Catalogue of Molecular Biology Programs Release 6.1 23 Jul 1999 All thanks are in the file biocatal.thanks. ===================================================================== AC BC00285 NAME AMPHI DOMAIN Structure prediction DOMAIN GCG tools DESCRIPTION Prediction of membran protein structure AUTHOR Jaehnig F. RX Medline; 90223529. RX SeqAnalRef; JAHF9001. RA Jahnig F.; RT "Structure predictions of membrane proteins are not that bad."; RL Trends Biochem. Sci. 15:93-95(1990). ADDRESS - CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/vms SITE-CONTACT Dan Davison dbd@theory.bchs.uh.edu OS Vax/VMS LANGUAGE FORTRAN VOLUME - REQUIRES GCG v6 for plotting AC BC00286 NAME ASSP DOMAIN Structure prediction DESCRIPTION Takes a multiple sequence alignment and estimates the lower DESCRIPTION limit in accuracy one should expect for a perfect consensus DESCRIPTION secondary structure prediction based on the alignment. AUTHOR - RA Russell R. B., Barton G. J.; RT "The Limits of Protein Structure Prediction Accuracy From RT Multiple Sequence Alignment."; RL J. Mol. Biol. 234:951-957(1993). RX Medline; 94087754. RX SeqAnalRef; RUSR9301. ADRESS University of Oxford Laboratory of Molecular Biophysics ADRESS Rex Richards Building , South Parks Road ADRESS Oxford OX1 3QU UK. CONTACT Barton, G. J.: gjb@bioch.ox.ac.uk SITE - SITE - SITE-CONTACT - OS Sun, SGI LANGUAGE C VOLUME - AC BC00287 NAME GARNIER DOMAIN Structure prediction DESCRIPTION A secondary structure prediction program DESCRIPTION using the method of Garnier, Osgusthorpe, DESCRIPTION and Robson, J. Mol. Biol. 120:97-120(1978). AUTHOR William R. Pearson RA Garnier J., Osguthorpe D.J., Robson B.; RT "Analysis of the accuracy and implications of simple methods for RT predicting the secondary structure of globular proteins."; RL J. Mol. Biol. 120:97-120(1978). RX Medline; 78153763. RX SeqAnalRef; GARJ7801. ADDRESS U. of Virginia Dept. of Biochemistry, USA CONTACT William R. Pearson wrp@virginia.edu SITE ftp anonymous ftp.virginia.edu SITE Directory /pub/fasta = fasta(version number) SITE-CONTACT William Pearson wrp@virginia.edu OS all LANGUAGE - VOLUME - AC BC00288 NAME HTH DOMAIN Structure prediction DESCRIPTION Prediction of helix-turn-helix regions in DESCRIPTION protein sequences AUTHOR Halling C. RT - ADDRESS - CONTACT - SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/search SITE-CONTACT D Gilbert: gilbertd@cricket.bio.indiana.edu 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 ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk OS Unix Vax/VMS LANGUAGE C VOLUME - AC BC00289 NAME MC-SYM DOMAIN Structure prediction DESCRIPTION Macromolecular Conformation by SYMbolic programming DESCRIPTION Software Package designed to predict and model the tridimentional DESCRIPTION structures nucleic acids when sequence and some secondary DESCRIPTION and tertiary structure information is known AUTHOR G. Lapalme, R.Cedergren, D. Gautheret, M Turcotte, F Major RA Major F., Turcotte M., Gautheret D., Lapalme G., Fillion E., RA Cedergren R.J.; RT "The combination of symbolic and numerical computation for three- RT dimensional modeling of RNA."; RL Science 253:1255-1260(1991). RX Medline; 91368195. RX SeqAnalRef; MAJF9101. RA Gautheret D., Major F., Cedergren R.; RT "Modeling the three-dimensional structure of RNA RT using discrete nucleotide conformational sets."; RL J. Mol. Biol. 229:1049-1064(1993). RX Medline; 93188000. ADDRESS Departement d'Informatique et de Recherche Operationnelle ADDRESS Departement de Biochimie Universite de Montreal ADDRESS National Center for Biotechnology Information National Library of ADDRESS Medecine National Institutes of Health CONTACT - SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /pub/MC-SYM read README.INSTALLATION Please, notify SITE that you installed MC-SYM at your site by sending an E-mail SITE message to: mcsym-request@ncbi.nlm.nih.gov SITE MC-SYM release 1.0 is a prototype. No technical support is SITE provided. New announcements will be sent to the user's mail SITE group 'mcsym-user'.A postscript version of the user's guide is SITE provided. SITE-CONTACT mcsym-request@ncbi.nlm.nih.gov OS SUN , Unix workstation-type computers LANGUAGE C++ VOLUME - AC BC00290 NAME PEBLS DOMAIN Structure prediction DESCRIPTION Parallel Exemplar-Based Learning System DESCRIPTION nearest-neighbor learning system designed for applications DESCRIPTION where the instances have symbolic feature values. DESCRIPTION PEBLS has been applied to the prediction of protein secondary DESCRIPTION structure based on the primary amino acid sequence of protein DESCRIPTION sub-units, and to the identification of DNA promoter sequences. AUTHOR Cost and Salzberg RA Cost S., Salzberg S.; RT "A weighted nearest neighbor algorithm for learning with RT symbolic features."; RL Machine Learning journal 10(1):57-78(1993). ADDRESS Prof. Steven Salzberg Dept. of Computer Science ADDRESS The Johns Hopkins University Baltimore, MD 21210, USA CONTACT salzberg@cs.jhu.edu SITE ftp anonymous blaze.cs.jhu.edu SITE Directory /pub/pebls SITE-CONTACT OS LANGUAGE ANSI C VOLUME - AC BC00291 NAME PREDICT_MULTI DOMAIN Structure prediction DESCRIPTION Program Predict_Multi makes secondary structure predictions DESCRIPTION according to the Chou-Fasman method of an aligned set of amino DESCRIPTION acid sequences. The results for each sequence and for the DESCRIPTION consensus are written into a file and furthermost graphicaly DESCRIPTION displayed. DESCRIPTION Predict_Multi uses the original method of Chou and Fasman DESCRIPTION (Adv.in Enzymol., ^*47\*; 45-148) to predict helices, sheets, DESCRIPTION and turns. It resolves overlapping regions of helix and DESCRIPTION beta-sheet with the "overall probability" procedure introduced DESCRIPTION by K.Nishikawa (Biochimica et Biophysica Acta, *748\*; 285-299). DESCRIPTION This same procedure also locates turns that are not in conflict DESCRIPTION with other secondary structures. AUTHOR Alfred Beck RT - ADDRESS Max-Plank-Institut fuer Molekulare Genetik ADDRESS Ihnestrasse 73 D-14195 Berlin (Dahlem) Germany CONTACT - SITE ftp anonymous denver.rz-berlin.mpg.de SITE Directory /molbio/predict_multi.txt SITE-CONTACT Dr. Alfred Beck SITE-CONTACT EAN-Mail: Beck@mpimg-berlin.mpg.d400.de SITE-CONTACT Internet-Mail: Beck@mpimg-berlin-dahlem.mpg.de OS - LANGUAGE - VOLUME - COMMENTS The program is programmed for gcg version 5 and not full adapted COMMENTS for gcg Version 7 but it is usebeal with this version. It use COMMENTS some subroutines from gcg's prediction programs. AC BC00292 NAME SOPM DOMAIN Structure prediction DESCRIPTION Self Optimised Prediction Method for protein secondary DESCRIPTION structure prediction AUTHOR C. Geourjon & G. Deleage RA Geourjon C., Deleage G.; RT "SOPM : a self optimised prediction method for protein secondary RT structure prediction."; RL Prot. Eng. 7:157-164(1994). RX Medline; 94224747. RX SeqAnalRef; GEOC9302. ADDRESS Institut de Biologie et Chimie des Proteines ADDRESS IBCP-CNRS UPR 412 ADDRESS Groupe de modelisation et RMN ADDRESS 7, Passage du vercors ADDRESS 69 367 Lyon cedex 07, FRANCE CONTACT deleage@ibcp.fr SITE ftp anonymous ibcp.fr SITE Directory /pub/SOPM SITE-CONTACT - OS Unix workstations and successfully checked onto IBM OS rs6000 workstations and SGI. LANGUAGE - VOLUME - COMMENTS Secondary structure prediction by SOPM can be performed by us COMMENTS provided you send the sequence by Email to deleage@ibcp.fr COMMENTS In this case, an automatic mail server will send you 3 files: COMMENTS 1) A detailed prediction of your sequence by SOPM COMMENTS 2) A consensus secondary structure derived from 4 methods COMMENTS Gibrat et al., J. Mol. Biol. 198:425-443(1987) COMMENTS Levin et al., Febs Lett. 205:303-308(1986) COMMENTS Deleage & Roux Prot. Eng. 1:289-294(1987) COMMENTS Geourjon & Deleage Prot. Eng. 7:157-164(1994) COMMENTS 3) An extensive search for sites is provided using the COMMENTS PATTERN program (PROSITE) COMMENTS Geourjon & Deleage Comput. Appl. Biosci. 9:87-91(1993) 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 BC00419 NAME PROTEIN DESIGNER DOMAIN Structure prediction DESCRIPTION Functions: DESCRIPTION - Homology by P. Argos (3). [ALIMATF, HPLOTTAK, ALIGNTAK] DESCRIPTION - Profiles according method described by Van Regenmortel (1). DESCRIPTION - Secondary structure prediction and surface probability performed DESCRIPTION based on method and statistical data proposed by P.Argos (2). DESCRIPTION 1. Van Regenmortel,M.H.V.(1989)Immunol.Today 10,266. DESCRIPTION 2. Argos,P.(1987). J.Mol.Biol. 193,331-348. DESCRIPTION 3. Argos,P.(1987). J.Mol.Biol. 193,385-396. DESCRIPTION - Prosite search and molecular graphics. AUTHOR Indulis Gusars RT - ADDRESS Biomedical research and study center ADDRESS LV-1067, Kirhensteina 1, Riga, Latvia CONTACT gibiomed@cclu.lv; gi@giprot.lu.lv ; gibiomed@mii.lu.lv SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/dos file gi0.arj SITE-CONTACT nethelp@ebi.ac.uk OS MS-DOS LANGUAGE - VOLUME - REQUIRES 4 Mb of EMS memory ; VGA (640*480); REQUIRES mouse, co-processor,about 600 kb real dos partition AC BC00445 NAME ANTHEPROT Web page DOMAIN WWW server DOMAIN Protein sequence analysis DOMAIN Structure prediction DOMAIN Pattern Identification DOMAIN Alignment browser SERVER http://www.ibcp.fr/predict.html DESCRIPTION ANTHEPROT is a server that allows to make: DESCRIPTION * Secondary structure predictions: GOR, DPM, HOMOLOGUE, SOPMA, DESCRIPTION Phd DESCRIPTION * Multiple alignment : Clustalw (Higgins), Multalin (Corpet) DESCRIPTION * Search for biological sites using PROSITE DESCRIPTION * Search for homologous protein : Program FASTA (W. Pearson) AUTHOR G. Deleage, C. Geourjon, C. Blanchet RA Geourjon C., Deleage G.; RT "SOPM: a self-optimised meyhod for protein secondary RT struture prediction."; RL Protein Eng. 7:157-164(1994) RX Medline; 94224747. RX SeqAnalRef; GEOC9302. RA Geourjon C., Deleage G.; RT "SOPMA:significant improvements in protein secondary RT structure prediction by consensus prediction from RT multiple alignments."; RL Comput. Appl. Biosci. 11(6):681-684(1995). ADDRESS Institut de Biologie et Chimie des Proteines ADDRESS IBCP-CNRS UPR 412, Groupe de modelisation et RMN ADDRESS 7, Passage du Vercors ADDRESS 69 367 Lyon cedex 07, FRANCE CONTACT deleage@ibcp.fr, geourjon@ibcp.fr SITE WWW server at URL http://www.ibcp.fr/predict.html SITE-CONTACT geourjon@ibcp.fr or deleage@ibcp.fr OS - LANGUAGE - VOLUME - REQUIRES - AC BC00450 NAME MaxSprout DOMAIN WWW server DOMAIN Structure prediction SERVER http://www2.ebi.ac.uk/dali/maxsprout/maxsprout_request.html DESCRIPTION MaxSprout is a fast database algorithm for generating protein DESCRIPTION backbone and side chain co-ordinates from a C(alpha) trace. The DESCRIPTION backbone is assembled from fragments taken from known DESCRIPTION structures. Side chain conformations are optimized in rotamer DESCRIPTION space using a rough potential energy function to avoid clashes. AUTHOR A. de Daruvar, L. Holm, C. Sander RA Holm L., Sander C.; RT "Database algorithm for generating protein backbone and RT side-chain co-ordinate from a C-alpha trace."; RL J. Mol. Biol. 218:183-194(1991). RX Medline; 91162641. RX SeqAnalRef; HOLL9101. 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://www2.ebi.ac.uk/dali/maxsprout/ SITE-CONTACT - OS VMS LANGUAGE Pascal,Fortran VOLUME - REQUIRES - AC BC00494 NAME DSC Protein Secondary Structure Prediction DOMAIN Structure prediction DESCRIPTION DSC Protein Secondary Structure Prediction DESCRIPTION I am pleased to announce the opening of a new web site for DESCRIPTION the prediction of protein secondary structure. DESCRIPTION Two prediction modes are available: DESCRIPTION 1) Given a single sequence. A multiple sequence alignmentt DESCRIPTION will be formed and DSC used to predict secondary structure. DESCRIPTION http://www.icnet.uk/bmm/dsc/dsc_form_align.html DESCRIPTION 2) Given a multiple sequence alignmnet. DSC will DESCRIPTION use this alignment to predict secondary structure. DESCRIPTION http://www.icnet.uk/bmm/dsc/dsc_read_align.html DESCRIPTION The advantages of DSC are: DESCRIPTION 1) It is very accurate. DSC has a prediction accuracy of 70.1% on a DESCRIPTION standard set of 126 proteins. This was not significantly different DESCRIPTION from PHD, a popular prediction method. For medium length sequences DESCRIPTION DSC was more accurate than PHD, and combining DSC and PHD produced DESCRIPTION a prediction method more accurate than either. DESCRIPTION 2) It is free. There is no charge for using DSC. DESCRIPTION 3) The C source code is available. This would allow you DESCRIPTION to run DSC on your own system if you had confidential sequences. DESCRIPTION DSC is based on simple linear statistics. A paper on the DESCRIPTION scientific basis of DSC will appear in Protein Science: DESCRIPTION "Identification and Application of the Concepts Important for DESCRIPTION Accurate and Reliable Protein Secondary Structure Prediction" DESCRIPTION by Ross D. King & Michael J.E. Sternberg AUTHOR King, R.D., Sternberg, M.J.E. RA King R.D., Sternberg M.J.E.; RT "Identification and Application of the Concepts Important for RT Accurate and Reliable Protein Secondary Structure Prediction."; RL Prot. Science (in press). ADDRESS Ross D. King ADDRESS Biomolecular Modelling Laboratory ADDRESS Imperial Cancer Research Fund ADDRESS Lincoln's Inn Fields, P. O. Box 123, ADDRESS London, WC2A 3PX, U.K. ADDRESS Tel: +44 171 269 3565, Fax: +44 171 269 3479, CONTACT rd_king@icrf.icnet.uk SITE ftp anonymous ftp.icnet.uk SITE Directory /icrf-public/bmm/king/dsc/ SITE-CONTACT - OS Unix LANGUAGE C VOLUME - REQUIRES - AC BC00495 NAME BlueGene DOMAIN Neural Networks DOMAIN Searching databases DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Sequence analysis DOMAIN Protein sequence analysis DOMAIN Structure prediction DOMAIN Database and analysis DESCRIPTION BlueGene uses a fast neural network for sequence similarity DESCRIPTION searches in Genbank and SWISS-PROT databases. DESCRIPTION BlueGene also includes graphically tools for sequence DESCRIPTION editing and analysing. DESCRIPTION BlueGene uses given and new sequence features to annotate DESCRIPTION the sequence editor and the map. AUTHOR Magic Works GmbH RT - ADDRESS Magic Works GmbH ADDRESS Potsdamer Str. 18a ADDRESS D-14513 Teltow ADDRESS GERMANY CONTACT info@magic-works.com SITE WWW Server at URL http://www.bluegene.com/ SITE-CONTACT - OS Win 3.1x or higher LANGUAGE - VOLUME 3.1MB REQUIRES 16MB RAM COMMENTS A free BlueGene demo version is ready for downloading on COMMENTS http://www.bluegene.com/. 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 BC00516 NAME RDP Recursive Dynamic Programming DOMAIN Structure prediction DOMAIN Alignment Search software DOMAIN WWW server SERVER http://cartan.gmd.de/ToPLign.html DESCRIPTION Protein Fold Prediction and Sequence-structure Alignment for DESCRIPTION Protein Sequences based on Aminoacidpair Interaction Potentials AUTHOR Ralf Thiele, Ralf Zimmer RA Thiele, R., Zimmer, R., Lengauer, T.; RT "Recursive Dynamic Programming for Adaptive RT Sequence and Structure Alignment"; RL Proc. of the Third International Conference on Intelligent RL Systems for Molecular Biology, 384-392(1995). ADDRESS Ralf Thiele Ralf Zimmer Thomas Lengauer ADDRESS German National Research Center for Information Technology ADDRESS Schloss Birlinghoven, D-53754 Sankt Augustin CONTACT Ralf.Thiele@gmd.de CONTACT Ralf.Zimmer@gmd.de SITE WWW Server at URL http://cartan.gmd.de/ToPLign.html OS - LANGUAGE - VOLUME - REQUIRES - AC BC00518 NAME 123D DOMAIN Structure prediction DOMAIN Alignment Search software DOMAIN WWW server SERVER http://cartan.gmd.de/ToPLign.html DESCRIPTION Protein Fold Prediction and Sequence-structure Alignment for DESCRIPTION Protein Sequences based on Contact Capacity Potentials AUTHOR Ralf Zimmer, Nick Alexandrov RA Alexandrov N., Nussinov R., Zimmer R.; RT "Fast Protein Fold Recognition via Sequence to RT Structure Alignment and Contact Capacity Potentials"; RL Proceedings of the First Pacific Symposium on Biocomputing, RL 53-72 (1996) ADDRESS Ralf Zimmer ADDRESS German National Research Center for Information Technology ADDRESS Schloss Birlinghoven, D-53754 Sankt Augustin ADDRESS Nick Alexandrov ADDRESS Amgen Inc. ADDRESS Thousands Oaks, CA, USA CONTACT Ralf.Zimmer@gmd.de SITE WWW Server at URL http://cartan.gmd.de/ToPLign.html OS - LANGUAGE - VOLUME - REQUIRES - 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 BC00555 NAME MacStripe 2.0 DOMAIN Structure prediction DESCRIPTION MacStripe is a program for the prediction and analysis of potential DESCRIPTION coiled-coil regions in protein sequences. A new and much improved DESCRIPTION version (2.0a1) is available to download now from: DESCRIPTION http://www.york.ac.uk/depts/biol/units/coils/coilcoil.html DESCRIPTION DESCRIPTION MacStripe is the ideal tool for anyone who wants to explore potential DESCRIPTION alpha-helical coiled coils in the sequence of their protein. With a full DESCRIPTION Macintosh interface, the results of analyses (raw data or publication DESCRIPTION quality plots) can easily be exported to other software. The "Inspector" DESCRIPTION window acts like a magnifying glass so you can study your protein on a DESCRIPTION residue-by-residue basis. MacStripe uses the algorithm of Andrei Lupas's DESCRIPTION COILS2 for detailed and reliable coiled-coil predictions. DESCRIPTION DESCRIPTION System Requirements: Macintosh with 68030, '040 or PowerPC processor; DESCRIPTION Colour Quickdraw; System 7.0 or better. DESCRIPTION DESCRIPTION Features: DESCRIPTION * Full Macintosh Interface DESCRIPTION * Uses established Lupas algorithm for coiled coil prediction DESCRIPTION * Full control of prediction parameters (matrix, window length, DESCRIPTION weighting) DESCRIPTION * Interactive exploration of coiled coil with "Inspector" window DESCRIPTION * Imports sequences from DNA Strider or DNASTAR formats DESCRIPTION * Reads sequences from text files in plain, FASTA or Staden formats DESCRIPTION * Uses FPU (where present) for maximum calculation speed DESCRIPTION * Plots optionally show 'skips' or 'stutters' in coiled coil which may DESCRIPTION be structurally important DESCRIPTION * Plots can be copied and pasted into other applications, saved as PICT DESCRIPTION files, or printed DESCRIPTION * Detailed statistics can be imported into spreadsheet or graphing DESCRIPTION programs DESCRIPTION * It's FREE! AUTHOR A.E. Knight RT - ADDRESS Alex Knight (aek4@york.ac.uk) ADDRESS Biology Department ADDRESS University of York ADDRESS Heslington, York Y01 5DD ADDRESS +44 1904 434381 ADDRESS +44 1904 432860 (FAX) CONTACT aek4@york.ac.uk SITE WWW Server at URL http://www.york.ac.uk/depts/biol/units/coils/coilcoil.html OS Macintosh LANGUAGE - VOLUME - REQUIRES Macintosh with 68030, '040 or PowerPC processor; AC BC00570 NAME RASA 2.2 DOMAIN Sequence analysis DOMAIN Structure prediction DOMAIN Pattern Identification DOMAIN Phylogeny DOMAIN Statistical significance DOMAIN Comparative analysis DESCRIPTION RASA 2.2 provides a set of tools for measuring DESCRIPTION phylogenetic signal and for studying its distribution DESCRIPTION among taxa. DESCRIPTION DESCRIPTION This software is used for DESCRIPTION * measuring signal DESCRIPTION * testing the suitability of available outgroup taxa DESCRIPTION * detecting long branches in the taxon variance plot DESCRIPTION * performing the mixed-character taxon test for differential DESCRIPTION lineage sorting DESCRIPTION * performing bootstrap power and effect to examine the DESCRIPTION power curve for your data. DESCRIPTION DESCRIPTION Exploratory options include DESCRIPTION * determining the signal spectrum for a set of sequences DESCRIPTION * removing noisy sites DESCRIPTION DESCRIPTION Some researchers have used the software to examine DESCRIPTION hypotheses of alignment using phylogenetic signal as the DESCRIPTION criterion. DESCRIPTION DESCRIPTION This software can be used on discrete data (molecular, DESCRIPTION morphological, or mixed). AUTHOR James Lyons-Weiler, PhD RA Lyons-Weiler, J., Hoelzer, G.A. and Tausch R.J.; RT "Relative Apparent Synapomorphy Analysis (RASA) I: RT the statistical measurement of phylogenetic signal."; RL Molecular Biology and Evolution 13:749-757(1996). RA Lyons-Weiler, J. and Milinkovitch, M.C.; RT "A phylogenetic approach to the problem of differential RT lineage sorting."; RL Molecular Biology and Evolution 14:968-975(1997). RA Lyons-Weiler, J. and Hoelzer, G.A.; RT "Escaping from the Felsenstein Zone by detecting long RT branches in phylogenetic data."; RL Molecular Phylogenetics and Evolution 8:375-384(1997). RA Lyons-Weiler, J. and Hoelzer, G.A.; RL "Optimal outgroup analysis."; RL Biological Journal of the Linnean Society 64:493(1998). RA Milinkovitch, M.C. and Lyons-Weiler, J.; RT "Finding optimal outgroup topologies and convexities RT when the choice of outgroups is not obvious."; RL Molecular Phylogenetics and Evolution 9:348-357(1998). ADDRESS - CONTACT jfl8@psu.edu SITE WWW Server at URL http://test1.bio.psu.edu/LW/list.htm OS Mac/PowerPC REQUIRES All superfluous extensions off. COMMENTS The software will be updated and bugs fixed at COMMENTS irregular intervals. Watch for updates. 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