESCRIPTION each atom in the pdb file to each atom in the ligand and records DESCRIPTION the minimum in the temperature field for that atom record. AS DESCRIPTION before, color by temperature (eg in RasMol) can be used to DESCRIPTION display the output pdb file. DESCRIPTION The usage for distalign is DESCRIPTION usage: distalign [-threshold ][-entropy] [-zvelebil] DESCRIPTION distalign reads the output from pdbdist and also the original DESCRIPTION GCG MSF file and produces an MSF file annotated with a measure DESCRIPTION of sequence variability and the distance of the residue at that DESCRIPTION position (of the sequence of known structure) from the ligand. DESCRIPTION Positions of high variabiity but close to the ligand can be DESCRIPTION immediately highlighted. AUTHOR Sayle R., Saqi M.A.S., Weir M.P., Lyall A. RA Sayle R., Saqi M.A.S., Weir M.P., Lyall A.; RT "PdbAlign,PdbDist and DistAlign: Tools to aid in RT relating sequence variability to structure."; RL Comput. Appl. Biosci. 11(5):571-573. ADDRESS Dr. Mansoor Saqi, Bioinformatics Group ADDRESS Dept. of Biomolecular Structure ADDRESS Glaxo Group Research ADDRESS Greenford, Middlx, UK. CONTACT ras32425@ggr.co.uk OR mass15599@ggr.co.uk SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix SITE-CONTACT nethelp@ebi.ac.uk OS Unix LANGUAGE C VOLUME - REQUIRES - Submitted by AC BC00487 NAME WinMGM DOMAIN Protein structure analysis DOMAIN Molecular modelling and graphics DESCRIPTION Visualisation and manipulation tools for biomolecules DESCRIPTION (proteins and nucleic acids) and organic molecules. DESCRIPTION Specific tools for proteins, allowing real-time manipulation DESCRIPTION of molecules represented as CPK, stick and ball, ribbons DESCRIPTION and cylinders. Specific colorations by atomic type, DESCRIPTION atoms of a selected area, of an active site,... DESCRIPTION Manipulation of a few molecules simultaneously. DESCRIPTION Nearly exhaustive parametrisation of all visualisation DESCRIPTION functions. DESCRIPTION Raytracing function for quality drawings. DESCRIPTION Specific build of peptides with geometry optimisation. DESCRIPTION Measure and representation of hydrophobic and DESCRIPTION electrostatic potentials. DESCRIPTION Computation and representation of solvant accessible DESCRIPTION surface. DESCRIPTION False colors representation of atoms by energy level. DESCRIPTION Computation and drawing of hydrogen bonds. DESCRIPTION Ramachandran map, interdistances map,... AUTHOR Mehdi Rahman, Robert Brasseur RA Brasseur, R.; RT "Differentiation of Lipid-associating Helices by Use of RT Three-dimensional Molecular Hydrophobicity Potential RT Calculations."; RL J. Biol. Chem. 266:16120-16127 (1991). RX Medline; 91340764. RX SeqAnalRef; BRAR9101. RA Rahman, M., Brasseur, R.; RT "WinMGM: a fast CPK molecular graphics program for RT analysing molecular structure."; RL J. Mol. Graph. 12:212-218(1994). ADDRESS Centre de biophysique moleculaire numerique ADDRESS 2, passage des Deportes ADDRESS B-5030, Gembloux ADDRESS Belgium ADDRESS Tel: (32)/81/62.25.25 Fax: (32)/81/62.25.22 CONTACT Mehdi Rahman CONTACT mehdirah@fsagx.ac.be SITE WWW Server at URL http://www.fsagx.ac.be/info_faculte/info_dep/info_bp/mehdi/winmgm/winmgmen.htm OS Windows 3.1, Windows 95, Windows NT LANGUAGE C VOLUME about 5 Mo REQUIRES i486 CPU, 8 Mo RAM, good graphic card AC BC00498 NAME Map123d SERVER http://www-bio.lirmm.fr:8090/map123d.html DOMAIN WWW server DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Structure prediction DOMAIN Alignment editing and display DOMAIN Molecular modelling and graphics SERVER http://www-bio.lirmm.fr:8090/map123d.html DESCRIPTION This server offers a set of tools for protein homology modelling. DESCRIPTION The "introduction" page provides a short overview on the DESCRIPTION problem of homology modelling and presents the tools DESCRIPTION available in this server: DESCRIPTION - Global multiple Alignment DESCRIPTION - Secondary structure prediction DESCRIPTION - Evaluation of a structural model AUTHOR H. Ripoche, J. Gracy, L. Chiche RT - ADDRESS LIRMM ADDRESS 161, Rue Ada ADDRESS 34392 MONTPELLIER Cedex 5 - France CONTACT hr@lirmm.fr SITE WWW Server at URL http://www-bio.lirmm.fr:8090/map123d.html OS - LANGUAGE - VOLUME - REQUIRES Java compatible browser (e.g. Netscape 2.0 or above) REQUIRES for some of the tools AC BC00519 NAME ONIX DOMAIN Protein structure analysis DOMAIN Molecular modelling and graphics DOMAIN Image analysis DESCRIPTION PC-based program for Windows, ONIX, allows DESCRIPTION users to examine proteins with known 3D structure from PDB. DESCRIPTION This program was designed for structure investigation of DESCRIPTION ligand binding site in proteins. The last one is a DESCRIPTION combination of certain fragments of protein sequence. Its DESCRIPTION examination requires active participation both of human and DESCRIPTION computer in the process of investigation. ONIX is an DESCRIPTION interactive software with high-performance interface, fast DESCRIPTION 3D molecular graphics and analysis of water-accessible DESCRIPTION surface. This program was designed based on protein DESCRIPTION structure hierarchy. Analysis of molecular surface makes DESCRIPTION possibly to find all elements of ligand binding site. AUTHOR A.S.Ivanov, A.B.Rumjantsev, V.S.Skvortsov, A.I.Archakov RA Ivanov A.S., Rumiantsev A.B., Skvortsov V.S., Archakov A.I.; RT "ONIX: an interactive PC program for the examination RT of protein 3D structure from PDB."; RL Comput. Appl. Biosci. 13:111-113(1997). ADDRESS Prof. Alexis S. Ivanov ADDRESS Institute of Biomedical Chemistry, ADDRESS Pogodinskaya str. 10, ADDRESS Moscow, 119832, Russia. CONTACT ivanov@ibmh.msk.su SITE ftp anonymous org.chem.msu.su SITE Directory pub/software/Onix/ SITE-CONTACT - OS Windows 3.1 or higher LANGUAGE - VOLUME 1.5 Mb REQUIRES PC 386/387 or higher, SVGA 512 kb, Windows 3.1 or higher, REQUIRES graphics mode 640 x 480 x 256 colors. COMMENTS For 3D visualization put marks in the lists and COMMENTS then press key F5 (read Manual in MS WinWord file). AC BC00526 NAME WebMol DOMAIN Protein structure analysis DOMAIN Molecular modelling and graphics DOMAIN WWW server DOMAIN JAVA SERVER http://www.embl-heidelberg.de/cgi/viewer.pl DESCRIPTION WebMol is a Java based program to display and analyze DESCRIPTION molecular structures stored in PDB format. The program DESCRIPTION comprises numerous graphical options as well as analysis DESCRIPTION tools as, for instance, Ramachandran and distance matrix DESCRIPTION plots, helix-helix packing geometrical analysis, detection DESCRIPTION of cavities, steric conflicts and others. AUTHOR Dirk Walther RA Walther D. (1997) RT "WebMol - a Java based PDB viewer."; RL Trends Biochem Sci, 22: 274-275(1997). ADDRESS Dirk Walther, PhD ADDRESS University of California, San Francisco ADDRESS Department of Cellular and Molecular Pharmacology ADDRESS San Francisco, CA 94143-0450, USA ADDRESS email: walther@cmpharm.ucsf.edu ADDRESS http://www.cmpharm.ucsf.edu/~walther/ CONTACT walther@cmpharm.ucsf.edu SITE WWW Server at URL http://www.embl-heidelberg.de/cgi/viewer.pl OS - LANGUAGE JAVA VOLUME - REQUIRES Java capable WWW-browser/ Java runtime system (stand-alone version) COMMENTS A stand-alone version is available from the server. AC BC00534 NAME DRAGON DOMAIN Structure prediction DOMAIN Molecular modelling and graphics DESCRIPTION DRAGON is a protein modelling tool using Distance Geometry. DESCRIPTION It was developed at the Division of Mathematical DESCRIPTION Biology of the NIMR between 1993 and 1996: the algorithms DESCRIPTION were designed by Willie R. Taylor and myself, while I am DESCRIPTION solely responsible for the implementation. DRAGON attempts DESCRIPTION to predict the tertiary structure of a small soluble DESCRIPTION protein, given its sequence, the secondary structure and DESCRIPTION possibly a set of structure-specific restraints. DRAGON DESCRIPTION communicates with you through a simple command-line DESCRIPTION interface which is used to specify parameter values and DESCRIPTION input filenames. During the run, DRAGON keeps you informed DESCRIPTION by writing a lot to the standard output. Finally, the DESCRIPTION model structures are written to coordinate files in PDB DESCRIPTION format. AUTHOR Andras Aszsdi, William R. Taylor RA Aszsdi, A. and Taylor, W. R.; RT "Folding polypeptide alpha-carbon backbones by distance RT geometry methods."; RL Biopolymers 34, 489-505(1994). RA Taylor, W. R. and Aszsdi, A.; RT "Building protein folds using distance geometry: Towards RT a general modelling and prediction method."; RL (In) Merz, K. M., Jr. and LeGrand, S. M. (eds): RL The Protein Folding Problem and Tertiary Structure Prediction, RL Birkhduser, Boston. (Book chapter):165-192(1994). RA Aszsdi, A. and Taylor, W. R.; RT "Secondary structure formation in model polypeptide chains."; RL Protein Engng. 7, 633-644(1994). RA Aszsdi, A., Gradwell, M. J. and Taylor, W. R.; RA "Global fold determination from a small number of RT distance restraints."; RL J. Mol. Biol. 251, 308-326(1995). RA Aszsdi, A. and Taylor, W. R.; RT "Estimating polypeptide alpha-carbon distances from RT multiple sequence alignments."; RL J. Math. Chem. 17, 167-184(1995). RA Aszsdi, A. and Taylor, W. R.; RT "Homology modelling by distance geometry."; RL Folding & Design 1, 325-334(1996). RA Aszsdi, A. and Taylor, W. R.; RT "Hierarchic inertial projection: A fast distance matrix RT embedding algorithm."; RL Computers & Chemistry 21, 13-23(1997). ADDRESS Division of Mathematical Biology ADDRESS National Institute for Medical Research ADDRESS The Ridgeway ADDRESS Mill Hill ADDRESS LONDON ADDRESS NW7 1AA CONTACT Robin Munro SITE WWW Server at URL http://www.nimr.mrc.ac.uk/~mathbio/a-aszodi/dragon.html OS IRIX LANGUAGE c++ VOLUME 1.6 Mb REQUIRES R4400 with 32Mb RAM COMMENTS User guide available at: COMMENTS URL: http://www.nimr.mrc.ac.uk/~mathbio/a-aszodi/ug.html AC BC00546 NAME MOLE DOMAIN Protein structure analysis DOMAIN Molecular modelling and graphics DOMAIN Database and analysis DESCRIPTION Molecular Visualization and Modeling Tool for Windows 95/NT. DESCRIPTION Provides fast ane high quality 3-d graphics based on Open GL DESCRIPTION graphics API. Comes on the CDs bundled with Protein Data Bank. DESCRIPTION Regular updates are offered AUTHOR George Privalov, Natalia Kurochkina RT - ADDRESS Applied Thermodynamics LLC ADDRESS 222 Schilling Circle, suite 130 ADDRESS Hunt Valley, MD 21031 ADDRESS USA CONTACT info@mole3d.com SITE WWW Server at URL http://www.mole3d.com OS Windows 95, Windows NT LANGUAGE C++ VOLUME 12 Mb REQUIRES CD-ROM drive, 256 Colours Graphics or more AC BC00573 NAME WebLab ViewerLite DOMAIN Molecular modelling and graphics DESCRIPTION The WebLab ViewerLite brings high quality molecular graphics DESCRIPTION to your desktop free of charge. DESCRIPTION Download your copy from http://www.msi.com/viewerlite/ AUTHOR Molecular Simulations Inc (MSI) http://www.msi.com RT - ADDRESS Molecular Simulations Inc. ADDRESS 240/250 The Quorum ADDRESS Barnwell Road ADDRESS Cambridge CB5 8RE ADDRESS UK ADDRESS ADDRESS 9685 Scranton Rd. ADDRESS San Diego, CA. 92121 ADDRESS USA CONTACT John Wintersteen, johnw@msi.com SITE WWW Server at URL http://www.msi.com/viewerlite/index.html OS Windows 3.1, Windows 95, Windows NT, Power Macintosh,680x0 Macintosh LANGUAGE - VOLUME - REQUIRES 10MB disk space, 16 MB RAM (32 recommended), REQUIRES 256 colors (32 bit recommended) COMMENTS - AC BC00594 NAME Protein Adviser for Windows DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Molecular modelling and graphics DOMAIN General tools DOMAIN Chemistry DOMAIN Image analysis DOMAIN Comparative analysis DOMAIN Protein 3D visualisation, editing and analysis (QSAR) DESCRIPTION FQS Protein Adviser displays and analyses 3D structures of DESCRIPTION biological molecules such as proteins or nucleic acids. DESCRIPTION Protein Adviser is a powerful tool for visual and numerical DESCRIPTION investigation of protein molecules and their 3D structures. DESCRIPTION The new implementation for Windows 95/98 and NT uses the DESCRIPTION innovative Microsoft technology for rendering molecular DESCRIPTION graphics known as Direct3D. Using Direct 3D technology FQS DESCRIPTION created the fastest biomolecular viewer available on PC DESCRIPTION platform. DESCRIPTION Versatile features to support protein analysis: DESCRIPTION - sequence based 3D analysis DESCRIPTION - Three level selections: atoms, residues, molecules DESCRIPTION - Display/Hide hydrogen's DESCRIPTION - Display/Hide side chain DESCRIPTION - Hydrogen generation DESCRIPTION - Measure atom-atom distances DESCRIPTION - Compare 3D structures DESCRIPTION - Compare aminoacid sequences DESCRIPTION - Analyze Ramachandran plots DESCRIPTION - Mutate and change side chain conformations DESCRIPTION - Build proteins, change torsional angles DESCRIPTION - Copy and paste molecules between the windows DESCRIPTION - Rotate and move selected molecules DESCRIPTION Windows specific features DESCRIPTION Protein Adviser can open as many documents DESCRIPTION as you wish and analyse them within one program session, DESCRIPTION Protein Adviser implements full ActiveX/OLE2 functionality. DESCRIPTION Its objects (molecules) may be placed on your WEB page and DESCRIPTION visualized by your colleagues everywhere through the DESCRIPTION internet. DESCRIPTION Plotting hydrophobicity and other properties DESCRIPTION Protein Adviser for Windows can plot DESCRIPTION different named properties. The program comes with 3 DESCRIPTION different scales of hydrophobicty, including Kyte&Doolittle DESCRIPTION scale. The program includes also 6 other predefined QSAR DESCRIPTION methods. DESCRIPTION Plotting Ramachandran diagrams DESCRIPTION Ramachandran plots show two-dimensional DESCRIPTION histograms of the values of conformational angles phi and DESCRIPTION psi. These histograms are superimposed on the areas of DESCRIPTION allowed and forbidden conformational angles pair values. DESCRIPTION Aminoacids DESCRIPTION Protein Adviser displays sequences of DESCRIPTION aminoacids as 3-letter codes, 1-letter codes or secondary DESCRIPTION structure symbols DESCRIPTION Protein's 3D structure comparison DESCRIPTION Protein Adviser for Windows allows for DESCRIPTION protein structure comparison command. The program DESCRIPTION superimposes the protein's 3D structures based on C(alpha) DESCRIPTION atoms coordinates and RMSD analysis. AUTHOR FQS Ltd. (Fujitsu Kyushu System Engineering Ltd.) RT - ADDRESS FQS Poland Sp. z o.o. ADDRESS Palac Pugetow ADDRESS ul. Starowislna 13-15 ADDRESS 31-038 Krakow ADDRESS Poland ADDRESS Tel. (+48 12) 4294345 ADDRESS Fax. (+48 12) 4296124 CONTACT info@fqspl.com.pl SITE WWW Server at URL http://www.fqspl.com.pl/protein OS Windows 95/98/NT, Macintosh LANGUAGE English, Japanese VOLUME 10 MB REQUIRES PC Pentium 166, 16MB RAM, Microsoft DirectX COMMENTS Commercial software. COMMENTS Price: COMMENTS 800 USD - commercial license & COMMENTS 400 USD - academic licence