Bioinformatics and Functional Genomics

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Chapter 9: Protein structure

Web resources from Chapter 9
Website URL
PBIL http://npsa-pbil.ibcp.fr
PDB http://www.rcsb.org/pdb/
PDB Current Holdings http://www.rcsb.org/pdb/holdings.html
The Macromolecular Structure database http://www.ebi.ac.uk/msd/
The NCBI structure page http://www.ncbi.nlm.nih.gov/Structure/
The SCOP database http://scop.mrc-lmb.cam.ac.uk/scop/
CATH http://www.biochem.ucl.ac.uk/bsm/cath_new/index.html
The SSAP algorithm http://www.biochem.ucl.ac.uk/cgi-bin/cath/GetSsapRasmol.pl
Dali http://www2.ebi.ac.uk/dali/
FSSP http://www.ebi.ac.uk/dali/fssp
Protein Structure Prediction Server http://www.bioinfo.rpi.edu/~bystrc/hmmstr/server.html
CASP http://predictioncenter.llnl.gov/

 

Tables

Table 9-1. Secondary structure prediction programs available on the internet. Additional sites are listed at ExPASy (http://kr.expasy.org/tools/#secondary), PBIL (http://npsa-pbil.ibcp.fr), and EVA (http://cubic.bioc.columbia.edu/eva/).
Program Comment
APSSP Based on neural networks
GOR4 From the Pole Bio-Informatique Lyonnais
Jpred From the Barton group (Dundee)
NNPREDICT An enhanced neural network approach (from UCSF)
PHD Based on neural networks
Predator From the Argos group
The PredictProtein server From Columbia University
PSIPRED From the University College London
SAM-T99 Uses Hidden Markov Models (Chapter 10)
Sosui From the Mitaku Group (Tokyo)
 
Table 9-3. Interactive visualization tools for protein structures. For Protein Data Bank URLs, see the help document at http://www.rcsb.org/pdb/help-graphics.html.
Tool Comment
Chime Plug-in for a web browser
Cn3D From NCBI
Mage Reads Kinemages
MICE Java Applet Molecular Interactive Collaborative Environment
RasMol A stand-alone package
SwissPDB viewer At ExPASy
VMD Visual Molecular Dynamics; U. of Illinois
VRML Uses MolScript
 
Table 9-6. Partial list of protein structure databases linked to the Protein Data Bank. Modified from Berman et al. (2000).
Database Comment
3dee Structural domain definitions
BMCD Crystallization information about biomacromoleucles
CATH Protein fold classifiction
CE Complete PDB and representative structure comparison and alignments
DSSP Secondary structure classification
Enzyme Structures Databases Enzyme classifications and nomenclature
FSSP Structurally similar families
GRASS Graphical representation and analysis
HSSP Homology derived secondary structures
MMDB Database of three dimensional structures
Medline Direct access to Medline at NCBI
NDB Database of three dimensional nucleic acid structures
PDBSum Summary information about protein structures
SCOP Structure classifications
STING Simultaneous display of structural and sequence information
Tops Protein strucutre motif comparisons topological diagram
VAST Vector Alignment Search Tool (NCBI)
Whatcheck Protein structure checks
 
 
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