Pairwise and Multimeric Protein-Protein Docking Using the LZerD Program Suite.
Protein Structure Prediction
Methods in molecular biology, March 2014
Esquivel-Rodriguez J, Filos-Gonzalez V, Li B, Kihara D, Juan Esquivel-Rodriguez, Vianney Filos-Gonzalez, Bin Li, Daisuke Kihara
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.
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