PMID: 3755181Mar 20, 1986Paper

Refined models for computer calculations in protein engineering. Calibration and testing of atomic potential functions compatible with more efficient calculations

Journal of Molecular Biology
B Robson, E Platt

Abstract

A reappraisal has been made of interatomic potential functions for protein structure calculations using the all-atom approximation (except CH, CH2 and CH3, which are treated as "united atoms"). Some key problems are identified and treated. The potential functions are somewhat novel in form and consistent with more efficient and robust folding algorithms. In addition, the potentials are calibrated for for the rigid geometry approximation, since use of fixed standard bond lengths and valence angles (and fixed trans planar peptide groups) reduces the number of conformational variables and saves a great deal of computer time. Though these algorithms demand the use of potential functions of this special type, these functions can be readily implemented in more classical programs for the conformational analysis of proteins. They are calibrated or tested against a large body of experimental data, including extended basis set ab initio, quantum mechanical calculations, nuclear magnetic resonance spectroscopic data and dipole moment data for di- and oligopeptides, characteristic ratio data for random coil homopolypeptides, extensive data from peptide solubility studies, and experimental structures of polyalanine fibres and globular prote...Continue Reading

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Citations

Mar 1, 1992·Biopolymers·J Edelman
Sep 1, 1993·Protein Science : a Publication of the Protein Society·V ColluraJ Garnier
Jun 1, 1994·Protein Science : a Publication of the Protein Society·D BouzidaC DeLisi
Feb 1, 1995·Journal of Computer-aided Molecular Design·D E ClarkD R Westhead
Feb 1, 1994·Journal of Computer-aided Molecular Design·D ByrneP Weiner
Jun 1, 1995·Journal of Computer-aided Molecular Design·D FrenkelD R Westhead
Apr 1, 1987·Journal of Computer-aided Molecular Design·B Robson, E Platt
May 4, 2011·Journal of Computer-aided Molecular Design·Barry RobsonStephen K Boyer
Aug 1, 1990·Biochimie·J Garnier
Jan 15, 1998·Biochimica Et Biophysica Acta·T Dandekar, R König
Dec 1, 1986·Proceedings of the National Academy of Sciences of the United States of America·E H LeeF C Hartman
Feb 1, 1989·Journal of Biomolecular Structure & Dynamics·A K Mazur, R A Abagyan
Jan 1, 1989·Annals of the New York Academy of Sciences·E C GriffithsB Robson
Jan 1, 1987·Journal of Child Psychology and Psychiatry, and Allied Disciplines·D R Offord
Nov 21, 1986·Journal of Theoretical Biology·C H Wynn, B Robson
Jan 1, 1995·Critical Reviews in Biochemistry and Molecular Biology·F EisenhaberP Argos
Jan 4, 1987·Nature·B RobsonC A Morrison
Mar 15, 1988·European Journal of Biochemistry·T BlundellM Sutcliffe
Aug 1, 1987·International Journal of Peptide and Protein Research·D J WardB Robson
Mar 20, 2003·Journal of Proteome Research·Barry RobsonAlessandro Curioni

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