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·
Primary structural databases
o
Protein Data Bank at
RCSB
o
Nucleic Acid Database
(Rutgers)
o
Beta-release of the RCSB Protein Data Bank (mostly
for expert-users)
o
SeqAlert
(alerts you when a structure has
been deposited that displays homology to a sequence you are
interested in; Weizmann)
·
Front-ends to
the structural databases
o
PDBsum
(EBI; new site !)
o
Entrez-Structure (NCBI)
o
MMDB, Molecular Modelling DataBase
(NCBI)
o
PDB at a Glance
(NIH)
o
PDBFINDER (CMBI)
o
SRS 3D (EBI)
·
Visualisation
software
o
Rasmol (Bernstein)
o
Chime (MDL)
o
Deep View Swiss-PdbViewer (Expasy)
o
MolScript
(Kraulis)
o
MolMol (ETH)
o
WebMol
(Java-based viewer; UCSF)
o
PyMOL
·
Structural macro-analysis
(folds, classification, similarity, sequence alignments)
o
CATH
(classification database; UCL)
o
SCOP (classification database;
MRC-LMB)
o
FSSP
(Fold classification based
on Structure-Structure alignment of Proteins; EBI)
o
TOPS
(protein
topology database; EBI)
o
STRUCTAL server
(superimposing two structures;
Yale)
·
Structural micro-analysis
(sites, small motifs, waters)
o
PROSITE patterns in PDB entries (EBI;
new site)
o
3MOTIF
(find sequence motifs in structures;
Stanford)
·
Model validation
o
PDBReport
(CMBI)
o
Biotech validation server (EBI)
o
ADIT server (PDB)
o
Ramachandran server (Bangalore)
·
Small molecules
o
LigBase
(Database of Aligned Ligand Binding
Sites; Rockefeller)
o
ChemPDB
(EBI)
o
MathMol (Library of 3-D Molecular
Structures; New York)
·
Specialised
and derived structural databases and servers
o
Structural databases in Nucleic Acids Research list
(not all are specialised)
o
PDBsum
(EBI; new site !)
o
SAS
(Sequences Annotated by Structure;
UCL)
o
CDD (conserved domain alignments;
NCBI)
o
PROMISE
(mirror of discontinued site in
Leeds; Scripps)
o
Protein side-chain interactions (UCL)
o
Side-chain and main-chain hydrogen bonding
(UCL)
·
Database for
specific protein families etc.
o
Protein databases in Nucleic Acids Research
list
(not all have a structural component)
·
Sequence databases
and analysis and comparison servers
o
SWISS-PROT
(ExPASy)
o
PIR
o
NCBI
o
GenBank
o
EBI
o
ExPASy
o
EMBL
o
Entrez (NCBI)
o
BLAST (NCBI)
·
Multiple-sequence
alignment
o
Tcoffee@igs (Marseille)
o
ClustalW
(EBI)
o
MULTALIN (NPS@)
o
MultAlin
(Toulouse)
·
Literature
o
PubMed/Entrez (NCBI)
o
PubMed Express
(NIH)
o
PubCrawler
o
Bioinformatics (journal)
·
Structure prediction
& modelling
o
GlobPlot
(predicts order and globularity;
EMBL)
o
Protein Structure Prediction Center (home
of CASP; LLNL)
·
Structural Genomics
o
TargetDB (PDB)
o
NIH Structural Genomics Initiatives
o
PRESAGE
o
Yeast Structural genomics
(France)
·
Education
o
2can bioinformatics educational resource
(EBI)
o
Bioinformatics: a tutorial for beginners exploring human visual
pigments (University of Southern
Maine)
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