DATABASES OF LINKS

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)

DATABASES

Major Public Sequence Databases

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

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

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

MOLECULAR GRAPHICS PACKAGES

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

CRITICAL ASSESSMENT OF STRUCTURE PREDICTION (CASP OR ASILOMAR)

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

ELECTRONIC JOURNALS

Nature

Science

Protein Science

Journal of Biological Chemistry

Journal of Molecular Biology

Frontiers in Bioscience

Network Science

SEQUENCE SIMILARITY SEARCHES

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

ALIGNMENT

Pairwise Sequence and Structure Alignment

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

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

SELECTED PREDICTION SERVERS

Gene Finding and Intron Splice Site Prediction

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

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

PREDICTION OF PROTEIN STRUCTURE FROM SEQUENCE

Miscellaneous links and Flowcharts

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 Mirror FTP site

The NIH Molecular Modeling Home Page

Swiss Model: automatic modeller

MOLECULAR BIOLOGY SOFTWARE LINKS

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

MoIScript

WHAT IF

SAM software for sequence consensus HMMs at UC Santa Cruz

HMMER (source code for hidden Markov model software)

ClustalW

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

Ph.D. COURSES OVER THE INTERNET

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

SITES

The AAA superfamily

Chaperonins web page

EMBL WWW Services

European Bioinformatics Institute (EBI)

EBI Industry support

Bioinformatics Sites

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

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

Tigr Database

Yeast Genome DerBrowser (JAVA)

Human Genome Project at Columbia University

Human Genome Sequencing Center, Baylor College

BioNet On-line

Bio Online

Search using Entrez (i.e. MEDLINE)

Cambridge Crystallographic Data Centre

Various crystallography pages

VARIOUS BIO-INCLINED RESEARCH GROUPS

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

OTHER LINKS OF INTEREST

Perl documentation/tutorials

Perl manual

WWW pages

NETSCAPE HOME

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)