Table 7. Tools for Structure Viewing and Analysis
Structure Databases
Program Website Comments
PDB http://www.rcsb.org/pdb/ Protein Data Bank. Repository of experimental determined protein structures
MMDB http://www.ncbi.nlm.nih.gov/Structure/ Structures obtained from PDB. Supports homology modeling & structure comparison
SwissModel http://swissmodel.expasy.org/repository/smr.php?job=1 Repository of automatically generated protein structure models (>367,642 models)
ModBase http://modbase.compbio.ucsf.edu/modbase-cgi-new/index.cgi Repository of automatically generated protein structure models (>547,473 models)
SCOP http://scop.mrc-lmb.cam.ac.uk/scop/
 
Structural classification of proteins
CATH http://www.cathdb.info/latest/index.html Structural classification of proteins
Structure Viewers
Program Website Comments
Chimera http://www.cgl.ucsf.edu/chimera/ Alignment viewer for structural analysis; molecular dynamics; electrostatics viewing
PyMol http://pymol.sourceforge.net/ High quality molecular graphics; electrostatics viewing; movie generation; scripts
VMD http://www.ks.uiuc.edu/Research/vmd/ Easy to use; quality graphics; handles many file types; movie generation; scripts
SwissPDB http://www.expasy.org/spdbv/ Easy to use; modeling; mutations, H-bonds, angles and distances between atoms
Cn3D http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.html Basic viewer; simultaneously display of structure, sequence & alignments
RasMol http://www.openrasmol.org/ Basic viewer; widely used; many severs return RasMol scripts for viewing of results
1) These viewers must be installed locally. The software is supported by Windows, Mac OS X (may require X11 window system) and UNIX.
Servers for Structural Analysis
Program Website Comments
ConSurf http://consurf.tau.ac.il/ Protein surface-mapping of phylogenetic information to identify functional regions
ProtSkin http://www.mcgnmr.ca/ProtSkin/intro/ Protein surface-mapping of sequence conservation (identity & similarity scores)
CASTp http://cast.engr.uic.edu/cast//calculation/?mode=request Identification & measurements of surface accessible pockets and interior regions
LigandProtein http://bip.weizmann.ac.il/oca-bin/lpccsu Analyzes protein-protein contacts in PDB files producing atom by atom description
Prediction Servers
Program Website Comments
PredictProtein http://www.embl-heidelberg.de/predictprotein/ Interface to many structure prediction servers
PhosphoBase http://www.cbs.dtu.dk/services/NetPhos/ Neural network prediction of phosphorylation sites in proteins and peptides
O-GlycoBase http://www.cbs.dtu.dk/services/NetOGlyc/ Neural network predictions of glycosylated proteins
Structure Modeling Servers
Program Website Comments
SwissModel
 
http://www.expasy.org/swissmod/ Automated protein structure homology-modeling. Accessible from SwissPDB viewer
ESyPred3D http://www.fundp.ac.be/urbm/bioinfo/esypred/ Structure prediction server
WhatIf http://www.cmbi.kun.nl/gv/servers/WIWWWI/ Structure analysis; modeling of amino acid mutations
EBI http://biotech.ebi.ac.uk:8400/ Interface to structure analysis software (Prove, ProCheck & What If)