Incorporation of flexibility into rigid‐body docking: Applications in rounds 3–5 of CAPRI

We have submitted models for all 9 targets in Rounds 3–5 of CAPRI and have predicted at least 30% of the correct contacts for 4 of the targets and at least 10% of the correct contacts for another 4 targets. We have employed a variety of techniques but have had the greatest success by combining established rigid‐body docking with a variety of initial conformations generated by molecular dynamics. Proteins 2005;60:263–268. © 2005 Wiley‐Liss, Inc.

[1]  Marc Graille,et al.  Activation of the LicT Transcriptional Antiterminator Involves a Domain Swing/Lock Mechanism Provoking Massive Structural Changes* , 2005, Journal of Biological Chemistry.

[2]  M. Sternberg,et al.  The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking. , 2005, Journal of molecular biology.

[3]  M. Nilges,et al.  Complementarity of structure ensembles in protein-protein binding. , 2004, Structure.

[4]  Jan A. Delcour,et al.  Structural Basis for Inhibition of Aspergillus niger Xylanase by Triticum aestivum Xylanase Inhibitor-I* , 2004, Journal of Biological Chemistry.

[5]  S. Vajda,et al.  Anchor residues in protein-protein interactions. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[6]  Human Rezaei,et al.  Insight into the PrPC-->PrPSc conversion from the structures of antibody-bound ovine prion scrapie-susceptibility variants. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[7]  Ruth Nussinov,et al.  FlexProt: Alignment of Flexible Protein Structures Without a Predefinition of Hinge Regions , 2004, J. Comput. Biol..

[8]  Roberto Dominguez,et al.  Structural basis of protein phosphatase 1 regulation , 2004, Nature.

[9]  Shoshana J Wodak,et al.  Prediction of protein-protein interactions: the CAPRI experiment, its evaluation and implications. , 2004, Current opinion in structural biology.

[10]  K. Stiasny,et al.  Structure of a flavivirus envelope glycoprotein in its low‐pH‐induced membrane fusion conformation , 2004, The EMBO journal.

[11]  Gary Williamson,et al.  XIP-I, a xylanase inhibitor protein from wheat: a novel protein function. , 2004, Biochimica et biophysica acta.

[12]  Wei Yang,et al.  Protein–nucleic acid interactions , 2004 .

[13]  Y. Modis,et al.  Structure of the dengue virus envelope protein after membrane fusion , 2004, Nature.

[14]  Harry J. Gilbert,et al.  Cellulosome assembly revealed by the crystal structure of the cohesin–dockerin complex , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[15]  Junichi Takagi,et al.  [Complex between nidogen and laminin fragments reveals a paradigmatic beta-propeller interface]. , 2003, Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme.

[16]  Jeffrey J. Gray,et al.  Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. , 2003, Journal of molecular biology.

[17]  Paul W. Fitzjohn,et al.  Guided docking: First step to locate potential binding sites , 2003, Proteins.

[18]  Sandor Vajda,et al.  CAPRI: A Critical Assessment of PRedicted Interactions , 2003, Proteins.

[19]  R. Abagyan,et al.  ICM‐DISCO docking by global energy optimization with fully flexible side‐chains , 2003, Proteins.

[20]  Martin Zacharias,et al.  Protein–protein docking with a reduced protein model accounting for side‐chain flexibility , 2003, Protein science : a publication of the Protein Society.

[21]  C. Dominguez,et al.  HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. , 2003, Journal of the American Chemical Society.

[22]  Jean-Guy Berrin,et al.  Specific Characterization of Substrate and Inhibitor Binding Sites of a Glycosyl Hydrolase Family 11 Xylanase fromAspergillus niger * , 2002, The Journal of Biological Chemistry.

[23]  Ruth Nussinov,et al.  Principles of docking: An overview of search algorithms and a guide to scoring functions , 2002, Proteins.

[24]  Pedro M Alzari,et al.  Mapping by site-directed mutagenesis of the region responsible for cohesin-dockerin interaction on the surface of the seventh cohesin domain of Clostridium thermocellum CipA. , 2002, Biochemistry.

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

[26]  Pedro M Alzari,et al.  Duplicated dockerin subdomains of Clostridium thermocellum endoglucanase CelD bind to a cohesin domain of the scaffolding protein CipA with distinct thermodynamic parameters and a negative cooperativity. , 2002, Biochemistry.

[27]  S. Vajda,et al.  Protein docking along smooth association pathways , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[28]  Pauline M. Rudd,et al.  Antibodies inhibit prion propagation and clear cell cultures of prion infectivity , 2001, Nature.

[29]  Berk Hess,et al.  GROMACS 3.0: a package for molecular simulation and trajectory analysis , 2001 .

[30]  X. Wu,et al.  Mutations in yeast protein phosphatase type 1 that affect targeting subunit binding. , 2001, Biochemistry.

[31]  D. Eisenberg,et al.  Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins. , 2001, Journal of molecular biology.

[32]  M J Sternberg,et al.  Enhancement of protein modeling by human intervention in applying the automatic programs 3D‐JIGSAW and 3D‐PSSM , 2001, Proteins.

[33]  D. Hartshorne,et al.  Study of the subunit interactions in myosin phosphatase by surface plasmon resonance. , 2000, European journal of biochemistry.

[34]  M J Sternberg,et al.  Use of pair potentials across protein interfaces in screening predicted docked complexes , 1999, Proteins.

[35]  M. Sternberg,et al.  Rapid refinement of protein interfaces incorporating solvation: application to the docking problem. , 1998, Journal of molecular biology.

[36]  M. Sternberg,et al.  Modelling protein docking using shape complementarity, electrostatics and biochemical information. , 1997, Journal of molecular biology.

[37]  R. Huber,et al.  Structure of the nidogen binding LE module of the laminin gamma1 chain in solution. , 1996, Journal of molecular biology.

[38]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[39]  J Hoebeke,et al.  Epitopic analysis of the Toxoplasma gondii major surface antigen SAG1. , 1994, Molecular and biochemical parasitology.

[40]  Claude Brezinski,et al.  Numerical recipes in Fortran (The art of scientific computing) : W.H. Press, S.A. Teukolsky, W.T. Vetterling and B.P. Flannery, Cambridge Univ. Press, Cambridge, 2nd ed., 1992. 963 pp., US$49.95, ISBN 0-521-43064-X.☆ , 1993 .

[41]  J. W. Humberston.  Classical mechanics , 1980, Nature.

[42]  D J Osguthorpe,et al.  Refined models for computer simulation of protein folding. Applications to the study of conserved secondary structure and flexible hinge points during the folding of pancreatic trypsin inhibitor. , 1979, Journal of molecular biology.