A Comprehensive
Resource for Candida glabrata Genome
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| Chromosome View | ||||||||
| A | B | C | D | E | F | G | ||
| H | I | J | K | L | M | |||
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1 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)
2 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)
3 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
4 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)
5 Structural micro-analysis (sites, small motifs, waters)
o PROSITE patterns in PDB entries (EBI; new site)
o 3MOTIF (find sequence motifs in structures; Stanford)
6 Model validation
o PDBReport (CMBI)
o Biotech validation server (EBI)
o ADIT server (PDB)
o Ramachandran server (Bangalore)
7 Small molecules
o LigBase (Database of Aligned Ligand Binding Sites; Rockefeller)
o ChemPDB (EBI)
o MathMol (Library of 3-D Molecular Structures; New York)
8 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)
9 Database for specific protein families etc.
o Protein databases in Nucleic Acids Research list (not all have a structural component)
10 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)
11 Multiple-sequence alignment
o Tcoffee@igs (Marseille)
o ClustalW (EBI)
o MULTALIN (NPS@)
o MultAlin (Toulouse)
12 Literature
o PubMed/Entrez (NCBI)
o PubMed Express (NIH)
o PubCrawler
o Bioinformatics (journal)
13 Structure prediction & modelling
o GlobPlot (predicts order and globularity; EMBL)
o Protein Structure Prediction Center (home of CASP; LLNL)
14 Structural Genomics
o TargetDB (PDB)
o NIH Structural Genomics Initiatives
o PRESAGE
o Yeast Structural genomics (France)
15 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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