title: Pairwise and multimeric protein-protein docking using the LZerD program suite.
abstract: 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.
authors.affiliation: Department of Computer Science, Purdue University, West Lafayette, IN, USA.
authors.forename: Juan
authors.initials: J
authors.lastname: Esquivel-Rodriguez
authors.forename: Vianney
authors.initials: V
authors.lastname: Filos-Gonzalez
authors.forename: Bin
authors.initials: B
authors.lastname: Li
authors.forename: Daisuke
authors.initials: D
authors.lastname: Kihara
mesh_terms: D019295:Computational Biology / Q000379:methods; D020407:Internet; D062105:Molecular Docking Simulation; D046912:Multiprotein Complexes / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D046912:Multiprotein Complexes; D011506:Proteins