title: ICOSA: A Distance-Dependent, Orientation-Specific Coarse-Grained Contact Potential for Protein Structure Modeling.
abstract: The relative distance and orientation in contacting residue pairs plays a significant role in protein folding and stabilization. We hereby devise a new knowledge-based, coarse-grained contact potential, so-called ICOSA, by correlating inter-residue contact distance and orientation in evaluating pair-wise inter-residue interactions. The rationale of our approach is to establish icosahedral local coordinates to estimate the statistical residue contact distributions in all spherical triangular shells within a sphere. We extend the theory of finite ideal gas reference state to icosahedral local coordinates. ICOSA incorporates long-range contact interactions, which is critical to ICOSA sensitivity and is justified in statistical rigor. With only backbone atoms information, ICOSA is at least comparable to all-atom, fine-grained potentials such as Rosetta, DFIRE, I-TASSER, and OPUS in discriminating near-natives from misfold protein conformations in the Rosetta and I-TASSER protein decoy sets. ICOSA also outperforms a set of widely used coarse-grained potentials and is comparable to all-atom, fine-grained potentials in identifying CASP10 models.
authors.affiliation: Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA.
authors.forename: Wessam
authors.initials: W
authors.lastname: Elhefnawy
authors.affiliation: Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA.
authors.forename: Lin
authors.initials: L
authors.lastname: Chen
authors.affiliation: Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA.
authors.forename: Yun
authors.initials: Y
authors.lastname: Han
authors.affiliation: Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA. Electronic address: yaohang@cs.odu.edu.
authors.forename: Yaohang
authors.initials: Y
authors.lastname: Li
mesh_terms: D000465:Algorithms; D053455:Caspase 10 / Q000737:chemistry; D019295:Computational Biology / Q000379:methods*; D051188:Knowledge Bases; D008958:Models, Molecular; D011487:Protein Conformation; D025941:Protein Interaction Mapping / Q000379:methods*; D060066:Protein Interaction Maps; D020539:Sequence Analysis, Protein / Q000379:methods; D012984:Software
chemical_list: D053455:Caspase 10
keywords: contact orientation and distance; finite ideal gas reference state; icosahedrons; inter-residue contact; knowledge-based potential