title: Search strategies and evaluation in protein-protein docking: principles, advances and challenges.
abstract: Protein-protein docking is attracting increasing attention in drug discovery research targeting protein-protein interactions, owing to its potential in predicting protein-protein interactions and identifying 'hot spot' residues at the protein-protein interface. Given the relative lack of information about binding sites and the fact that proteins are generally larger than ligand, the search algorithms and evaluation methods for protein-protein docking differ somewhat from those for protein-ligand docking and, hence, require different research strategies. Here, we review the basic concepts, principles and advances of current search strategies and evaluation methods for protein-protein docking. We also discuss the current challenges and limitations, as well as future directions, of established approaches.
authors.affiliation: Research Support Computing, University of Missouri, Columbia, MO 65211, USA; University of Missouri Bioinformatics Consortium, University of Missouri, Columbia, MO 65211, USA; Department of Computer Science, University of Missouri, Columbia, MO 65211, USA. Electronic address: huangshe@missouri.edu.
authors.forename: Sheng-You
authors.initials: SY
authors.lastname: Huang
mesh_terms: D001665:Binding Sites; D055808:Drug Discovery / Q000379:methods; D008024:Ligands; D062105:Molecular Docking Simulation / Q000379:methods; D011485:Protein Binding; D060066:Protein Interaction Maps; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D008024:Ligands; D011506:Proteins