Table 7. Tools for Structure Viewing and Analysis
Structure Databases
Program Website Comments
PDB Protein Data Bank. Repository of experimental determined protein structures
MMDB Structures obtained from PDB. Supports homology modeling & structure comparison
SwissModel Repository of automatically generated protein structure models (>367,642 models)
ModBase Repository of automatically generated protein structure models (>547,473 models)
Structural classification of proteins
CATH Structural classification of proteins
Structure Viewers
Program Website Comments
Chimera Alignment viewer for structural analysis; molecular dynamics; electrostatics viewing
PyMol High quality molecular graphics; electrostatics viewing; movie generation; scripts
VMD Easy to use; quality graphics; handles many file types; movie generation; scripts
SwissPDB Easy to use; modeling; mutations, H-bonds, angles and distances between atoms
Cn3D Basic viewer; simultaneously display of structure, sequence & alignments
RasMol 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 Protein surface-mapping of phylogenetic information to identify functional regions
ProtSkin Protein surface-mapping of sequence conservation (identity & similarity scores)
CASTp Identification & measurements of surface accessible pockets and interior regions
LigandProtein Analyzes protein-protein contacts in PDB files producing atom by atom description
Prediction Servers
Program Website Comments
PredictProtein Interface to many structure prediction servers
PhosphoBase Neural network prediction of phosphorylation sites in proteins and peptides
O-GlycoBase Neural network predictions of glycosylated proteins
Structure Modeling Servers
Program Website Comments
SwissModel Automated protein structure homology-modeling. Accessible from SwissPDB viewer
ESyPred3D Structure prediction server
WhatIf Structure analysis; modeling of amino acid mutations
EBI Interface to structure analysis software (Prove, ProCheck & What If)