The Protein Data Bank (PDB), Its Related Services and Software Tools as Key Components for
In Silico Guided Drug Discovery.

Johannes Kirchmair, Patrick Markt, Simona Distinto, Daniela Schuster, Gudrun M. Spitzer, Klaus R. Liedl,
Thierry Langer, and Gerhard Wolber.

Perspective published in the Journal of Medicinal Chemistry, 2008 51, 7021–7040. DOI:10.1021/jm8005977

Here is a collection of URLs to services discussed in this publication. New services will be added in future.
If you encounter dead links or if you have comments/questions, please dont't hesitate to contact us. Thank you!

service/tool name description free for academics?*
wwPDB portals and partner sites
wwPDB Worldwide Protein Data Bank portal y
RCSB PDB RCSB PDB portal y
PDBj PDBj portal y
BMRB BMRB portal y
MSD-EBI MSD-EBI portal y
TargetDB target search for structural genomics y
PepcDB information on the current status of solutions of structures in production y
cross-linked datasources
Gene Ontology controlled vocabulary to describe gene and gene product attributes in any organism y
ENZYME repository of information on the nomenclature of enzymes y
OMIM compendium of human genes and genetic phenotypes y
SCOP hierarchical classification of proteins y
UNIPROT comprehensive protein sequence repository y
protein visualization tools
AstexViewer protein structure viewer y
Chimera popular tool for protein visualization and the investigation of electron density maps y
Coot popular tool for investigation of electron density maps and model building y
LIGPLOT 2D diagrams of protein-ligand interactions y
RASMOL protein structure viewer y
tools for PDB data validation and manipulation
PQS analyze and predict quaternary protein structures y
WHAT_CHECK tool for protein structure checks y
PDBREPORT repository of WHAT_CHECK reports y
PROCHECK tool for protein structure checks y
PROCHECK-NMR tool for protein structure checks y
MolProbity tool for protein structure checks y
NQ Flipper erroneous Asn and Gln rotamer detection y
PSVS protein structure validation software suite y
modeling suites featuring ligand structure interpretation and correction algorithms
MOE comprehensive modeling package n
SYBYL comprehensive modeling package n
LigandScout modeling suite for structure-based pharmacophore modeling and virtual screening n, free eval lic
tools for visualizing and manipulating electron density maps
SFCHECK tool for structure factor file checks y
EDS electron density server - repository of ED maps; collection of structure validation tools y
Chimera popular tool for protein visualization and the investigation of electron density maps y
Coot popular tool for investigation of electron density maps and model building y
AFITT real-space fitting of ligands in protein-ligand complexes y
protein interface, binding site, and cavity analyses
PASS identification of protein cavities y
SURFNET identification of protein cavities y
Q-SiteFinder identification of protein cavities y
InSite software tool for the identification of protein-protein interaction sites y
Protemot prediction of protein binding sites with automatically extracted geometrical templates y
SitesBase comparative investigation of protein-ligand binding sites y
PDBSITE protein binding site analysis y
PSIbase repository of PDB-derived protein interface information y
PROTCOM data pool of protein interface structures y
Molsurfer analysis and visualization of protein interfaces y
iPFAM visualization and browsing of protein interfaces y
DMAPS database of multiple alignments for protein structures y
binding data collections
Binding DB affinity data collection y
PDBbind affinity data collection y
AffinDB affinity data collection y
KiBank affinity data collection y
Binding MOAD affinity data collection y
ligand collections based on PDB structures
Binding DB-CN collection of all small organic molecules of the PDB; affinity data collection y
SuperLigands ligand structure repository y
PDB-Ligand ligand structure repository y
Ligand Expo (formerly Ligand Depot) ligand structure repository y
HIC-up ligand structure repository y
PDB-derived subsets and recalculated data repositores
sc-PDB PDB subset of structures prepared for virtual screening y
LigBase ligand-binding proteins aligned to structural templates y
PLD protein-ligand database y
PDB-REPRDB representative protein chains from PDB y
RECOORD a REcalculated COORdinates Database of 500+ NMR structures y
Membrane Protein DB collection of PDB data on membrane proteins y
PiQSi database for comparing the quarternary structure of protein complexes y
iMolTalk web toolkit for analyzing and searching PDB complexes y
PSAP protein structure analysis package y
PDBsum at-a-glance overviews on PDB structures; cross-linking to second-party databases y
EZCatDB database of enzyme catalytic mechanisms y
data mining and analysis tools
PDB-UF prediction of enzymatic functions of not-annotated PDB entries y
pKNOT analyses tools and structural data on knotted proteins y
PDBSprotEC links PDB chains with Swiss-Prot codes and EC numbers y
SuMo analysis and comparison of protein binding sites y
Relibase+ analysis and datamining interface for protein structures y
pdbFun collection of PDB data mining tools y
SURFACE surface-based structural comparison and similarity assessment of protein structures y
PAST fast protein structure search y
3dLogo identification of conserved residues in a set of structurally superimposed proteins y
FeatureMap3D align query sequences to PDB structures y
PISCES PDB sequence culling y
MMsINC ligand structure and substructure search y
DBAli database of structure alignments y
MaxSprout generating protein backbone and side chain co-ordinates from a C(alpha) trace y
SABBAC reconstruction of protein backbones and amino acid side chains based on alpha-carbon trace y
TIP - Target Informatics Platform database of pairwise structure alignments for the PDB; assessment of structural similarities; data mining free basic access to the database
EVE - Eidogen Visualization Environment visualization and comparison of target active sites and interfaces n
misc. tools online service for the selection of PDB subsets
Columba y
PDB Goodies web-based manipulation of PDB files y
PMG online movie generator for PDB structures y
ZINC free database of commercially-available compounds for virtual screening y
DUD directory of useful decoys and known active compounds y

*to our best knowledge