Catalogue of Molecular Biology Programs Release 6.1 23 Jul 1999 All thanks are in the file biocatal.thanks. ===================================================================== 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 BC00188 NAME ABACUS DOMAIN Protein structure analysis DESCRIPTION ABaCUS is a no-frills program developed to investigate DESCRIPTION the significance of the putative correspondence between exons DESCRIPTION and units of protein structure. DESCRIPTION This type of analysis takes the form of an attempt to eliminate the DESCRIPTION reference hypothesis (sometimes called a "null" hypothesis) that no DESCRIPTION correspondence exists. A reference hypothesis in this case consists DESCRIPTION of a reference model for random gene structures, and a scoring rule DESCRIPTION for quantifying correspondences. AUTHOR Arlin Stoltzfus RA Stoltzfus A., Spencer D.F., Doolittle W.F.; RT "Methods for evaluating exon-protein correspondances."; RL Comput. Appl. Biosci. 11(5):509-515(1995). ADDRESS CIAR program in Evolutionary Biology, Depart. of Biochemistry, ADDRESS Dalhousie University, Halifax, Nova Scotia, B3H 4H7 Canada. CONTACT arlin@ac.dal.ca SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/unix SITE-CONTACT archive@bio.indiana.edu OS Unix LANGUAGE C VOLUME - AC BC00189 NAME COILS2 DOMAIN Protein structure analysis DESCRIPTION COILS is a program that compares a sequence to a database of known DESCRIPTION parallel two-stranded coiled-coils and derives a similarity score. DESCRIPTION By comparing this score to the distribution of scores in globular DESCRIPTION and coiled-coil proteins, the program then calculates the probability DESCRIPTION that the sequence will adopt a coiled-coil conformation. AUTHOR A. N. Lupas,J. M. Lupas RA Lupas A., van Dyke M., Stock, J.; RT "Predicting Coled Coils from Protein Sequences."; RL Science 252:1162-1164(1991). RX Medline; 91233366. RX SeqAnalRef; LUPA9101. RA Parry D.A.D.; RT "Coiled-coils in alpha-helix-containing proteins: RT analysis of the residue types within the heptad repeat and the use of RT these data in the prediction of coiled coils in other proteins."; RL Biosci. Rep. 2:1017-1024(1982). ADDRESS - CONTACT lupas@vms.biochem.mpg.de SITE ftp anonymous ftp.biochem.mpg.de SITE Directory /vms/coils SITE-CONTACT - OS VMS LANGUAGE PASCAL VOLUME - REQUIRES - COMMENTS The program works well for parallel two-stranded structures COMMENTS that are solvent-exposed but runs progressively into COMMENTS problems with the addition of more helices, their COMMENTS antiparallel orientation and their decreasing length. COMMENTS The program fails entirely on buried structures. AC BC00190 NAME CSI DOMAIN Protein structure analysis DESCRIPTION CSI is a program for determining secondary structure in proteins DESCRIPTION from the chemical shift indices of 1-H and 13-C nuclei. AUTHOR David Wishart, Brian D. Sykes RA Wishart D.S., Sykes B.D.; RT "The 13-C Chemical Shift Index: A Simple Method for the RT Identification of Protein Secondary Structure using 13-C RT Chemical Shift Data"; RL J. Biomol. NMR 4:171:180(1994). RX Medline; 94289984. ADDRESS Protein Engineering Network of Centres of Excellence ADDRESS University of Alberta, Edmonton, Alberta, Canada,T6G 2H7 CONTACT dsw@rigel.biochem.ualberta.ca, leigh@procyon.biochem.ualberta.ca SITE ftp anonymous canopus.biochem.ualberta.ca SITE Directory /pub/ SITE-CONTACT - OS Unix (SUN and SGI) LANGUAGE C VOLUME - REQUIRES - AC BC00191 NAME DSSP DOMAIN Protein structure analysis DESCRIPTION Definition of secondary structure of proteins. DESCRIPTION Produce Dictionary of secondary structure of proteins. DESCRIPTION Defines secondary structure and solvent exposure of proteins, given DESCRIPTION atomic coordinates in Brookhaven Protein Data Bank format. DESCRIPTION NOT a prediction program. AUTHOR Wolfgang Kabsch, Chris Sander RA Kabsch W., Sander C.; RT "Dictionary of protein secondary structure: pattern recognition of RT hydrogen-bonded and geometrical features."; RL Biopolymers 22:2577-2637(1983). RX Medline; 84128824. RX SeqAnalRef; KABW8302. RA Hobohm U., Scharf M., Schneider R., Sander C.; RT "Selection of representative protein data sets."; RL Protein Sci. 1:409-417(1992). RX Medline; 93278275. RX SeqAnalRef; HOBU9201. RA Sander C., Schneider R.; RT "Database of homology-derived protein structures and the structural RT meaning of sequence alignment."; RL Proteins 9:56-68(1991). RX Medline; 91204686. RX SeqAnalRef; SANC9101. RT Holm L., Ouzounis C., Sander C., Tuparev G., Vriend G.; RT "A database of protein structure families with RT common folding motifs."; RL Protein Sci. 1:1691-1698(1992). RX Medline; 93284107. RX SeqAnalRef; HOLL9203. ADDRESS EMBL - 69012 Heidelberg - Germany ADDRESS Fax : +49-6221-387 517 CONTACT Sander@embl-heidelberg.de SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix SITE-CONTACT nethelp@ebi.ac.uk SITE WWW Server at URL http://www.ebi.ac.uk OS Unix, VMS LANGUAGE - VOLUME - REQUIRES - COMMENTS You need to fill a licence agreement to get this program. AC BC00192 NAME LIGPLOT DOMAIN Protein structure analysis DESCRIPTION LIGPLOT generates schematic diagrams of protein-ligand DESCRIPTION interactions directly from the 3D coordinates of the protein and DESCRIPTION its bound ligand. It produces clear and simple diagrams DESCRIPTION illustrating the key interactions involved, giving an DESCRIPTION at-a-glance representation of the important atoms and residues DESCRIPTION in both protein and ligand. Diagrams of this sort are often DESCRIPTION presented in the literature to clarify the interactions; to DESCRIPTION show, for example,which atoms of the ligand are hydrogen-bonded DESCRIPTION to which residues in the protein. The diagrams are often drawn DESCRIPTION by hand and can be time-comsuming to produce. LIGPLOT makes the DESCRIPTION process entirely automatic. The interactions shown are those DESCRIPTION mediated by hydrogen bonds and by hydrophobic contacts. DESCRIPTION Hydrogen-bond distances can be printed on the bonds if required. DESCRIPTION Atom accessibilities can also be depicted, indicating which DESCRIPTION parts of the ligand are buried and which are DESCRIPTION solvent-accessible. In essence, the program unrolls and unfolds DESCRIPTION what can often be a complicated 3D network of interactions into DESCRIPTION a clear and simple 2D picture that gives an at-a-glance DESCRIPTION depiction of the key interactions. The output is a PostScript DESCRIPTION file and can be in colour as well as in black-and-white. AUTHOR Andrew Wallace, Roman Laskowski RT - ADDRESS University College London, UK CONTACT wallace@bsm.bioc.ucl.ac.uk CONTACT roman@bsm.bioc.ucl.ac.uk SITE ftp anonymous ftp.biochem.ucl.ac.uk SITE Directory /pub/ligplot SITE-CONTACT - OS Unix LANGUAGE C VOLUME - REQUIRES - COMMENTS The inputs to the program are the PDB file to be processed and a COMMENTS list of hydrogen bonds and non-bonded contacts in the structure. COMMENTS (The program does not currently calculate these itself). You can COMMENTS generate these lists using your own software, but we recommend COMMENTS using HBPLUS (written by Ian McDonald at UCL) which many sites COMMENTS now have. LIGPLOT will read HBPLUS output automatically. If you COMMENTS do not have HBPLUS, you can obtain a copy from the same COMMENTS anonymous ftp site as that for LIGPLOT (described below), from COMMENTS the directory pub/hbplus. AC BC00193 NAME MEMSAT DOMAIN Protein structure analysis DESCRIPTION MEMbrane protein Structure And Topology AUTHOR Dr David T. Jones RA Jones D.T., Taylor W.R., Thornton J.M.; RT "A model recognition approach to the prediction of all-helical RT membrane protein structure and topology."; RL Biochemistry 33:3038-3049(1994). RX Medline; 94176498. RX SeqAnalRef; JONE9401. ADDRESS Biomolecular Structure and Modelling Unit ADDRESS Department of Biochemistry and Molecular Biology ADDRESS University College ADDRESS Gower Street ADDRESS London WC1E 6BT ADDRESS United Kingdom CONTACT jones@bsm.bioc.ucl.ac.uk SITE ftp anonymous ftp.biochem.ucl.ac.uk SITE Directory /pub/MEMSAT SITE-CONTACT - OS PC (386), Unix LANGUAGE C VOLUME - COMMENTS The source code is available, by sending by the COMMENTS licence agreement. It compiles without problems COMMENTS under Unix. REQUIRES - 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 BC00195 NAME PROSA DOMAIN Protein structure analysis DESCRIPTION Prosa II is a powerful tool in protein structure research. DESCRIPTION It supports and guides your studies aimed at the determination of DESCRIPTION a protein's native fold. It is helpful for experimental structure DESCRIPTION determinations and modeling studies. DESCRIPTION Prosa II assists you in protein structure quality control. DESCRIPTION It calculates a score for your input-structure. DESCRIPTION Scores of native protein folds are in a characteristic range. DESCRIPTION If your score is outside this range then your structure may have problems. DESCRIPTION Energy graphs display the energetic architecture of protei DESCRIPTION folds as a function of amino acid sequence position. AUTHOR Manfred.J.Sippl (sippl@olga.came.sbg.ac.at) RT - ADDRESS Center of Applied Molecular Engineering, ADDRESS Jakob-Haringer-Str. 1, A-5020 SALZBURG / Austria CONTACT prosa@agnes.came.sbg.ac.at SITE ftp anonymous gundi.came.sbg.ac.at SITE Directory /PROSA SITE-CONTACT floeckn@wst.edvz.sbg.ac.at OS SGI with IRIX 5.x, DEC ALPHA OSF1(2.0) LANGUAGE C VOLUME - REQUIRES To run the program you need a licence and code number REQUIRES Free licences for academic users are valid for one year. REQUIRES Contact prosa@agnes.came.sbg.ac.at REQUIRES For commercial usage please contact: sippl@irina.came.sbg.ac.at AC BC00346 NAME TOPS DOMAIN Protein structure analysis DESCRIPTION Program to automatically generate and edit protein DESCRIPTION topology cartoons. These cartoons are two dimensional DESCRIPTION representations of the secondary structure of proteins, DESCRIPTION where helices are represented by circles and strands DESCRIPTION by triangles. TOPS is made of two parts: Tops, the main DESCRIPTION ansi C program and Xtops, an X windows topology cartoon DESCRIPTION editor. AUTHOR Tom Flores RA Flores T.P., Moss D.S., Thornton J.M.; RT "An Algorithm to Automatically Generate Protein RT Topology Cartoons."; RL Protein Eng. 7:31-37(1993). RX Medline; 94188348. RX SeqAnalRef; FLOT9401. ADDRESS EMBL Outstation, Hinxton - the European Bioinformatics Institute ADDRESS Hinxton Hall, Hinxton, ADDRESS Cambridge CB10 1RQ, UK CONTACT flores@ebi.ac.uk SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/contrib/TOPS SITE WWW server at URL http://www.ebi.ac.uk/contrib/flores/TOPS/tops.html SITE-CONTACT nethelp@ebi.ac.uk OS unix, dos LANGUAGE C, tcl/tk VOLUME - REQUIRES tcl/tk AC BC00359 NAME PROTEAN DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Protein analysis tools DESCRIPTION PROTEAN finds structural motifs, beta sheets, alpha helices DESCRIPTION and turns, and plots hydrophobicity and charge, among DESCRIPTION other functions. A large library of analytical methods is DESCRIPTION available to predict protein structure. The software can also DESCRIPTION locate antigenic determinants and predict protease digestion DESCRIPTION patterns. The simple, elegant interface presents the most DESCRIPTION comprehensive suite of protein analysis tools available. AUTHOR - RT - ADDRESS DNASTAR, Inc. ADDRESS 1228 South Park Street ADDRESS Madison, WI 53715,U.S.A. ADDRESS Tel: +1-608-2587420, Fax: +1-608-2587439 CONTACT - sales@dnastar.com SITE - SITE-CONTACT - OS Win95/NT and MacIntosh LANGUAGE - VOLUME - REQUIRES LaserGene protein and DNA sequence analysis package COMMENTS Commercial software AC BC00379 NAME TopPredII DOMAIN Protein structure analysis DESCRIPTION Prediction of transmembrane segments in integral DESCRIPTION membrane proteins, and the putative topologies. AUTHOR Claros M.G and von Heijne G. RA Claros M.G., von Heijne G.; RT "TopPred II: an improved software for membrane protein RT structures predictions."; RL Comput. Appl. Biosc. 10(6):685-685(1994). RX SeqAnalRef; CLAM9401. ADDRESS Manuel G. CLAROS ADDRESS Biologia Molecular, Facultad Ciencias, E-29071 Malaga CONTACT claros@cica.es or gvh@cbs.ki.se SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/mac SITE-CONTACT nethelp@ebi.ac.uk OS MacOS LANGUAGE - VOLUME 614k REQUIRES - COMMENTS TopPred II is now available in two different versions: COMMENTS - "TopPredII 1.1" which is "compatible" with any kind of macintosh COMMENTS computer. COMMENTS - "TopPredII 1.1 FPU" which is a "rapid" version of TopPred. This one COMMENTS needs a macintosh with a 68020 processor or later, containing an FPU. COMMENTS This version is significatively faster making profiles and COMMENTS constructing protein topologies (in several cases up to 6-fold COMMENTS faster) AC BC00384 NAME PROANAL DOMAIN Protein structure analysis DESCRIPTION ProAnal isfor analysis of the structure-activity relationship in DESCRIPTION a family of evolutionarily related (and/or artificially mutated) DESCRIPTION proteins/peptides. The program uses aligned amino acid DESCRIPTION sequences with data of their activity (pK, Km, ED50 or any DESCRIPTION other) and searches for correlations between data on activity DESCRIPTION and various physico-chemical characteristics of different DESCRIPTION regions in primary structures. In automatic mode, the program DESCRIPTION generates and verifies hypotheses on the disposition of a DESCRIPTION sequential modulating region in a protein, and key DESCRIPTION characteristics of the region. In manual mode, users can DESCRIPTION generate and analyze their own hypotheses. The program is DESCRIPTION implemented on IBM PC or compatible computers. It is designed to DESCRIPTION be easily handled by the occasional computer user and yet it is DESCRIPTION powerful enough for experienced professionals. Pro__Anal DESCRIPTION operation is demonstrated on the example of finding modulating DESCRIPTION centers in a family of disintegrins-proteins from snake venoms DESCRIPTION which inhibit fibrinogen interaction with platelet receptors. In DESCRIPTION another example it is shown that the immunogenicity of peptides DESCRIPTION is connected with their positive charge. AUTHOR Alexey Eroshkin RA Eroshkin A.M., Fomin V.I., Zhilkin P.A.; RT "Algorithm and computer program ProAnal for analysis of RT relationship between structure and activity in a family RT of proteins or peptides."; RL Comput. Appl. Biosci. 9:491-497(1993). RX Medline; 94123132. RX SeqAnalRef; EROA9301. RA Eroshkin A.M., Fomin V.I., Zhilkin P.A., Ivanisenko V.V., RA Kondrakhin Y.V.; RT "PROANAL version 2: multifunctional program for analysis RT of multiple protein sequence alignments and for studying RT the structure-activity relationships in protein families."; RL Comput. Appl. Biosci. 11:39-44(1995). ADDRESS Research Institute of Molecular Biology, ADDRESS SRC VB "Vector", Koltsovo, Novosibirsk Region. ADDRESS 633159 Russia ADDRESS Tel: +7 (3832) - 647774 ADDRESS Fax: +7 (3832) - 328831 CONTACT eroshkin@vector.nsk.su SITE ftp anonymous ft.ebi.ac.uk SITE Directory /pub/software/dos SITE-CONTACT nethelp@ebi.ac.uk SITE WWW Server at URL http://www.ebi.ac.uk/ OS MS-DOS LANGUAGE - VOLUME - REQUIRES EGA/VGA card AC BC00391 NAME BCM Search Launcher DOMAIN WWW server DOMAIN Sequence format conversion tools DOMAIN Sequence analysis DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Structure prediction DOMAIN Pattern Identification DOMAIN Alignment Search software DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN Restriction maps DOMAIN Database and analysis DOMAIN Searching databases DOMAIN Statistical significance DOMAIN Comparative analysis SERVER http://www.hgsc.bcm.tmc.edu/SearchLauncher/ DESCRIPTION The BCM Search Launcher is an integrated set of World- DESCRIPTION Wide Web (WWW) pages that organize molecular biology- DESCRIPTION related search and analysis services available on the DESCRIPTION WWW by function, and provide a single point-of-entry for DESCRIPTION related searches. The Protein Sequence Search Page, for DESCRIPTION example, provides a single sequence entry form for DESCRIPTION submitting sequences to WWW servers that provide remote DESCRIPTION access to a variety of different protein sequence search DESCRIPTION tools, including BLAST, FASTA, Smith-Waterman, BEAUTY, DESCRIPTION PROSITE, and BLOCKS searches. Other Launch pages provide DESCRIPTION access to 1) nucleic acid sequence searches, 2) multiple DESCRIPTION and pairwise sequence alignments, 3) gene feature searches, DESCRIPTION 4) protein secondary structure prediction, and 5) DESCRIPTION miscellaneous sequence utilities (e.g., 6-frame DESCRIPTION translation). The BCM Search Launcher also provides a DESCRIPTION mechanism to extend the utility of other WWW services by DESCRIPTION adding supplementary hypertext links to results returned DESCRIPTION by remote servers. For example, links to the NCBI's DESCRIPTION Entrez database and to the Sequence Retrieval System DESCRIPTION (SRS) are added to search results returned by the NCBI's DESCRIPTION WWW BLAST server. These links provide easy access to DESCRIPTION auxiliary information, such as Medline abstracts, that DESCRIPTION can be extremely helpful when analyzing BLAST database DESCRIPTION hits. For new or infrequent users of sequence database DESCRIPTION search tools, we have pre-set the default search parameters DESCRIPTION to provide the most informative first-pass sequence DESCRIPTION analysis possible. We have also developed a batch client DESCRIPTION interface for Unix and Macintosh computers that allows DESCRIPTION multiple input sequences to be automatically searched as DESCRIPTION a background task, with the results returned as individual DESCRIPTION HTML documents directly to the user's system. AUTHOR Randall F. Smith, Brent A. Wiese, Mary K. Wojzynski, AUTHOR Daniel B. Davison , and Kim C. Worley RA Smith R.F., Wiese B.A., Wojzynski M.K., Davison D.B., Worley K.C.; RT "BCM Search Launcher--An integrated interface to molecular RT biology database search and analysis services available on RT the World-Wide Web."; RL Submitted. ADDRESS Randall F. Smith, Ph.D. ADDRESS Department of Molecular and Human Genetics, T-921, ADDRESS Baylor College of Medicine ADDRESS One Baylor Plaza, Houston, TX 77030, USA ADDRESS Tel: +1 (713) 798-4735 Fax: +1 (713) 798-5386 CONTACT rsmith@bcm.tmc.edu CONTACT kworley@bcm.tmc.edu SITE WWW Server at URL http://www.hgsc.bcm.tmc.edu/SearchLauncher/ SITE-CONTACT rsmith@bcm.tmc.edu SITE WWW Server at URL http://dot.imgen.bcm.tmc.edu:9331/downloads/software/batch_client.html SITE give information about the downloads SITE ftp anonymous dot.imgen.bcm.tmc.edu for a batch client SITE Directory /pub/software/search-launcher OS Unix and Macintosh for the batch client LANGUAGE Perl (on Unix), AppleScript (on Macintosh) VOLUME - REQUIRES MacTCP on Macintosh and AppleScript, Perl on Unix AC BC00397 NAME ProFIT DOMAIN Protein structure analysis DESCRIPTION ProFIT (Protein Fold Identification Tool) combines an aminoacid DESCRIPTION sequence with a database of 3D structures, and has the potential DESCRIPTION to detect a fold related to the native structure DESCRIPTION of the input sequence. This is a beta-release. It is DESCRIPTION still experimental and will change during the following months. AUTHOR Manfred.J.Sippl RT - ADDRESS Center Of Applied Molecular Engineering ADDRESS Jakob-Haringer Str. 1 ADDRESS A-5020 Salzburg / AUSTRIA CONTACT sippl@olga.came.sbg.ac.at SITE ftp anonymous Gundi.came.sbg.ac.at SITE Directory /pub/Profit SITE-CONTACT root@gundi.came.sbg.ac.at OS UNIX (SGI and DEC ALPHA Workstations) LANGUAGE - VOLUME - REQUIRES - COMMENTS Licenses are distributed on a one machine one license basis. COMMENTS A licence is valid for one year. COMMENTS Licenses are free of charge for academic users. COMMENTS For commercial licenses please contact Manfred.J.Sippl 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 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 BC00410 NAME TMAP DOMAIN e-mail Server ANALYSIS DOMAIN Protein structure analysis SERVER Tmap@EMBL-Heidelberg.de DESCRIPTION The TMAP program predicts transmembrane segments in proteins DESCRIPTION It uses information in multiple sequence alignments of DESCRIPTION related proteins (higher prediction accuracy can be achieved DESCRIPTION with multiple alignments than with single sequences) to DESCRIPTION 1 - identify helical transmembrane segments DESCRIPTION 2 - predict the membrane topology of the family. AUTHOR Bengt Persson, Frank Milpetz & Patrick Argos RA Persson B., Argos, P.; RT "Prediction of transmembrane Segments in proteins RT utilising multiple sequence alignments."; RL J. Mol. Biol. 237:182-192(1994). RX Medline; 94172640. RX SeqAnalRef; PERB9401. RA Milpetz F., Argos P., Persson B.; RT "TMAP: a new email and WWW service for membrane-proein RT structural predictions."; RL Trends Biochem. Sci. 20:204-205(1995). RX Medline; 95334825. RX SeqAnalRef; MILF9501. ADDRESS European Molecular Biology Laboratory, ADDRESS Meyerhofstrasse 1, Postfach 10.2209, ADDRESS D-69012 heidelberg, Germany CONTACT Milpetz@EMBL-Heidelberg.de SITE WWW Server at URL http://www.embl-heidelberg.de/tmap/tmap_info.html OS - LANGUAGE - VOLUME - REQUIRES - AC BC00426 NAME SAMSON DOMAIN Sequence analysis DOMAIN RNA analysis DOMAIN Protein structure analysis DESCRIPTION The SAMSON package is a tool for advanced analysis of DESCRIPTION primary DNA, RNA and protein structures. The package consists DESCRIPTION of 16 programs performing statistical analysis and comparison DESCRIPTION of biopolymer sequences, search for homologies, translation of DESCRIPTION DNA and RNA sequences into amino acid sequences, splicing of DESCRIPTION RNA sequences and restriction map construction, recognition of DESCRIPTION functionally related sites in biopolymer molecules, textual DESCRIPTION analysis of DNA and RNA regulatory sites and prediction of DESCRIPTION intermolecular hybridization sites in DNA and RNA molecules. DESCRIPTION The SAMSON package consists of: DESCRIPTION - 16 applied programs in form of executable modules under DESCRIPTION MS-DOS v. 3.0 or higher; DESCRIPTION - the Microsoft FORTRAN 5.0 source library containing DESCRIPTION standard input-output and simple sequence processing routines; DESCRIPTION - ASCII-files with manuals (in russian); DESCRIPTION - helpfiles and other things that are need for learning DESCRIPTION the software usage. AUTHOR Nazipova N.N., Shabalina S.A., Ogurtsov A.Yu., Kondrashov A.S., AUTHOR Roytberg M.A., Butryakov G.V., Vernoslov S.E.; RA Nazipova N.N., Shabalina S.A., Ogurtsov A.Yu., RA Kondrashov A.S., Roytberg M.A., Butryakov G.V., RA Vernoslov S.E.; RT "SAMSON: a software package for the biopolymer RT primary structure analysis."; RL Comput. Appl. Biosci. 11(4):423-426 (1995). ADDRESS Institute of Mathematical Problems of Biology, ADDRESS Russian Academy of Sciences, Pushchino, Moscow region,142292 Russia CONTACT NNN@impb.serpukhov.su or shab@imbp.serpukhov.su SITE - SITE-CONTACT - OS MS-DOS LANGUAGE MS FORTRAN 5.0 VOLUME - REQUIRES MS-DOS v. 3.0 or higher AC BC00448 NAME FSSP DOMAIN WWW server DOMAIN Protein structure analysis DOMAIN Alignment browser SERVER http://www.embl-heidelberg.de/dali/fssp/ DESCRIPTION Use WWW browsers to view fold classification DESCRIPTION and multiple structure alignments. AUTHOR L. Holm RA Holm L., Sander C.; RT The FSSP database of structurally aligned protein fold families. RL Nucleic Acids Res. 22:3600-3609(1994). RX Medline; 95023099. RX SeqAnalRef; HOLL9401. ADDRESS L. Holm, EMBL Outstation - EBI, Hinxton Hall, Cambridge CB10 1RQ, U.K. CONTACT dali-help@embl-heidelberg.de SITE WWW server at URL http://www.embl-heidelberg.de/dali/fssp/ SITE-CONTACT - OS - LANGUAGE Perl VOLUME - REQUIRES - AC BC00460 NAME ProFit DOMAIN Protein structure analysis DESCRIPTION Designed to be the "ultimate" protein least squares fitting DESCRIPTION program. Uses a simple command language to specify atoms, DESCRIPTION zones, etc. to be fitted. RMS may be displayed over the DESCRIPTION same, or different, atoms and zones. ProFit also alows DESCRIPTION fitting zones to be calculated automatically from a DESCRIPTION sequence alignment, or an alignment file may be supplied DESCRIPTION to specify the zones. Includes an on-line help facility. 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/#profit OS unix, vms, AmigaDOS, any? LANGUAGE C VOLUME - REQUIRES - 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 BC00538 NAME DRAWHCA SERVER http://www.lmcp.jussieu.fr/~mornon DOMAIN WWW server DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DESCRIPTION This WWW page enables you to draw an HCA (Hydrophobic Cluster DESCRIPTION Analysis)plot using the program drawhca. This server provides DESCRIPTION plots as colour or b&w PostScript files. AUTHOR Luc Canard, Alain Soyer RT - ADDRESS Jean-Paul Mornon ADDRESS Laboratoire de Mineralogie-Cristallographie - CNRS URA09 ADDRESS Universite Pierre et Marie Curie ADDRESS Tour 16, 2e etage, Boite 115 ADDRESS 4, place Jussieu ADDRESS F-75252 PARIS CEDEX 05 ADDRESS FRANCE CONTACT mornon@lmcp.jussieu.fr SITE WWW Server at URL http://www.lmcp.jussieu.fr/~mornon/ OS - LANGUAGE - VOLUME - REQUIRES - 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 BC00549 NAME k2d DOMAIN Protein structure analysis DOMAIN Neural Networks DOMAIN WWW server SERVER http://kal-el.ugr.es/k2d/spectra.html DESCRIPTION Algorithm for the estimation of the percentages of DESCRIPTION protein secondary structure from UV circular dichroism DESCRIPTION spectra using a Kohonen neural network with a 2-dimensional DESCRIPTION output layer. You can either use k2d via a web server or DESCRIPTION get the program and run it on your machine. AUTHOR M.A. Andrade, P. Chacon, J.J. Merelo, F. Moran RA Andrade, M.A., Chacon P., Merelo J.J and Moran F.; RT "Evaluation of secondary structure of proteins from RT UV circular dichroism using an unsupervised learning RT neural network."; RL Prot. Eng. 6:383-390(1993). RA Merelo, J.J., Andrade M.A., Prieto A. and Moran F.; RT "Proteinotopic Feature Maps."; RL Neurocomputing. 6:443-454(1994). ADDRESS Miguel A. Andrade ADDRESS EMBL Outstation - European Bioinformatics Institute, ADDRESS Wellcome Trust Genome Campus ADDRESS Hinxton, Cambridge CB10 1SD, UK CONTACT andrade@ebi.ac.uk SITE WWW Server at URL http://kal-el.ugr.es/k2d/spectra.html SITE-CONTACT andrade@ebi.ac.uk OS Unix, DOS LANGUAGE C VOLUME 4Mb REQUIRES - COMMENTS More information at COMMENTS http://columba.ebi.ac.uk:8765/~andrade/k2d.html AC BC00553 NAME USF - Uppsala Software Factory DOMAIN Protein structure analysis DOMAIN Crystallography DESCRIPTION The Uppsala Software Factory provides software, DESCRIPTION web-based services and other resources for DESCRIPTION structural biologists (in particular, but not exclusively, DESCRIPTION for macromolecular crystallographers). DESCRIPTION All software can be downloaded free of charge by DESCRIPTION academics. For-profit insitutes and companies DESCRIPTION need to obtain a license. AUTHOR Gerard J Kleywegt AB http://alpha2.bmc.uu.se/~gerard/manuals/references.html AB http://alpha2.bmc.uu.se/~gerard/manuals/citing.html ADDRESS Dr. Gerard J. Kleywegt ADDRESS Department of Molecular Biology ADDRESS Uppsala University ADDRESS Biomedical Centre ADDRESS Box 590 ADDRESS SE-751 24 Uppsala ADDRESS SWEDEN CONTACT gerard@xray.bmc.uu.se SITE WWW Server at URL http://alpha2.bmc.uu.se/~gerard/manuals/ OS SGI, DEC Alpha OSF1, ESV LANGUAGE Fortran VOLUME varies REQUIRES varies AC BC00568 NAME JOY SERVER http://www-cryst.bioc.cam.ac.uk/cgi-bin/joy.cgi DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Alignment editing and display DOMAIN WWW server DOMAIN Comparative analysis DESCRIPTION JOY is a program to annotate protein sequence alignments DESCRIPTION with three-dimensional (3D) structural features. It was DESCRIPTION developed to display 3D structural information in a sequence DESCRIPTION alignment and to help understand the conservation of amino DESCRIPTION acids in their specific local environments. The JOY DESCRIPTION representation now constitutes an essential part of the two DESCRIPTION databases of protein structure alignments: HOMSTRAD DESCRIPTION (http://www-cryst.bioc.cam.ac.uk/~homstrad) and CAMPASS DESCRIPTION (http://www-cryst.bioc.cam.ac.uk/~campass). It has also been DESCRIPTION successfully used for identifying distant evolutionary DESCRIPTION relationships. DESCRIPTION DESCRIPTION JOY takes an input alignment (or a single sequence) in a DESCRIPTION format similar to that of the NBRF/PIR format and produces a DESCRIPTION number of output files, including the annotated alignment in DESCRIPTION PostScript, LATEX and HTML. JOY requires a series of DESCRIPTION datafiles containing information about secondary structures, DESCRIPTION solvent accessibility and hydrogen bonding. These are DESCRIPTION produced automatically from a PDB file by supporting DESCRIPTION programs. AUTHOR Kenji Mizuguchi, Charlotte M. Deane, Tom L. Blundell, AUTHOR Mark S. Johnson, John P. Overington RA Mizuguchi K., Deane C.M., Johnson M.S., Blundell T.L., Overington J.P.; RT "JOY: protein sequence-structure representation and analysis."; RL Bioinformatics 14:617-623(1998). ADDRESS Department of Biochemistry ADDRESS University of Cambridge ADDRESS 80 Tennis Court Road ADDRESS Cambridge CB2 1GA ADDRESS UK CONTACT kenji@cryst.bioc.cam.ac.uk SITE WWW Server at URL http://www-cryst.bioc.cam.ac.uk/cgi-bin/joy.cgi OS UNIX LANGUAGE Fortran, C, Perl VOLUME - REQUIRES - COMMENTS Currently only executable files for IRIX5.3 or highter are COMMENTS available, but distribution of the source code to academic COMMENTS users will follow. AC NC00581 NAME SIMLYS DOMAIN Protein structure analysis DOMAIN WWW server SERVER http://bionm4.biochem.rwth-aachen.de/FB2/Simlys/simlys0.html DESCRIPTION SIMLYS a program for trajectory/conformational analysis of DESCRIPTION (bio)molecular simulations and/or experimental X-ray, NMR DESCRIPTION structures (PDB-format). Version 4.0 (1998) free available. DESCRIPTION Installation possible on various operating systems. AUTHOR Peter Krueger, Angelika Szameit RA Krueger, Lueke, Szameit; RL Comput.Phys.Commun. 62:371-380(1991). RA Krueger, Szameit; RL Comput.Phys.Commun. 72:265-268(1992). ADDRESS Peter Krueger ADDRESS Laboratory of Chemical and Biological Dynamics ADDRESS Katholieke Universiteit Leuven ADDRESS Celestijnenlaan 200 D ADDRESS B-3001 Leuven Belgium CONTACT E-mail: peter@lcbdiris.fys.kuleuven.ac.be CONTACT or : peter@bionm1.biochem.rwth-aachen.de SITE WWW Server at URL http://bionm4.biochem.rwth-aachen.de/FB2/Simlys/simlys0.html SITE-CONTACT - OS Unix, MS-Dos, Windos 95/NT LANGUAGE Fortran VOLUME 580 KB REQUIRES Fortran compiler AC BC00588 NAME DAMBE (Data analysis in molecular biology and evolution) DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN Genetic tools DOMAIN Molecular Evolution DOMAIN Phylogeny DOMAIN Database and analysis DOMAIN Searching databases DOMAIN General tools DOMAIN Statistical significance DOMAIN Comparative analysis DESCRIPTION DAMBE (Data Analysis in Molecular Biology DESCRIPTION and Evolution) is an integrated software package for DESCRIPTION converting, manipulating, statistically and graphically DESCRIPTION describing and analyzing molecular sequence data, with a DESCRIPTION user-friendly Windows 95 interface. AUTHOR Xuhua Xia RT - ADDRESS Department of Ecology & Biodiversity, ADDRESS University of Hong Kong, Hong Kong CONTACT xxia@hkusua.hku.hk SITE WWW Server at URL http://web.hku.hk/~xxia/software/software.htm OS Windows 95 LANGUAGE - VOLUME 10 MB REQUIRES Windows 95 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 AC BC00600 NAME Jpred - consensus secondary structure prediction server DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Structure prediction DOMAIN JAVA DOMAIN WWW server SERVER http://barton.ebi.ac.uk/servers/jpred.html DESCRIPTION Jpred is a internet web server that takes DESCRIPTION either a protein sequence or a mulitple alignment of DESCRIPTION protein sequences, and predicts secondary structure. It DESCRIPTION works by combining a number of modern, high quality DESCRIPTION prediction methods to form a consensus. DESCRIPTION DESCRIPTION Jpred runs DSC, PHD, PREDATOR and NNSSP to build it's consensus DESCRIPTION prediction, but predictions from older algorithms Mulpred and DESCRIPTION Zpred are also included in the final output. DESCRIPTION DESCRIPTION The consensus method has been shown, to be DESCRIPTION on average more accurate than any of the component methods, DESCRIPTION by ca. 1%. However the strength of this server lies in the DESCRIPTION fact that it leaves the final decision to the user who can DESCRIPTION use the supplied coloured HTML and Java viewer to decide DESCRIPTION where the best or most sensible consensus may be. AUTHOR Cuff J. A., Clamp M. E., Siddiqui A. S., Finlay M., Barton G. J. RA Cuff J. A. and Barton G. J.; RT "Evaluation and improvement of multiple sequence methods RT for protein secondary structure prediction."; RL PROTEINS: Structure, Function and Genetics. 34:508-519 (1999). RA Cuff, J. A., Clamp, M. E., Siddiqui, A. S., Finlay, M. RA and Barton, G. J. RT "Jpred: a consensus secondary structure prediction server."; RL Bioinformatics 14:892-893 (1998). ADDRESS EMBL-European BioInformatics Institute, ADDRESS Wellcome Trust Genome Campus, Hinxton Cambs. ADDRESS CB10 1SD, UK CONTACT geoff@ebi.ac.uk SITE WWW Server at URL http://barton.ebi.ac.uk/servers/jpred.html OS - LANGUAGE - VOLUME - REQUIRES Netscape/IE > 4, with JAVA