List of Biotechnology Databases

 

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Aidstar Team

Brookhaven National Laboratory Genmoe Sequences Facility
0-glycosylation sites in manunalian proteins
123D Zimmer & Alexandrov
16SMDB and 23SMDB |16S and 23S ribosomal RNA mutation database 
3Dee |database of protein structure domain definitions 
A Guide to Structure Prediction |This server 
Advanced BLAST2 Search at EMBL
Alfonso Valencia Group
Algorithms in molecular biology
ALIGN |compendium of protein sequence alignments 
ALIGNMENT
ALIGNMENT 
AMAS |analyse multiply aligned sequences 
AMAS Server|Livinstone & Barton 
Andrej Sali Group
ANU Bioinformatics Hypermedia Serk,er |virus databases, classification and nomenclature of viruses 
ANU Molecular biology
Archives for biological software and databases
Argicultural Biotechnology Center, Hungary
Asilomar Protein Structure Prediction Challenge
ATCC |American type culture collection 
Australian National University Bioinformatics
Barry Honig Group
Barton group software |ALSCRIPT, AMPS, AMAS, STAMP, ASSP, and SCANPS 
Bayesian bioinformatics at Wadsworth Center
BCM Genefinder
BCM Search Launcher |makes multiple searches from one input 
BCM Search Launcher |pairwise sequence alignment 
BCM search launcher for multiple sequence alignments
BCNI Search Launcher |protein secondary structure prediction 
Beckman Institute Theoretical Biophysics Group
Best of Web 1994
Bio Online
Biocomputing course resource list: course syllabi
Bioinformatics and Computational Biology at George Mason University
Bioinformatics Sites
Bioinformatics Sites 
Bioinformatics WWW Sites
BioMedNet Library
BioNet On-line
BioSCAN online at U. North Carolina
Biotectmological Software and Internet journal
Birkbeck College mirror
Birkbeck Home Page
BLITZ ULTRA Fast Search at EMBL
Blocking Gibbs sampling for linkage analysis in very large pedigrees
Blocks database |system for protein classification 
BMERC PSA Server Boston University
Bootscanriing for viral recombinations
Brookhanen FTP site |very, very slow from UK 
Brookhaven Protein Data Bank |PDB  WWW
Brookhaven Protein Data Bank WWW Server |get a PDB structure 
Cambridge Centre for Protein Engineering
Cambridge Crystallographic Data Centre
Cambridge Structural Database
Carbohydrate databases
CASP2 |1996  Web page |UK 
CASP2 |1996  Web page |US 
CATH: Protein Structure Classification
Center for Biological Sequence Analysis |Denmark 
CEPH genotype database
CGI guide
Chaperonins web page
Chris Sander Group
Cladistic software |a list from the Willi Hennig Society 
ClustalW
ClustalW |multiple sequence alignment at BCM 
Cohen group software rotamer library, BLoop, QPack, FOLD, Match,
COILS |prediction of coiled coil regions in proteins 
CollaboratiN,e course in protein structure
Compare your sequence to COG database
Compilation of TRNA sequences and sequences of TRNA genes
CONTENTS
CRITICAL ASSESSMENT OF STRUCTURE PREDICTION |CASP OR ASILOMAR 
CRITICAL ASSESSMENT OF STRUCTURE PREDICTION |CASP OR ASILOMAR  
Cytokines web
DALI compare protein structures in 3D
DALI server for protein 3D structure searching |Liisa Holm’s method 
Daresbury Lab WWW server
DARWIN system at ETH Zurich
DAS |Dense Alignment Surface; prediction of transmembrane regions in proteins 
DashPat find sequence similarity using a hashcode comparison with a pattern library
Database of Enzymes and Metabolic Pathways |Ei\IP 
DATABASES
DATABASES OF LINKS
DATABASES OF LINKS 
DATABASES 
David Eisenberg Group
DBGET Database Links
DBWatcher for Sun/Solaris
DIALIGN |aligment program without explicit gap penalties 
DNA sequences 
DRAGON protein modelling tool using distance geometry
DSC King & Sternberg |this server 
DSSP program
E.coli database collection |ECDC  |compilation of DNA sequences of E coli K 1 2 
EBI Industry support
EBI PDB retreival |very fast from UK 
EBI Protein topology atlas
EBI Sequence searching
EBI Server
EcoCyc: Encyclopedia of Escherichia coli Genes and Metabolism
ELECTRONIC JOURNALS
ELECTRONIC JOURNALS 
EMBL Server
EMBL WWW services
ENZYME |nomenclature of enzymes 
Eukaryotic Pol 11 promoter prediction
European Bioinformatics Institute |EBI 
ExPASy Molecular Biology Server
ExPASy Molecular Biology Server |SwissProt, etc. 
FASTA-SWAP or FASTA-PAT search of a pattern database |profile and pattern searches 
FlyBase |Drosophila database 
Fred Cohen Group
Frontiers in Bioscience
FSSP |fold classification based on structure-structure aligmnent of proteins 
FTP of the above
GenBank Database Query Form |get a GenBank entry 
Gene Discovery Page
Gene Finding and Intron Splice Site Prediction
Gene Finding and Intron Splice Site Prediction 
GENEMARK |WWW system for predicting protein coding regions 
GeneQuiz |automated analysis of genomes 
Genome data, etc.
Genome data, etc. 
GenProtEc |genes and proteins of Escherichia coli 
GenQuest |Fasta, Blast, Smith Waterman; search in an@, database 
GENSCAN Web Ser-v,er: Complete gene structures in genomic DNA
Geoff Barton Group
George Church Group
Glucocorticoid receptor resource
Glycolsylation site prediction server
GNA’s Virtual School of Natural Sciences
GPCRD |G protein-coupled receptor data
Graham Richards Group
GRAIL and GENQUEST |E-mail sequence analysis, gene assembly, and sequence comparison 
GRAIL interface |protein coding regions and functional sites 
GRASP Anthony Nicholls, Columbia, USA.
GRBase |database linking information on proteins involved in gene regulation 
Guide to HTML documents
Guides for evaluation from Asilomar
Haemophilus influenzae database |HIDC  |genetic map, contigs, searchable index 
HAMSTeRS |haemophilia A mutation database  and factor VIII mutation database
Harvard Genome Research Databases and Selected Servers
Heidelberg FTP server
Heidelberg Gopher server
Histone sequence database of highl@r conser,%,ed nucleoprotein sequences
HIV Molecular Immunology Database, Los Alamos
HIV Sequence Database, Los Alamos
HMMER |source code for hidden Markov model software 
Homology Modelling
Homology Modelling 
Hopkins Bio-Informatics Home Page
HSSP |homology-derived secondary structure of proteins 
HTTPD software
Human 2-D PAGE databases for proteome analysis in health and disease
Human Genome Center Applications Baylor College of Medicine
Human Genome Project at Columbia University
Human Genome Project Information
Human Genome Sequencing Center, Baylor College
Human p53, hprt and lacz genes and mutations
Human papillomaviruses database
ICGEB Trieste
IMGT |immunogenetics database 
Imperial College FTP site
Imperial College, Department of Biochemistry
Index of Biology Internet Servers, USGS
Indiana Urtiversit@, IUBIO software and data
Institute for Molecular Viriology
Irwin D. Kuntz Group
ISSD:Integrated Sequence-Structure Databsase incorporating Codons
Janet Thornton Group
John Moult Group
Johns Hopkins Univ. OWL Web Server
Journal of Biological Chemistry
Journal of Molecular Biology
K2D Secondary Structure from CD spectra Merelo & Andrade |Granada, Spain 
KabatMan |database of antibody structure and sequence information 
Keith Robison’s Journal list
Kidne@, development database
Laboratory of Molecular Biophysics Home Page
Lawrence Livermore National Laboratory
Links to other Bio-Web servers
List of genome sequencing projects
LISTA, LISTA-HOP and LISTA-HON |compilation of homology databases from yeast 
Locus specific mutation database
Ludwig Institute for Cancer Research
Macromolecular Structures Database
Major 3D Structure Public Databases
Major 3D Structure Public Databases 
Major Public Sequence Databases
Major Public Sequence Databases 
Manchester Structural Chemistry Group
Mandalay Scientific |Maryland 
Manfred Sippl Group
Mark Sansom Group
Marketa Zvelebil’s page
MHCPEP |database of MHC-binding peptides 
Mike Sutcliffe Group
Mirror of the above in Cambridge
Miscellaneous links and Flowcharts
Miscellaneous links and Flowcharts 
MIT GNU FTP site
MITOMAP |human mitochondrial genome database 
Model Database FTP site
MODELLER |Sali 
MODELLER Mirror FTP site
MoIScript
Molecular Biology Institute |UCLA 
MOLECULAR BIOLOGY SOFTWARE LINKS
MOLECULAR BIOLOGY SOFTWARE LINKS 
Molecular biology software list at NIH
Molecular Biophysics, Washingnton University, St. Louis
Molecular Graphics and Modelling Society
MOLECULAR GRAPHICS PACKAGES
MOLECULAR GRAPHICS PACKAGES 
Molecular Modelling Servers and Databases
Molecular Simulations – Quanta/Charmm etc
Molecular Surface Package
Molecules R Us |search and view a protein molecule 
MolMol Reto Koradi, ETH, Zurrich, C.H.
Mosaic home page
Mouse genome database
Mouse knockout database
MPDB |molecular probe database 
MuItPredict |predict secondary structure based on multiple sequence aligmuent 
Multiple Alignment and Phylogeny
Multiple Alignment and Phylogeny 
National Biotechnology Information Facility
Natonal Center for Biotechnology Information
Nature
NCBI: BLAST notebook
NetGene |prediction of intron splice sites in human genes 
NetPlantGene |prediction of intron splice sites in Arabidopsis thaliana 
NETSCAPE HOME
Network Science
NIH Molecular Modeling Homepage |modelling homepage with links 
NIH PDB at a glance classification |useful 
nnPredict Cohen et al.
NNSSP |prediction of protein secondary sturcture by nearest-neighbor algorithms 
NRL-3D |sequence-str-ucture database derived from PDB, pictures and searches 
NRSub |non-redundant database for Bacillus subtilis 
OCMS publications list
OCMS publishers list
O-GLYCBASE |a revised database of 0-glycosylated proteins 
Other information
Other information 
OTHER LINKS OF INTEREST
OTHER LINKS OF INTEREST 
Other organisms genome databases |ACeDB-C. elegans, DictyDB-Dictyostelium dis-coideum, MycDB-Mycobacteria, PathoGenes-fungal pat
Other pages
Other pages 
Other phylogen@, programs, a complication from PH’Y’LIP documentation
Other Prediction Servers
Other Prediction Servers 
Oxford Centre for Molecular Sciences Home Page
Oxford University
P,NA structure-sequence logo
PAH mutation analysis |disease-producing human PAH loci 
Pairwise DNA alignment |LFASTA  ACNUC at Lyon
Pairwise protein alignment |SIM 
Pairwise Sequence and Structure Alignment
Pairwise Sequence and Structure Alignment 
Pasteur Institute
Pattern scan of proteins or nucleotides
PDB Browser
PDB Mirror at the EBI
PEDROS List of Molecular Biology Search and Analysis Tools
Peer Bork search list |motif/pattern/profile searches 
Perl documentation/tutorials
Perl documentation/tutorials 
Perl manual
Peter Kollman Group
Ph.D COURSES OVER THE INTERNET
Ph.D. course in biological sequence analysis and protein modeling
Ph.D. COURSES OVER THE INTERNET 
PHD home page Rost & Sander
PhD Threader
PHYLIP |programs for inferring phylogenies 
Phylip Web Page
Phylogenetic analysis programs |the tree of life list 
Pimall find sequence similarity using dynamic programming
PIR-International Protein Sequence Database
PREDATORFrischman & Argos |EMBL 
Prediction of HLA-binding peptides from sequences
Prediction of HLA-binding peptides in HIV sequences
PREDICTION OF PROTEIN STRUCTURE FROM SEQUENCE
PREDICTION OF PROTEIN STRUCTURE FROM SEQUENCE 
Prepi Suhail Islam, ICRF, U.K.
PRINTS |protein fingerprint database 
ProDom |protein domain database 
ProFit |protein least squares fitting software 
PROPSEARCH |search based on an-iino acid composition, EMBL 
PROSITE |functional protein sites 
PROSITE Database Searches |search for functional sites in your sequence 
Protein 3D structure
Protein 3D structure 
Protein Disease Database |PDD 
Protein FOLD recognition
Protein FOLD recognition 
Protein Modelling Discussion Group
Protein Motif Searching |IBCP, France 
Protein Science
Protein Science Gopher Server
Protein Secondary structure prediction
Protein secondary structure prediction 
Protein sequence analysis email server |Boston 
Protein sequence logos using relative entropy
Protein structural analysis, BMERC
Protein Structure Course |Birckbeck 
Protein Structure Prediction Center |US 
Proteome Research: New Frontiers in Functional Genomics |book contents 
PROWL-Protein Information Retrieval at Skirball Institute
PSORT |prediction of protein-sorting signals and localization from sequence 
Publishing/publications pages
Publishing/publications pages 
Quest Protein Database Center |Cold Spring Harbour 
RasMol manual
Rasmol software and script documentation
RasMol Roger Sayle, Glaxo, U.K.
RDP |the Ribosomal Database Project 
REBASE |database of restriction enzymes and meth@rlases 
RNA modification database
RNaseP database
SAM Sequence alignment and modelling system
SAM software for sequence consensus HMMs at UC Santa Cruz
SBASE protein domains |an-notated protein sequence segments 
ScanProsite |ExPASy 
Science
SCOP |structural classification of proteins , MRC
Search using Entrez |i.e. MEDLINE 
SELECTED PREDICTION SERVERS
SELECTED PREDICTION SERVERS 
Self Optomised Prediction method Deleage |IBCP, France 
SEQNET UK data service
Sequence data
Sequence data 
Sequence search protocol |integrated pattern search 
Sequence similarity search page at EBI
SEQUENCE SIMILARITY SEARCHES
SEQUENCE SIMILARITY SEARCHES 
Shoshanna Wodak Group
SignalP |signal peptide and cleavage sites in gram+, gram-, and eukaryotic amino acid sequences 
SITES
SITES 
Small RNA database, Baylor College of Medicine
SMSS-2DPAGE |database of two-dimensional polyacrylamide gel electrophoresis 
Specialized Databases
Specialized Databases 
SR-PDB |signal recognition particle database 
SRS Database Server
SRS Sequence Retrieval System |network browser for databanks in molecular biology 
SSCP |secondary structure prediction content with amino acid composition 
SSearch |searches against a specified database 
SSP |Nearest-neighbor segment method  Solovyev and Salamov |Baylor College
SSPRED Argos et al.
Structural Classification of Protein Domains Analytical Biostatistics Section
Structure of large ribosomal subunit RNA
Structure of small ribosomal subunit RNA
Submission form for protein domain and foldclass prediction
SUN site Northern Europe
Survey of Molecular Biology Databases and Servers
Swiss Model: automatic modeller
SWISS-PROT |protein sequences 
The AAA superfamily
The Antibody Resource Page
The BioCatalog
The EBI molecular biology software archive
The NCBI WWW Entrez Browser
The NIH Molecular Modeling Home Page
The PRINTS/PROSITE scanner |search motif databases with query, sequence 
The URNA database, University of Texas
The Virtual School of Niolecular Sciences
Thyroid hormone receptor resource
TIFR Molecular Biology Page |Bombay 
TIGR Database
Times Higher Education Jobs gopher
TMAP Argos
TMpred Baylor College
TRANSFAC |database on transcription factors and their DNA binding sites 
Translation start in vertebrate and A. thaliana DNA
Transmembrane protein structure prediction
Transmembrane protein structure prediction 
TransTerm |database of translational signals 
Tree of Life Home Page |information about phylogeny and biodiversity
U.S. patent citation database
UCLA-DOE Fold-Recognition Benchmark Home Page
UCLA-DOE Fold-Recognition server
UK MRC Human Genome Mapping Project Resource Centre
UK Protein & Peptide Science Group
University College Dept. of Biochemistry
University of California at San Francisco
Various Bio-inclined organisations
Various Bio-inclined organisations 
VARIOUS BIO-INCLINED RESEARCH GROUPS
VARIOUS BIO-INCLINED RESEARCH GROUPS 
Various crystallography pages
Various institutions
Various institutions 
VAST home page |NCBI 
VBASE human variable immunogluhn gene sequences
Web Signal Scan Service |scan DNA sequences for eukaryotic transcriptional elements 
WebLogo |sequence logo
WHAT IF
WWW Consortium
WWW for the Molecular Biologists and Biochemists
WWW home page
WWW pages
WWW pages 
WWW Sequence query |in Lyon 
WWW Server for Virology, UW-Madison
Yeast Genome DerBrowser |JAVA 
YPD |proteins from Saccharomyces cerevisiae 

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