title: Focused grid-based resampling for protein docking and mapping.
abstract: The fast Fourier transform (FFT) sampling algorithm has been used with success in application to protein-protein docking and for protein mapping, the latter docking a variety of small organic molecules for the identification of binding hot spots on the target protein. Here we explore the local rather than global usage of the FFT sampling approach in docking applications. If the global FFT based search yields a near-native cluster of docked structures for a protein complex, then focused resampling of the cluster generally leads to a substantial increase in the number of conformations close to the native structure. In protein mapping, focused resampling of the selected hot spot regions generally reveals further hot spots that, while not as strong as the primary hot spots, also contribute to ligand binding. The detection of additional ligand binding regions is shown by the improved overlap between hot spots and bound ligands.
authors.affiliation: Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215.
authors.forename: Artem B
authors.initials: AB
authors.lastname: Mamonov
authors.affiliation: Center for Information and Systems Engineering, Boston University, Boston, Massachusetts, 02215.
authors.forename: Mohammad
authors.initials: M
authors.lastname: Moghadasi
authors.affiliation: Center for Information and Systems Engineering, Boston University, Boston, Massachusetts, 02215.
authors.forename: Hanieh
authors.initials: H
authors.lastname: Mirzaei
authors.affiliation: Department of Mechanical Engineering, Boston University, Boston, Massachusetts, 02215.
authors.forename: Shahrooz
authors.initials: S
authors.lastname: Zarbafian
authors.affiliation: Department of Sciences, Wentworth Institute of Technology, Boston, Massachusetts, 02115.
authors.forename: Laurie E
authors.initials: LE
authors.lastname: Grove
authors.affiliation: Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215.
authors.forename: Tanggis
authors.initials: T
authors.lastname: Bohnuud
authors.affiliation: Center for Information and Systems Engineering, Boston University, Boston, Massachusetts, 02215.|Department of Mechanical Engineering, Boston University, Boston, Massachusetts, 02215.
authors.forename: Pirooz
authors.initials: P
authors.lastname: Vakili
authors.affiliation: Center for Information and Systems Engineering, Boston University, Boston, Massachusetts, 02215.|Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, 02215.
authors.forename: Ioannis
authors.initials: I
authors.lastname: Ch Paschalidis
authors.affiliation: Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215.|Center for Information and Systems Engineering, Boston University, Boston, Massachusetts, 02215.|Department of Chemistry, Boston University, Boston, Massachusetts, 02215.
authors.forename: Sandor
authors.initials: S
authors.lastname: Vajda
authors.affiliation: Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215.|Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, 11790.
authors.forename: Dima
authors.initials: D
authors.lastname: Kozakov
mesh_terms: D000465:Algorithms; D005583:Fourier Analysis; D008024:Ligands; D062105:Molecular Docking Simulation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
chemical_list: D008024:Ligands; D011506:Proteins
keywords: binding hot spots; fast Fourier transform; protein mapping; protein-protein docking; systematic sampling
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