title: Prediction of loop geometries using a generalized born model of solvation effects.
abstract: We have carried out an extensive exploration of the possibility of predicting the structure of long loops in proteins, using an 8- and a 12-residue loop in ribonuclease A as models. The native X-ray structure is used as a template while allowing for template flexibility; this makes our work relevant to the problem of homology modeling in which the template is not precisely known. Energies are calculated with the AMBER* and AMBER94 molecular mechanics potentials and the generalized Born continuum solvation model; and conformational space is sampled by means of a combination of Monte Carlo and molecular dynamics methods. Our AMBER94 results demonstrate that we can successfully generate loops with low root-mean-square deviations from the native as well as excellent energetic rankings.
authors.affiliation: Department of Chemistry and Center for Biomolecular Simulation, Columbia University, New York, New York 10027, USA.
authors.forename: C S
authors.initials: CS
authors.lastname: Rapp
authors.forename: R A
authors.initials: RA
authors.lastname: Friesner
mesh_terms: D003198:Computer Simulation; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D011487:Protein Conformation; D012259:Ribonuclease, Pancreatic / Q000737:chemistry*; D012997:Solvents
chemical_list: D012997:Solvents; D012259:Ribonuclease, Pancreatic