Gabriels hot List



    A Guide to Structure Prediction (This server)

    SRS Sequence Retrieval System (network browser for databanks in molecular biology)

    Survey of Molecular Biology Databases and Servers

    BioMedNet Library

    DBGET Database Links

    Harvard Genome Research Databases and Selected Servers

    Johns Hopkins Univ. OWL Web Server

    Index of Biology Internet Servers, USGS

    WWW Server for Virology, UW-Madison

    UK MRC Human Genome Mapping Project Resource Centre

    PEDROS List of Molecular Biology Search and Analysis Tools

    WWW for the Molecular Biologists and Biochemists

    Links to other Bio-Web servers

    Molecular Modelling Servers and Databases

    ExPASy Molecular Biology Server

    The Antibody Resource Page

    Bioinformatics WWW Sites

    Bioinformatics and Computational Biology at George Mason University

    National Biotechnology Information Facility

    Human Genome Project Information

    Proteome Research: New Frontiers in Functional Genomics (book contents)


    Major Public Sequence Databases

    Blocks database (system for protein classification)

    PRINTS (protein fingerprint database)

    SRS Sequence Retrieval System (network browser for databanks in molecular biology)

    GenBank Database Query Form (get a GenBank entry)

    SWISS-PROT (protein sequences)

    PROSITE (functional protein sites)

    PIR-International Protein Sequence Database

    HIV Sequence Database, Los Alamos

    HIV Molecular Immunology Database, Los Alamos

    TIGR Database

    The NCBI WWW Entrez Browser

    Major 3D Structure Public Databases

    EBI PDB retreival (very fast from UK)

    DALI compare protein structures in 3D

    3Dee (database of protein structure domain definitions)

    NRL-3D (sequence-str-ucture database derived from PDB, pictures and searches)

    HSSP (homology-derived secondary structure of proteins)

    FSSP (fold classification based on structure-structure aligmnent of proteins)

    Brookhaven Protein Data Bank WWW Server (get a PDB structure)

    EBI Protein topology atlas

    Macromolecular Structures Database

    Molecules R Us (search and view a protein molecule)

    SCOP (structural classification of proteins), MRC

    Cambridge Structural Database

    VAST home page (NCBI)

    CATH: Protein Structure Classification

    DALI server for protein 3D structure searching (Liisa Holm's method)

    NIH PDB at a glance classification (useful)

    Structural Classification of Protein Domains Analytical Biostatistics Section

    Specialized Databases

    ISSD:Integrated Sequence-Structure Databsase incorporating Codons

    Brookhaven National Laboratory Genmoe Sequences Facility

    Protein Motif Searching (IBCP, France)

    Protein Disease Database (PDD)

    ANU Bioinformatics Hypermedia Serk,er (virus databases, classification and nomenclature of viruses)

    O-GLYCBASE (a revised database of 0-glycosylated proteins)

    DNA sequences)

    Database of Enzymes and Metabolic Pathways (Ei\IP)

    E.coli database collection (ECDC) (compilation of DNA sequences of E coli K 1 2)

    Haemophilus influenzae database (HIDC) (genetic map, contigs, searchable index)

    EcoCyc: Encyclopedia of Escherichia coli Genes and Metabolism

    GenProtEc (genes and proteins of Escherichia coli)

    NRSub (non-redundant database for Bacillus subtilis)

    YPD (proteins from Saccharomyces cerevisiae)

    LISTA, LISTA-HOP and LISTA-HON (compilation of homology databases from yeast)

    FlyBase (Drosophila database)

    MPDB (molecular probe database)

    Compilation of TRNA sequences and sequences of TRNA genes

    Small RNA database, Baylor College of Medicine

    The URNA database, University of Texas

    SR-PDB (signal recognition particle database)

    RDP (the Ribosomal Database Project)

    Structure of small ribosomal subunit RNA

    Structure of large ribosomal subunit RNA

    RNA modification database

    HAMSTeRS (haemophilia A mutation database) and factor VIII mutation database

    Human p53, hprt and lacz genes and mutations

    PAH mutation analysis (disease-producing human PAH loci)

    IMGT (immunogenetics database)

    Glucocorticoid receptor resource

    Thyroid hormone receptor resource

    16SMDB and 23SMDB (16S and 23S ribosomal RNA mutation database)

    MITOMAP (human mitochondrial genome database)

    SMSS-2DPAGE (database of two-dimensional polyacrylamide gel electrophoresis)

    KabatMan (database of antibody structure and sequence information)

    ALIGN (compendium of protein sequence alignments)

    ProDom (protein domain database)

    SBASE protein domains (an-notated protein sequence segments)

    TransTerm (database of translational signals)

    GRBase (database linking information on proteins involved in gene regulation)

    ENZYME (nomenclature of enzymes)

    REBASE (database of restriction enzymes and meth@rlases)

    RNaseP database

    TRANSFAC (database on transcription factors and their DNA binding sites)

    MHCPEP (database of MHC-binding peptides)

    Mouse genome database

    Mouse knockout database

    ATCC (American type culture collection)

    Histone sequence database of highl@r conser,%,ed nucleoprotein sequences

    VBASE human variable immunogluhn gene sequences

    GPCRD (G protein-coupled receptor data)

    Other organisms genome databases (ACeDB-C. elegans, DictyDB-Dictyostelium dis-coideum, MycDB-Mycobacteria, PathoGenes-fungal pat

    Locus specific mutation database

    Carbohydrate databases

    Human papillomaviruses database

    Human 2-D PAGE databases for proteome analysis in health and disease

    Kidne@, development database

    U.S. patent citation database


    GRASP Anthony Nicholls, Columbia, USA.

    MolMol Reto Koradi, ETH, Zurrich, C.H.

    Prepi Suhail Islam, ICRF, U.K.

    RasMol Roger Sayle, Glaxo, U.K.

    Molecular Simulations - Quanta/Charmm etc


    Protein Structure Prediction Center (US)

    CASP2 (1996) Web page (UK)

    CASP2 (1996) Web page (US)

    Asilomar Protein Structure Prediction Challenge

    Mirror of the above in Cambridge

    Model Database FTP site




    Protein Science

    Journal of Biological Chemistry

    Journal of Molecular Biology

    Frontiers in Bioscience

    Network Science


    SAM Sequence alignment and modelling system

    ScanProsite (ExPASy)

    EBI Sequence searching

    Sequence similarity search page at EBI

    NCBI: BLAST notebook

    BLITZ ULTRA Fast Search at EMBL

    EMBL WWW services

    BioSCAN online at U. North Carolina

    Pattern scan of proteins or nucleotides

    The PRINTS/PROSITE scanner (search motif databases with query, sequence)

    DARWIN system at ETH Zurich

    Pimall find sequence similarity using dynamic programming

    DashPat find sequence similarity using a hashcode comparison with a pattern library

    PROPSEARCH (search based on an-iino acid composition, EMBL)

    Sequence search protocol (integrated pattern search)

    GenQuest (Fasta, Blast, Smith Waterman; search in an@, database)

    SSearch (searches against a specified database)

    BCM Search Launcher (makes multiple searches from one input)

    Peer Bork search list (motif/pattern/profile searches)

    PROSITE Database Searches (search for functional sites in your sequence)

    PROWL-Protein Information Retrieval at Skirball Institute

    FASTA-SWAP or FASTA-PAT search of a pattern database (profile and pattern searches)

    CEPH genotype database

    Advanced BLAST2 Search at EMBL


    Pairwise Sequence and Structure Alignment

    Pairwise protein alignment (SIM)

    Pairwise DNA alignment (LFASTA) ACNUC at Lyon

    AMAS (analyse multiply aligned sequences)

    BCM Search Launcher (pairwise sequence alignment)

    DIALIGN (aligment program without explicit gap penalties)

    Multiple Alignment and Phylogeny

    AMAS Server(Livinstone & Barton)

    ClustalW (multiple sequence alignment at BCM)

    PHYLIP (programs for inferring phylogenies)

    Other phylogen@, programs, a complication from PH'Y'LIP documentation

    Tree of Life Home Page (information about phylogeny and biodiversity)

    Phylogenetic analysis programs (the tree of life list)

    Cladistic software (a list from the Willi Hennig Society)

    BCM search launcher for multiple sequence alignments

    WebLogo (sequence logo)

    Protein sequence logos using relative entropy

    P,NA structure-sequence logo


    Gene Finding and Intron Splice Site Prediction

    BCM Genefinder

    NetGene (prediction of intron splice sites in human genes)

    NetPlantGene (prediction of intron splice sites in Arabidopsis thaliana)

    GeneQuiz (automated analysis of genomes)

    GRAIL interface (protein coding regions and functional sites)

    GENEMARK (WWW system for predicting protein coding regions)

    GENSCAN Web Ser-v,er: Complete gene structures in genomic DNA

    GRAIL and GENQUEST (E-mail sequence analysis, gene assembly, and sequence comparison)

    Eukaryotic Pol 11 promoter prediction

    Web Signal Scan Service (scan DNA sequences for eukaryotic transcriptional elements)

    Gene Discovery Page

    List of genome sequencing projects

    Other Prediction Servers

    Translation start in vertebrate and A. thaliana DNA

    0-glycosylation sites in manunalian proteins

    SignalP (signal peptide and cleavage sites in gram+, gram-, and eukaryotic amino acid sequences)

    PSORT (prediction of protein-sorting signals and localization from sequence)

    Compare your sequence to COG database

    Prediction of HLA-binding peptides from sequences

    Prediction of HLA-binding peptides in HIV sequences


    Miscellaneous links and Flowcharts

    A Guide to Structure Prediction (This server)

    Protein structural analysis, BMERC

    Submission form for protein domain and foldclass prediction

    NIH Molecular Modeling Homepage (modelling homepage with links)

    Protein secondary structure prediction

    BCNI Search Launcher (protein secondary structure prediction)

    COILS (prediction of coiled coil regions in proteins)

    MuItPredict (predict secondary structure based on multiple sequence aligmuent)

    SSCP (secondary structure prediction content with amino acid composition)

    NNSSP (prediction of protein secondary sturcture by nearest-neighbor algorithms)

    DSC King & Sternberg (this server)

    PREDATORFrischman & Argos (EMBL)

    PHD home page Rost & Sander

    ZPRED server Zvelebil et al.

    BMERC PSA Server Boston University

    SSP (Nearest-neighbor segment method) Solovyev and Salamov (Baylor College)

    nnPredict Cohen et al.

    Self Optomised Prediction method Deleage (IBCP, France)

    SSPRED Argos et al.

    K2D Secondary Structure from CD spectra Merelo & Andrade (Granada, Spain)

    Transmembrane protein structure prediction

    DAS (Dense Alignment Surface; prediction of transmembrane regions in proteins)

    TMAP Argos

    TMpred Baylor College

    Protein FOLD recognition

    Guides for evaluation from Asilomar

    PhD Threader

    123D Zimmer & Alexandrov

    UCLA-DOE Fold-Recognition Benchmark Home Page

    UCLA-DOE Fold-Recognition server

    Homology Modelling

    MODELLER (Sali)

    MODELLER Mirror FTP site

    The NIH Molecular Modeling Home Page

    Swiss Model: automatic modeller


    The EBI molecular biology software archive

    The BioCatalog

    Archives for biological software and databases

    Barton group software (ALSCRIPT, AMPS, AMAS, STAMP, ASSP, and SCANPS)

    Cohen group software rotamer library, BLoop, QPack, FOLD, Match,

    Bayesian bioinformatics at Wadsworth Center

    Rasmol software and script documentation



    SAM software for sequence consensus HMMs at UC Santa Cruz

    HMMER (source code for hidden Markov model software)


    DSSP program

    Bootscanriing for viral recombinations

    Blocking Gibbs sampling for linkage analysis in very large pedigrees

    DBWatcher for Sun/Solaris

    ProFit (protein least squares fitting software)

    Indiana Urtiversit@, IUBIO software and data

    Molecular biology software list at NIH

    DRAGON protein modelling tool using distance geometry

    Molecular Surface Package

    Biotectmological Software and Internet journal


    Biocomputing course resource list: course syllabi

    Ph.D. course in biological sequence analysis and protein modeling

    The Virtual School of Niolecular Sciences

    CollaboratiN,e course in protein structure

    GNA's Virtual School of Natural Sciences

    Algorithms in molecular biology


    Cytokines web

    The AAA superfamily

    Chaperonins web page

    EMBL WWW Services

    European Bioinformatics Institute (EBI)

    EBI Industry support

    Bioinformatics Sites

  • Protein 3D structure

    Brookhaven Protein Data Bank (PDB) WWW

    PDB Mirror at the EBI

    PDB Browser

    Brookhanen FTP site (very, very slow from UK)

    EBI PDB retreival (very fast from UK)

    Birkbeck College mirror

  • Sequence data

    Protein sequence analysis email server (Boston)

    ExPASy Molecular Biology Server (SwissProt, etc.)

    Heidelberg FTP server

    Heidelberg Gopher server

    EMBL Server

    EBI Server

    SRS Database Server

    Natonal Center for Biotechnology Information

    SEQNET UK data service

    Daresbury Lab WWW server

    Quest Protein Database Center (Cold Spring Harbour)

    WWW Sequence query (in Lyon)

    Human Genome Center Applications Baylor College of Medicine

  • Genome data, etc.

    Tigr Database

    Yeast Genome DerBrowser (JAVA)

    Human Genome Project at Columbia University

    Human Genome Sequencing Center, Baylor College

  • Other information

    BioNet On-line

    Bio Online

    Search using Entrez (i.e. MEDLINE)

    Cambridge Crystallographic Data Centre

    Various crystallography pages


    Argicultural Biotechnology Center, Hungary

    Australian National University Bioinformatics

    ANU Molecular biology

    Geoff Barton Group

    Beckman Institute Theoretical Biophysics Group

    Birkbeck Home Page

    Cambridge Centre for Protein Engineering

    Center for Biological Sequence Analysis (Denmark)

    George Church Group

    Fred Cohen Group

    David Eisenberg Group

    Barry Honig Group

    Peter Kollman Group

    Irwin D. Kuntz Group

    Laboratory of Molecular Biophysics Home Page

    Lawrence Livermore National Laboratory

    Manchester Structural Chemistry Group

    Mandalay Scientific (Maryland)

    Molecular Biology Institute (UCLA)

    John Moult Group

    Oxford Centre for Molecular Sciences Home Page

    Hopkins Bio-Informatics Home Page

    ICGEB Trieste

    Pasteur Institute

    Graham Richards Group

    Andrej Sali Group

    Chris Sander Group

    Mark Sansom Group

    Manfred Sippl Group

    Mike Sutcliffe Group

    Janet Thornton Group

    TIFR Molecular Biology Page (Bombay)

    Shoshanna Wodak Group

    UK Protein & Peptide Science Group

    Alfonso Valencia Group

    York Protein Structure Group

    Marketa Zvelebil's page

    Various Bio-inclined organisations

    Molecular Graphics and Modelling Society

    Protein Modelling Discussion Group


    Perl documentation/tutorials

    Perl manual

    WWW pages


    WWW home page

    WWW Consortium

    HTTPD software

    FTP of the above

    Mosaic home page

    Guide to HTML documents

    Best of Web 1994

    CGI guide

    Various institutions

    Institute for Molecular Viriology

    Molecular Biophysics, Washingnton University, St. Louis

    University College Dept. of Biochemistry

    University of California at San Francisco

    SUN site Northern Europe

    Oxford University

    Ludwig Institute for Cancer Research

    Imperial College, Department of Biochemistry

    Publishing/publications pages

    Keith Robison's Journal list

    Protein Science Gopher Server

    OCMS publications list

    OCMS publishers list

    Other pages

    MIT GNU FTP site

    Imperial College FTP site

    Times Higher Education Jobs gopher

    RasMol manual

    Glycolsylation site prediction server

    Phylip Web Page

    Protein Structure Course (Birckbeck)