The PDBbind database: methodologies and updates.

We have developed the PDBbind database to provide a comprehensive collection of binding affinities for the protein-ligand complexes in the Protein Data Bank (PDB). This paper gives a full description of the latest version, i.e., version 2003, which is an update to our recently reported work. Out of 23 790 entries in the PDB release No.107 (January 2004), 5897 entries were identified as protein-ligand complexes that meet our definition. Experimentally determined binding affinities (K(d), K(i), and IC(50)) for 1622 of these were retrieved from the references associated with these complexes. A total of 900 complexes were selected to form a "refined set", which is of particular value as a standard data set for docking and scoring studies. All of the final data, including binding affinity data, reference citations, and processed structural files, have been incorporated into the PDBbind database accessible on-line at http:// www.pdbbind.org/.

[1]  I. Kuntz.  Structure-Based Strategies for Drug Design and Discovery , 1992, Science.

[2]  C L Verlinde,et al.  Structure-based drug design: progress, results and challenges. , 1994, Structure.

[3]  Hans-Joachim Böhm,et al.  The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure , 1994, J. Comput. Aided Mol. Des..

[4]  Ajay N. Jain.  Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities , 1996, J. Comput. Aided Mol. Des..

[5]  Garland R. Marshall,et al.  VALIDATE: A New Method for the Receptor-Based Prediction of Binding Affinities of Novel Ligands , 1996 .

[6]  G. V. Paolini,et al.  Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes , 1997, J. Comput. Aided Mol. Des..

[7]  Luhua Lai,et al.  SCORE: A New Empirical Method for Estimating the Binding Affinity of a Protein-Ligand Complex , 1998 .

[8]  Hans-Joachim Böhm,et al.  Prediction of binding constants of protein ligands: A fast method for the prioritization of hits obtained from de novo design or 3D database search programs , 1998, J. Comput. Aided Mol. Des..

[9]  Y. Martin,et al.  A general and fast scoring function for protein-ligand interactions: a simplified potential approach. , 1999, Journal of medicinal chemistry.

[10]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[11]  I. Muegge.  A knowledge-based scoring function for protein-ligand interactions: Probing the reference state , 2000 .

[12]  P. Dean,et al.  Recent advances in structure-based rational drug design. , 2000, Current opinion in structural biology.

[13]  Ferenc Csizmadia.  JChem: Java Applets and Modules Supporting Chemical Database Handling from Web Browsers , 2000, J. Chem. Inf. Comput. Sci..

[14]  G. Klebe,et al.  Knowledge-based scoring function to predict protein-ligand interactions. , 2000, Journal of molecular biology.

[15]  C L Brooks,et al.  Ligand-protein database: linking protein-ligand complex structures to binding data. , 2001, Journal of medicinal chemistry.

[16]  X Chen,et al.  The binding database: overview and user's guide. , 2001, Biopolymers.

[17]  I. Muegge.  Effect of ligand volume correction on PMF scoring , 2001, J. Comput. Chem..

[18]  X Chen,et al.  BindingDB: a web-accessible molecular recognition database. , 2001, Combinatorial chemistry & high throughput screening.

[19]  Luhua Lai,et al.  Further development and validation of empirical scoring functions for structure-based binding affinity prediction , 2002, J. Comput. Aided Mol. Des..

[20]  Xi Chen,et al.  The Binding Database: data management and interface design , 2002, Bioinform..

[21]  E. Shakhnovich,et al.  SMall Molecule Growth 2001 (SMoG2001): an improved knowledge-based scoring function for protein-ligand interactions. , 2002, Journal of medicinal chemistry.

[22]  Gerhard Klebe,et al.  Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions. , 2003, Journal of molecular biology.

[23]  John B. O. Mitchell,et al.  Protein Ligand Database (PLD): additional understanding of the nature and specificity of protein-ligand complexes , 2003, Bioinform..

[24]  Martin Stahl,et al.  The Use of Scoring Functions in Drug Discovery Applications , 2003 .

[25]  John P. Overington,et al.  PDBLIG: classification of small molecular protein binding in the Protein Data Bank. , 2004, Journal of medicinal chemistry.

[26]  Junwei Zhang,et al.  Development of KiBank, a database supporting structure-based drug design , 2004, Comput. Biol. Chem..

[27]  Renxiao Wang,et al.  The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures. , 2004, Journal of medicinal chemistry.

[28]  Shaomeng Wang,et al.  An Extensive Test of 14 Scoring Functions Using the PDBbind Refined Set of 800 Protein-Ligand Complexes , 2004, J. Chem. Inf. Model..

[29]  Michael G. Lerner,et al.  Binding MOAD (Mother Of All Databases) , 2005, Proteins.