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Human Genome Project Non-Human Genome Projects Genome Analysis Systems Protein analysis Sequence search / alignments Primary structure Secondary structure 3D structure / Threading  Quaternary Structure Direct links to protein databases Metabolism Virology Bibliography BioComputing Miscellany List of Molecular Biology databases ==>

The sixteen institutions that form the Human Genome Sequencing Consortium include:

Baylor College	Baylor College of Medicine, Houston, Texas, USA
Beijing HGC	Beijing Human Genome Center, Institute of Genetics, Chinese Academy of Sciences, Beijing, China
Braunschweig GBF	Gesellschaft für Biotechnologische Forschung mbH, Braunschweig, Germany
Genoscope	Genoscope, Evry, France
Waltham GTC	Genome Therapeutics Corporation, Waltham, MA, USA
Jena IMB	Institute for Molecular Biotechnology, Jena, Germany
Joint Genome	Joint Genome Institute, U.S. Department of Energy, Walnut Creek, CA, USA
Keio University	Keio University, Tokyo, Japan
Max Planck	Max Planck Institute for Molecular Genetics, Berlin, Germany
RIKEN	RIKEN Genomic Sciences Center, Saitama, Japan
The Sanger Centre	The Sanger Centre, Hinxton, U.K.
Stanford TDC	Stanford DNA Sequencing and Technology Development Center, Palo Alto, CA, USA
Washington Univ. Genome Center	University of Washington Genome Center, Seattle, WA, USA
Washington Univ. Mult. Seq. Center	University of Washington Multimegabase Sequencing Center, Seattle, WA,USA
Whitehead Institute	Whitehead Institute for Biomedical Research, MIT, Cambridge, MA, USA
Washington Univ. Genome Seq. Center	Washington University Genome Sequencing Center, St. Louis, MO, USA

Computational support and analysis (Consortium):

NCBI	The National Center for Biotechnology Information at NIH
EBI	The European Bioinformatics Institute in Cambridge, UK

Celera:

Celera Genomics

Celera Genomics (A PE Corporation Business) homepage.

 

Non-Human Genome Projects
 

Mouse	Mouse Genome Informatics
Microbial	The TIGR Microbial Database
Parasite	Parasite Genome
Arabidopsis	The Arabidopsis cDNA Sequence Analysis Project
Mosquitoes	The Mosquito Genomics WWW Server
C. elegans	Wormbase
Drosophila	Flybase
Rat	RATMAP
Saccharomyces	Saccharomyces Genome Database

 
 

 Sequence search / alignments.

Primary structure.
 

PFAM	Protein families database of alignments and HMMs (Sanger, UK)
Prosite	ProfileScan Server (ISREC, CH)
ProDom	ProDom protein domain database (INRA, FR)
InterPro	Integrated resource of protein domains and functional sites. (EBI, UK)
PRINTS	Protein Motif Fingerprint Database (UCL, UK)
SMART	Simple Modular Architecture Research Tool. Domains/motif  detection (EMBL)
Blocks/Prints	Searching both Blocks+ and Prints databases (FHCRC, USA)
SignalP	Predicts the presence and location of signal peptide (CBS, DK)

 

PredictProtein	The PredictProtein server  (Columbia, USA)
PredictProtein (local)	The PredictProtein server  (EMBnet / CNB, ES)
ExPASy Tools	ExPASy Proteomics tools

Secondary structure.
 

TMHMM	Prediction of transmembrane helices in proteins (CBS, DK)
COILS	Prediction of Coiled Coil Regions in Proteins (ISREC, CH)
MultiCoil	Program for Predicting Two- and Three-Stranded Coiled Coils (MIT, USA)
Jpred	A consensus method for protein secondary structure prediction (EBI, UK)
Psi-Pred	Protein structure prediction server  (secondary structure & transmembrane topology) (Brunel, UK)
TOPS	Protein Topology Home Page (EBI, UK)
SAM-T99	SAM-T99 secondary structure prediction.

 

PredictProtein	The PredictProtein server  (Columbia, USA)
PredictProtein (local)	The PredictProtein server  (EMBnet / CNB, ES)
ExPASy Tools	ExPASy Proteomics tools

3D structure / Threading
 

Swiss-Model	SWISS-MODEL. An Automated Comparative Protein Modelling Server (ExPASy, CH)
SWISS-MODEL Repository	SWISS-MODEL Repository. A database for theoretical protein models (ExPASy, CH)
PredictProtein	The PredictProtein server (TOPITS) (Columbia, USA)
PredictProtein (local)	The PredictProtein server (TOPITS) (EMBnet / CNB, ES)
3D-PSSM	3D-PSSM Protein Fold Recognition (Threading) Server (ICNET, UK)
UCLA-DOE	UCLA-DOE Fold-Recognition server (UCLA, USA)
Psi-Pred (GenThreader)	Protein structure prediction server  (sequence profile based fold recognition) (Brunel, UK)
SAM-T99	SAM-T99 protein structure HMM library search.
FFAS	Fold & Function Assignment System. (Burnham Institute, USA)
Fold-Pred	Protein Fold Prediction in the context of SCOP.
FUGUE	FUGUE Profile Library Search Against HOMSTRAD (Cambridge, UK)

 

AQUA	AQUA - Alignment Quality Assessment
BIOTECH Validation Suite	Biotech Validation Suite for Protein Structures (PROCHECK, PROVE & WHAT IF)

 

PDB - EBI	Protein Data Bank (EBI)
PDB - RCSB	Protein Data Bank (RCSB)
PDBsum	Summaries and structural analyses of PDB data files (UCL, UK)
OCA	PDB advanced browser(EBI)
PDBselect	Subset of the structures in the PDB that does not contain (highly) homolog sequences
EC->PDB	Enzyme Structures deposited in PDB (UCL, UK)
Prosite->PDB	PROSITE patterns in PDB entries (UCL, UK)
Ligans->PDB	List of ligands bound to PDB srtuctures (UCL, UK)
NDB	The Nucleic Acid Database Project (UK) (Nucleic Acid Structures)
IMB Jena	IMB Jena Image Library of Biological Macromolecules (Jena, Germany)

 

Get ExPDB	Get ExPDB entries for a PDB code (Swiss-Model, ExPASy, CH)
SCOP	Structural Classification of Proteins (MRC-LMB, UK)
CATH	CATH Protein Structure Classification (UCL-BSM, UK)
The Dali server	The Dali server: Network service for comparing protein (query) structures in 3D (EBI)
FSSP	Fold classification based on Structure-Structure alignment of Proteins (FSSP) (EBI)
DaliDD	Dali Domain Dictionary: structural classification of protein domains (EBI)
Homstrad	Homologous Structure Alignment Database (CrystBioc, UK)
3Dee	3 Dee - A Database of Protein Domain Definitions (EBI)
CAMPASS	CAMbridge database of Protein Alignments organised as Structural Superfamilies (CrystBioc, UK)
ProSup	Structure Comparison Server (Manfred J. Sippl - CAME)

Quaternary structure
 

PQS	Protein Quaternary Structure Database Searches at the EBI
NDB	The Nucleic Acid Database Project (UK) (Protein/Nucleic Acid Complexes)

Direct links to databases