title: Method for identification of rigid domains and hinge residues in proteins based on exhaustive enumeration.
abstract: Many proteins undergo large-scale motions where relatively rigid domains move against each other. The identification of rigid domains, as well as the hinge residues important for their relative movements, is important for various applications including flexible docking simulations. In this work, we develop a method for protein rigid domain identification based on an exhaustive enumeration of maximal rigid domains, the rigid domains not fully contained within other domains. The computation is performed by mapping the problem to that of finding maximal cliques in a graph. A minimal set of rigid domains are then selected, which cover most of the protein with minimal overlap. In contrast to the results of existing methods that partition a protein into non-overlapping domains using approximate algorithms, the rigid domains obtained from exact enumeration naturally contain overlapping regions, which correspond to the hinges of the inter-domain bending motion. The performance of the algorithm is demonstrated on several proteins.
authors.affiliation: Department of Oral Microbiology and Immunology, School of Dentistry, Seoul National University, Seoul, 110-749, Korea.
authors.forename: Jaehyun
authors.initials: J
authors.lastname: Sim
authors.affiliation: Department of Bioinformatics and Life Science, Soongsil University, Seoul, 156-743, Korea.
authors.forename: Jun
authors.initials: J
authors.lastname: Sim
authors.affiliation: Administrative Service Division, Apsun Dental Hospital, Seoul, 135-590, Korea.
authors.forename: Eunsung
authors.initials: E
authors.lastname: Park
authors.affiliation: Department of Oral Microbiology and Immunology, School of Dentistry, Seoul National University, Seoul, 110-749, Korea.
authors.forename: Julian
authors.initials: J
authors.lastname: Lee
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D056004:Molecular Dynamics Simulation; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins
keywords: DAGR; elastic network model; exact; exhaustive enumeration; graph theory; hinge; maximal clique; normal mode analysis; protein structure; rigid domain