GAPDOCK: A genetic algorithm approach to protein docking in CAPRI round 1

As part of the first Critical Assessment of PRotein Interactions, round 1, we predict the structure of two protein–protein complexes, by using a genetic algorithm, GAPDOCK, in combination with surface complementarity, buried surface area, biochemical information, and human intervention. Among the five models submitted for target 1, HPr phosphocarrier protein (B. subtilis) and the hexameric HPr kinase (L. lactis), the best correctly predicts 17 of 52 interprotein contacts, whereas for target 2, bovine rotavirus VP6 protein‐monoclonal antibody, the best model predicts 27 of 52 correct contacts. Given the difficult nature of the targets, these predictions are very encouraging and compare well with those obtained by other methods. Nevertheless, it is clear that there is a need for improved methods for distinguishing between “correct” and “plausible but incorrect” complexes. Proteins 2003;52:10–14. © 2003 Wiley‐Liss, Inc.

[1]  J. Cherfils,et al.  Molecular docking programs successfully predict the binding of a β-lactamase inhibitory protein to TEM-1 β-lactamase , 1996, Nature Structural Biology.

[2]  W N Hunter,et al.  Structure of trypanothione reductase from Crithidia fasciculata at 2.6 A resolution; enzyme-NADP interactions at 2.8 A resolution. , 1994, Acta crystallographica. Section D, Biological crystallography.

[3]  P. Kraulis.  A program to produce both detailed and schematic plots of protein structures , 1991 .

[4]  M. Sternberg,et al.  Prediction of protein-protein interactions by docking methods. , 2002, Current opinion in structural biology.

[5]  Magali Mathieu,et al.  Atomic structure of the major capsid protein of rotavirus: implications for the architecture of the virion , 2001, The EMBO journal.

[6]  L. Delbaere,et al.  Mg2+–Mn2+ clusters in enzyme-catalyzed phosphoryl-transfer reactions , 1997, Nature Structural Biology.

[7]  J. S. Dixon,et al.  Evaluation of the CASP2 docking section , 1997, Proteins.

[8]  M. Lawrence,et al.  Shape complementarity at protein/protein interfaces. , 1993, Journal of molecular biology.

[9]  Ivan Mijakovic,et al.  X-ray structure of a bifunctional protein kinase in complex with its protein substrate HPr , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[10]  Collaborative Computational,et al.  The CCP4 suite: programs for protein crystallography. , 1994, Acta crystallographica. Section D, Biological crystallography.

[11]  P Willett,et al.  Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm. , 1993, Journal of molecular biology.

[12]  R Abagyan,et al.  Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase. , 1996, Nature structural biology.

[13]  Eleanor J. Gardiner,et al.  Protein docking using a genetic algorithm , 2001, Proteins.

[14]  E A Merritt,et al.  Raster3D Version 2.0. A program for photorealistic molecular graphics. , 1994, Acta crystallographica. Section D, Biological crystallography.

[15]  J. Janin,et al.  X‐ray structure of HPr kinase: a bacterial protein kinase with a P‐loop nucleotide‐binding domain , 2001, The EMBO journal.

[16]  Wolfgang Hengstenberg,et al.  Evolutionary relationship between the bacterial HPr kinase and the ubiquitous PEP‐carboxykinase: expanding the P‐loop nucleotidyl transferase superfamily , 2002, FEBS letters.

[17]  M. L. Connolly.  Solvent-accessible surfaces of proteins and nucleic acids. , 1983, Science.

[18]  M. L. Connolly.  Analytical molecular surface calculation , 1983 .

[19]  I. Vakser,et al.  Evaluation of GRAMM low‐resolution docking methodology on the hemagglutinin‐antibody complex , 1997, Proteins.