title: The protein local optimization program and G-protein-coupled receptors: loop restoration and applications to homology modeling.
abstract: The protein local optimization program (PLOP) uses sophisticated sampling algorithms and a highly refined physics-based energy function to restore loops within a protein structure. In this chapter, we highlight some of the recent successes we have had with PLOP restoring long loops in their native environment as well as the intra- and extracellular loops of four G-protein-coupled receptors. This includes the very long second extracellular loops of bovine rhodopsin and the turkey β1- and human β2-adrenergic receptors. We then provide an extremely detailed description of PLOP's algorithms, as well as a sample file and explicit keywords so that a new user can successfully run PLOP.
authors: Department of Chemistry, Columbia University, New York, USA. dag2115@columbia.edu
authors: Dahlia A
authors: DA
authors: Goldfeld
authors: Richard A
authors: RA
authors: Friesner
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D002417:Cattle; D006801:Humans; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D008969:Molecular Sequence Data; D019151:Peptide Library; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D018342:Receptors, Adrenergic, beta-1 / Q000737:chemistry*; D018343:Receptors, Adrenergic, beta-2 / Q000737:chemistry*; D012243:Rhodopsin / Q000737:chemistry*; D040681:Structural Homology, Protein; D013816:Thermodynamics; D014422:Turkeys
chemical_list: D019151:Peptide Library; D018342:Receptors, Adrenergic, beta-1; D018343:Receptors, Adrenergic, beta-2; D012243:Rhodopsin