Pairwise and multimeric protein-protein docking using the LZerD program suite.

Physical interactions between proteins are involved in many important cell functions and are key for understanding the mechanisms of biological processes. Protein-protein docking programs provide a means to computationally construct three-dimensional (3D) models of a protein complex structure from its component protein units. A protein docking program takes two or more individual 3D protein structures, which are either experimentally solved or computationally modeled, and outputs a series of probable complex structures.In this chapter we present the LZerD protein docking suite, which includes programs for pairwise docking, LZerD and PI-LZerD, and multiple protein docking, Multi-LZerD, developed by our group. PI-LZerD takes protein docking interface residues as additional input information. The methods use a combination of shape-based protein surface features as well as physics-based scoring terms to generate protein complex models. The programs are provided as stand-alone programs and can be downloaded from http://kiharalab.org/proteindocking.

[1]  Alexandre M. J. J. Bonvin,et al.  Building Macromolecular Assemblies by Information-driven Docking , 2010, Molecular & Cellular Proteomics.

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

[3]  Daisuke Kihara,et al.  Protein-protein docking using region-based 3D Zernike descriptors , 2009, BMC Bioinformatics.

[4]  Daisuke Kihara,et al.  Fitting multimeric protein complexes into electron microscopy maps using 3D Zernike descriptors. , 2012, The journal of physical chemistry. B.

[5]  J. Thornton,et al.  Satisfying hydrogen bonding potential in proteins. , 1994, Journal of molecular biology.

[6]  Daisuke Kihara,et al.  Effect of conformation sampling strategies in genetic algorithm for multiple protein docking , 2012, BMC Proceedings.

[7]  Nikolaos Canterakis,et al.  3D Zernike Moments and Zernike Affine Invariants for 3D Image Analysis and Recognition , 1999 .

[8]  Marcin Novotni,et al.  3D zernike descriptors for content based shape retrieval , 2003, SM '03.

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

[10]  Zhiping Weng,et al.  Protein–protein docking benchmark version 4.0 , 2010, Proteins.

[11]  Yifeng D. Yang,et al.  Multi‐LZerD: Multiple protein docking for asymmetric complexes , 2012, Proteins.

[12]  H. Wolfson,et al.  Prediction of multimolecular assemblies by multiple docking. , 2005, Journal of molecular biology.

[13]  M. Eisenstein,et al.  Construction of molecular assemblies via docking: Modeling of tetramers with D2 symmetry , 2003, Proteins.

[14]  Daisuke Kihara,et al.  Evaluation of multiple protein docking structures using correctly predicted pairwise subunits , 2012, BMC Bioinformatics.

[15]  Huan-Xiang Zhou,et al.  meta-PPISP: a meta web server for protein-protein interaction site prediction , 2007, Bioinform..

[16]  Daisuke Kihara,et al.  Molecular surface representation using 3D Zernike descriptors for protein shape comparison and docking. , 2011, Current protein & peptide science.

[17]  Haim J. Wolfson,et al.  Geometric hashing: an overview , 1997 .

[18]  David S. Goodsell,et al.  The RCSB Protein Data Bank: new resources for research and education , 2012, Nucleic Acids Res..

[19]  David Baker,et al.  Prediction of the structure of symmetrical protein assemblies , 2007, Proceedings of the National Academy of Sciences.

[20]  Z. Weng,et al.  ZDOCK: An initial‐stage protein‐docking algorithm , 2003, Proteins.

[21]  D. Kihara,et al.  A novel method for protein–protein interaction site prediction using phylogenetic substitution models , 2012, Proteins.

[22]  Andrey Tovchigrechko,et al.  GRAMM-X public web server for protein–protein docking , 2006, Nucleic Acids Res..

[23]  Pedro Alexandrino Fernandes,et al.  Protein–protein docking dealing with the unknown , 2009, J. Comput. Chem..

[24]  David W Ritchie,et al.  Recent progress and future directions in protein-protein docking. , 2008, Current protein & peptide science.

[25]  W. Delano.  The PyMOL Molecular Graphics System , 2002 .

[26]  Daisuke Kihara,et al.  Protein Surface Representation and Comparison: New Approaches in Structural Proteomics , 2011 .

[27]  Miriam Eisenstein,et al.  Weighted geometric docking: Incorporating external information in the rotation‐translation scan , 2003, Proteins.

[28]  Stephen R. Comeau,et al.  Predicting oligomeric assemblies: N-mers a primer. , 2005, Journal of structural biology.

[29]  Zhiping Weng,et al.  ZRANK: Reranking protein docking predictions with an optimized energy function , 2007, Proteins.

[30]  Bin Li,et al.  Protein docking prediction using predicted protein-protein interface , 2012, BMC Bioinformatics.

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