Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling Export

@article{citeulike:1177290, abstract = {The kinetic and thermodynamic aspects of the helix-coil transition in polyalanine-based peptides have been studied at the ensemble level using a distributed computing network. This study builds on a previous report, which critically assessed the performance of several contemporary force fields in reproducing experimental measurements and elucidated the complex nature of helix-coil systems. Here we consider the effects of modifying backbone torsions and the scaling of noncovalent interactions. Although these elements determine the potential of mean force between atoms separated by three covalent bonds (and thus largely determine the local conformational distributions observed in simulation), we demonstrate that the interplay between these factors is both complex and force field dependent. We quantitatively assess the heliophilicity of several helix-stabilizing potentials as well as the changes in heliophilicity resulting from such modifications, which can ldquomake or breakrdquo the accuracy of a given force field, and our findings suggests that future force field development may need to better consider effect that vary with peptide length. This report also serves as an example of the utility of distributed computing in analyzing and improving upon contemporary force fields at the level of absolute ensemble equilibrium, the next step in force field development. {\copyright} 2005 Wiley Periodicals, Inc. J Comput Chem 26: 682-690, 2005}, address = {Department of Chemistry, Stanford University, Structural Biology Department and SSRL85, Stanford, California 94305-5080}, author = {Sorin, Eric J. and Pande, Vijay S.}, citeulike-article-id = {1177290}, citeulike-linkout-0 = {http://dx.doi.org/10.1002/jcc.20208}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/15754305}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=15754305}, citeulike-linkout-3 = {http://www3.interscience.wiley.com/cgi-bin/abstract/110426169/ABSTRACT}, doi = {10.1002/jcc.20208}, issn = {1096-987X}, journal = {Journal of Computational Chemistry}, keywords = {force\_field, parametrization}, month = {May}, number = {7}, pages = {682--690}, posted-at = {2009-10-01 16:12:43}, priority = {2}, title = {Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling}, url = {http://dx.doi.org/10.1002/jcc.20208}, volume = {26}, year = {2005} }

TY - JOUR ID - citeulike:1177290 L3 - citeulike-article-id:1177290 N2 - The kinetic and thermodynamic aspects of the helix-coil transition in polyalanine-based peptides have been studied at the ensemble level using a distributed computing network. This study builds on a previous report, which critically assessed the performance of several contemporary force fields in reproducing experimental measurements and elucidated the complex nature of helix-coil systems. Here we consider the effects of modifying backbone torsions and the scaling of noncovalent interactions. Although these elements determine the potential of mean force between atoms separated by three covalent bonds (and thus largely determine the local conformational distributions observed in simulation), we demonstrate that the interplay between these factors is both complex and force field dependent. We quantitatively assess the heliophilicity of several helix-stabilizing potentials as well as the changes in heliophilicity resulting from such modifications, which can ldquomake or breakrdquo the accuracy of a given force field, and our findings suggests that future force field development may need to better consider effect that vary with peptide length. This report also serves as an example of the utility of distributed computing in analyzing and improving upon contemporary force fields at the level of absolute ensemble equilibrium, the next step in force field development. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 682-690, 2005 IS - 7 JF - Journal of Computational Chemistry SN - 1096-987X AD - Department of Chemistry, Stanford University, Structural Biology Department and SSRL85, Stanford, California 94305-5080 EP - 690 TI - Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling VL - 26 SP - 682 KW - force_field KW - parametrization AU - Sorin, Eric AU - Pande, Vijay PY - 2005/05// UR - http://dx.doi.org/10.1002/jcc.20208 ER -