GRAMM-X public web server for protein–protein docking

Protein docking software GRAMM-X and its web interface () extend the original GRAMM Fast Fourier Transformation methodology by employing smoothed potentials, refinement stage, and knowledge-based scoring. The web server frees users from complex installation of database-dependent parallel software and maintaining large hardware resources needed for protein docking simulations. Docking problems submitted to GRAMM-X server are processed by a 320 processor Linux cluster. The server was extensively tested by benchmarking, several months of public use, and participation in the CAPRI server track.

[1]  Ilya A Vakser,et al.  Development and testing of an automated approach to protein docking , 2005, Proteins.

[2]  I. Vakser,et al.  How common is the funnel‐like energy landscape in protein‐protein interactions? , 2001, Protein science : a publication of the Protein Society.

[3]  I. Vakser.  Protein docking for low-resolution structures. , 1995, Protein engineering.

[4]  Zhiping Weng,et al.  ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5 , 2005, Proteins.

[5]  Wilfred F. van Gunsteren,et al.  Estimating relative free energies from a single ensemble: Hydration free energies , 1999, J. Comput. Chem..

[6]  C. Aflalo,et al.  Hydrophobic docking: A proposed enhancement to molecular recognition techniques , 1994, Proteins.

[7]  C. Camacho,et al.  Modeling side‐chains using molecular dynamics improve recognition of binding region in CAPRI targets , 2005, Proteins.

[8]  Rebecca C. Wade,et al.  Protein‐Protein Docking , 2001 .

[9]  Ilya A Vakser,et al.  The role of geometric complementarity in secondary structure packing: A systematic docking study , 2003, Protein science : a publication of the Protein Society.

[10]  I A Vakser.  Long-distance potentials: an approach to the multiple-minima problem in ligand-receptor interaction. , 1996, Protein engineering.

[11]  Jeffrey J. Gray,et al.  CAPRI rounds 3–5 reveal promising successes and future challenges for RosettaDock , 2005, Proteins.

[12]  Gabriel Waksman,et al.  Proteomics and protein-protein interactions : biology, chemistry, bionformatics, and drug design , 2005 .

[13]  I. Vakser,et al.  A systematic study of low-resolution recognition in protein--protein complexes. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[14]  E. Katchalski‐Katzir,et al.  Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[15]  Genki Terashi,et al.  Searching for protein–protein interaction sites and docking by the methods of molecular dynamics, grid scoring, and the pairwise interaction potential of amino acid residues , 2005, Proteins.

[16]  Sandor Vajda,et al.  ClusPro: an automated docking and discrimination method for the prediction of protein complexes , 2004, Bioinform..

[17]  Ruth Nussinov,et al.  PatchDock and SymmDock: servers for rigid and symmetric docking , 2005, Nucleic Acids Res..

[18]  Garland R. Marshall,et al.  Protein-Protein Docking Methods , 2005 .

[19]  L. T. Ten Eyck,et al.  Protein docking using continuum electrostatics and geometric fit. , 2001, Protein engineering.

[20]  Zhiping Weng,et al.  A protein–protein docking benchmark , 2003, Proteins.