title: Finding needles in haystacks: Reranking DOT results by using shape complementarity, cluster analysis, and biological information.
abstract: We present an evaluation of our results for the first Critical Assessment of PRedicted Interaction (CAPRI). The methods used include the molecular docking program DOT, shape analysis tool FADE, cluster analysis and filtering based on biological data. Good results were obtained for most of the seven CAPRI targets, and for two systems, submissions having the highest number of correctly predicted contacts were produced.
authors.affiliation: San Diego Supercomputer Center, University of California at San Diego, La Jolla 92093-0527, USA.
authors.forename: Dennis S
authors.initials: DS
authors.lastname: Law
authors.forename: Lynn F
authors.initials: LF
authors.lastname: Ten Eyck
authors.forename: Omer
authors.initials: O
authors.lastname: Katzenelson
authors.forename: Igor
authors.initials: I
authors.lastname: Tsigelny
authors.forename: Victoria A
authors.initials: VA
authors.lastname: Roberts
authors.forename: Mike E
authors.initials: ME
authors.lastname: Pique
authors.forename: Julie C
authors.initials: JC
authors.lastname: Mitchell
mesh_terms: D000465:Algorithms; D000956:Antigens, Viral; D001426:Bacterial Proteins; D001665:Binding Sites; D036022:Capsid Proteins / Q000737:chemistry / Q000276:immunology; D016000:Cluster Analysis; D005098:Exotoxins / Q000737:chemistry / Q000378:metabolism; D006388:Hemagglutinins / Q000737:chemistry / Q000276:immunology; D007140:Immunoglobulin Fab Fragments / Q000737:chemistry / Q000276:immunology; D007135:Immunoglobulin Variable Region / Q000737:chemistry / Q000276:immunology; D046911:Macromolecular Substances; D008958:Models, Molecular; D015394:Molecular Structure; 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; D055672:Static Electricity; D000516:alpha-Amylases / Q000737:chemistry / Q000276:immunology
chemical_list: D000956:Antigens, Viral; D001426:Bacterial Proteins; D036022:Capsid Proteins; D005098:Exotoxins; D006388:Hemagglutinins; D007140:Immunoglobulin Fab Fragments; D007135:Immunoglobulin Variable Region; D046911:Macromolecular Substances; D011506:Proteins; D016693:Receptors, Antigen, T-Cell, alpha-beta; C061332:VP6 protein, Rotavirus; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System; C030182:phosphocarrier protein HPr; C110847:HPr kinase; D017346:Protein Serine-Threonine Kinases; D000516:alpha-Amylases