title: GAPDOCK: a Genetic Algorithm Approach to Protein Docking in CAPRI round 1.
abstract: 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.
authors.affiliation: Department of Information Studies, Krebs Institute, Sheffield University, Sheffield, United Kingdom. e.gardiner@sheffield.ac.uk
authors.forename: Eleanor J
authors.initials: EJ
authors.lastname: Gardiner
authors.forename: Peter
authors.initials: P
authors.lastname: Willett
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Artymiuk
mesh_terms: D000465:Algorithms; D000956:Antigens, Viral; D001426:Bacterial Proteins; D001665:Binding Sites; D036022:Capsid Proteins / Q000737:chemistry / Q000378:metabolism; D007140:Immunoglobulin Fab Fragments / Q000737:chemistry / Q000378:metabolism; D046911:Macromolecular Substances; D008957:Models, Genetic; D008958:Models, Molecular; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System / Q000737:chemistry / Q000378:metabolism; D025941:Protein Interaction Mapping; D017346:Protein Serine-Threonine Kinases / Q000737:chemistry / Q000378:metabolism; D011506:Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*
chemical_list: D000956:Antigens, Viral; D001426:Bacterial Proteins; D036022:Capsid Proteins; D007140:Immunoglobulin Fab Fragments; D046911:Macromolecular Substances; D011506:Proteins; C061332:VP6 protein, Rotavirus; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System; C030182:phosphocarrier protein HPr; C110847:HPr kinase; D017346:Protein Serine-Threonine Kinases