title: ZDOCK predictions for the CAPRI challenge.
abstract: The CAPRI Challenge is a blind test of protein-protein-docking algorithms that predict the complex structure from the crystal structures of the interacting proteins. We participated in both rounds of this blind test and submitted predictions for all seven targets, relying mainly on our Fast Fourier Transform based algorithm ZDOCK that combines shape complementarity, desolvation, and electrostatics. Our group made good predictions for three targets and had at least some success with three others. Implications of the treatment of prior biological information as well as contributions of manual inspection to docking predictions are also discussed.
authors.affiliation: Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA.
authors.forename: Rong
authors.initials: R
authors.lastname: Chen
authors.forename: Weiwei
authors.initials: W
authors.lastname: Tong
authors.forename: Julian
authors.initials: J
authors.lastname: Mintseris
authors.forename: Li
authors.initials: L
authors.lastname: Li
authors.forename: Zhiping
authors.initials: Z
authors.lastname: Weng
mesh_terms: D000465:Algorithms; D000818:Animals; D000906:Antibodies / Q000737:chemistry / Q000276:immunology; D000956:Antigens, Viral; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D036022:Capsid Proteins / Q000737:chemistry / Q000276:immunology; D005098:Exotoxins / Q000737:chemistry / Q000378:metabolism; D006388:Hemagglutinins / Q000737:chemistry / Q000276:immunology; D046911:Macromolecular Substances; D008565:Membrane Proteins / Q000737:chemistry / Q000378:metabolism; 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* / Q000378:metabolism*; D016693:Receptors, Antigen, T-Cell, alpha-beta / Q000737:chemistry / Q000378:metabolism; D000516:alpha-Amylases / Q000737:chemistry / Q000378:metabolism
chemical_list: D000906:Antibodies; D000956:Antigens, Viral; D001426:Bacterial Proteins; D036022:Capsid Proteins; D005098:Exotoxins; D006388:Hemagglutinins; D046911:Macromolecular Substances; D008565:Membrane Proteins; D011506:Proteins; D016693:Receptors, Antigen, T-Cell, alpha-beta; C117980:SpeA protein, Streptococcus pyogenes; C061332:VP6 protein, Rotavirus; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System; C030182:phosphocarrier protein HPr; C110847:HPr kinase; D017346:Protein Serine-Threonine Kinases; D000516:alpha-Amylases