The statistical-thermodynamic basis for computation of binding affinities: a critical review. Export

@article{citeulike:741701, abstract = {Although the statistical thermodynamics of noncovalent binding has been considered in a number of theoretical papers, few methods of computing binding affinities are derived explicitly from this underlying theory. This has contributed to uncertainty and controversy in certain areas. This article therefore reviews and extends the connections of some important computational methods with the underlying statistical thermodynamics. A derivation of the standard free energy of binding forms the basis of this review. This derivation should be useful in formulating novel computational methods for predicting binding affinities. It also permits several important points to be established. For example, it is found that the double-annihilation method of computing binding energy does not yield the standard free energy of binding, but can be modified to yield this quantity. The derivation also makes it possible to define clearly the changes in translational, rotational, configurational, and solvent entropy upon binding. It is argued that molecular mass has a negligible effect upon the standard free energy of binding for biomolecular systems, and that the cratic entropy defined by Gurney is not a useful concept. In addition, the use of continuum models of the solvent in binding calculations is reviewed, and a formalism is presented for incorporating a limited number of solvent molecules explicitly.}, address = {Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, Rockville, Maryland 20850-3479, USA. gilson@indigo14.carb.nist.gov}, author = {Gilson, M. K. and Given, J. A. and Bush, B. L. and McCammon, J. A.}, citeulike-article-id = {741701}, citeulike-linkout-0 = {http://www.biophysj.org/cgi/content/abstract/72/3/1047}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/9138555}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=9138555}, issn = {0006-3495}, journal = {Biophys J}, keywords = {entropy, free\_energy, molecular\_dynamics, physics, protein\_structure, review}, month = {March}, number = {3}, pages = {1047--1069}, posted-at = {2008-04-03 20:07:07}, priority = {2}, title = {The statistical-thermodynamic basis for computation of binding affinities: a critical review.}, url = {http://www.biophysj.org/cgi/content/abstract/72/3/1047}, volume = {72}, year = {1997} }

TY - JOUR ID - citeulike:741701 L3 - citeulike-article-id:741701 N2 - Although the statistical thermodynamics of noncovalent binding has been considered in a number of theoretical papers, few methods of computing binding affinities are derived explicitly from this underlying theory. This has contributed to uncertainty and controversy in certain areas. This article therefore reviews and extends the connections of some important computational methods with the underlying statistical thermodynamics. A derivation of the standard free energy of binding forms the basis of this review. This derivation should be useful in formulating novel computational methods for predicting binding affinities. It also permits several important points to be established. For example, it is found that the double-annihilation method of computing binding energy does not yield the standard free energy of binding, but can be modified to yield this quantity. The derivation also makes it possible to define clearly the changes in translational, rotational, configurational, and solvent entropy upon binding. It is argued that molecular mass has a negligible effect upon the standard free energy of binding for biomolecular systems, and that the cratic entropy defined by Gurney is not a useful concept. In addition, the use of continuum models of the solvent in binding calculations is reviewed, and a formalism is presented for incorporating a limited number of solvent molecules explicitly. IS - 3 JF - Biophys J SN - 0006-3495 AD - Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, Rockville, Maryland 20850-3479, USA. gilson@indigo14.carb.nist.gov EP - 1069 TI - The statistical-thermodynamic basis for computation of binding affinities: a critical review. VL - 72 SP - 1047 KW - entropy KW - free_energy KW - molecular_dynamics KW - physics KW - protein_structure KW - review AU - Gilson, MK AU - Given, JA AU - Bush, BL AU - McCammon, JA PY - 1997/03// UR - http://www.biophysj.org/cgi/content/abstract/72/3/1047 ER -