An Information Theoretic Approach to Macromolecular Modeling: II. Force Fields. Export

@article{citeulike:423120, abstract = {In this article, we explore the information content of molecular force-field calculations. We make use of exhaustive lattice models of molecular conformations and reduced alphabet sequences to determine the relative resolving power of pairwise interaction-based force fields. We find that sequence-specific interactions that operate over longer distances offer greater amounts of information than nearest-neighbor or non-sequence-specific interactions. In a companion article in this issue, we explored the information content of sequence alignment procedures and the calculation of gap penalties. Both articles have implications for protein and nucleic-acid computations.}, address = {Graduate Group in Biophysics, and Department of Pharmaceutical Chemistry, University of California, San Francisco, California.}, author = {Aynechi, T. and Kuntz, I. D.}, citeulike-article-id = {423120}, citeulike-linkout-0 = {http://dx.doi.org/10.1529/biophysj.105.059618}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/16254390}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=16254390}, doi = {10.1529/biophysj.105.059618}, issn = {0006-3495}, journal = {Biophys J}, keywords = {algorithm, force-field, information-theory}, month = {November}, number = {5}, pages = {3008--3016}, posted-at = {2005-12-06 01:47:19}, priority = {2}, title = {An Information Theoretic Approach to Macromolecular Modeling: II. Force Fields.}, url = {http://dx.doi.org/10.1529/biophysj.105.059618}, volume = {89}, year = {2005} }

TY - JOUR ID - citeulike:423120 L3 - citeulike-article-id:423120 N2 - In this article, we explore the information content of molecular force-field calculations. We make use of exhaustive lattice models of molecular conformations and reduced alphabet sequences to determine the relative resolving power of pairwise interaction-based force fields. We find that sequence-specific interactions that operate over longer distances offer greater amounts of information than nearest-neighbor or non-sequence-specific interactions. In a companion article in this issue, we explored the information content of sequence alignment procedures and the calculation of gap penalties. Both articles have implications for protein and nucleic-acid computations. IS - 5 JF - Biophys J SN - 0006-3495 AD - Graduate Group in Biophysics, and Department of Pharmaceutical Chemistry, University of California, San Francisco, California. EP - 3016 TI - An Information Theoretic Approach to Macromolecular Modeling: II. Force Fields. VL - 89 SP - 3008 KW - algorithm KW - force-field KW - information-theory AU - Aynechi, T AU - Kuntz, ID PY - 2005/11// UR - http://dx.doi.org/10.1529/biophysj.105.059618 ER -