dorsal/arxiv
View SchemaA physically meaningful method for the comparison of potential energy functions
| Authors | J. L. Alonso, Pablo Echenique |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0504029 |
| URL | https://arxiv.org/abs/q-bio/0504029 |
| DOI | 10.1002/jcc.20337 |
| Journal | J. Comp. Chem. 27 (2006) 238-252 |
Abstract
In the study of the conformational behavior of complex systems, such as proteins, several related statistical measures are commonly used to compare two different potential energy functions. Among them, the Pearson's correlation coefficient r has no units and allows only semi-quantitative statements to be made. Those that do have units of energy and whose value may be compared to a physically relevant scale, such as the root mean square deviation (RMSD), the mean error of the energies (ER), the standard deviation of the error (SDER) or the mean absolute error (AER), overestimate the distance between potentials. Moreover, their precise statistical meaning is far from clear. In this article, a new measure of the distance between potential energy functions is defined which overcomes the aforementioned difficulties. In addition, its precise physical meaning is discussed, the important issue of its additivity is investigated and some possible applications are proposed. Finally, two of these applications are illustrated with practical examples: the study of the van der Waals energy, as implemented in CHARMM, in the Trp-Cage protein (PDB code 1L2Y) and the comparison of different levels of the theory in the ab initio study of the Ramachandran map of the model peptide HCO-L-Ala-NH2.
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"abstract": "In the study of the conformational behavior of complex systems, such as\nproteins, several related statistical measures are commonly used to compare two\ndifferent potential energy functions. Among them, the Pearson\u0027s correlation\ncoefficient r has no units and allows only semi-quantitative statements to be\nmade. Those that do have units of energy and whose value may be compared to a\nphysically relevant scale, such as the root mean square deviation (RMSD), the\nmean error of the energies (ER), the standard deviation of the error (SDER) or\nthe mean absolute error (AER), overestimate the distance between potentials.\nMoreover, their precise statistical meaning is far from clear. In this article,\na new measure of the distance between potential energy functions is defined\nwhich overcomes the aforementioned difficulties. In addition, its precise\nphysical meaning is discussed, the important issue of its additivity is\ninvestigated and some possible applications are proposed. Finally, two of these\napplications are illustrated with practical examples: the study of the van der\nWaals energy, as implemented in CHARMM, in the Trp-Cage protein (PDB code 1L2Y)\nand the comparison of different levels of the theory in the ab initio study of\nthe Ramachandran map of the model peptide HCO-L-Ala-NH2.",
"arxiv_id": "q-bio/0504029",
"authors": [
"J. L. Alonso",
"Pablo Echenique"
],
"categories": [
"q-bio.QM",
"cond-mat.soft",
"q-bio.BM"
],
"doi": "10.1002/jcc.20337",
"journal_ref": "J. Comp. Chem. 27 (2006) 238-252",
"title": "A physically meaningful method for the comparison of potential energy functions",
"url": "https://arxiv.org/abs/q-bio/0504029"
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