Skip to main content

Binding Affinity and Specificity from Computational Studies

Buy Article:

$63.00 plus tax (Refund Policy)

Abstract:



Computational methods available for the calculation of relative and absolute binding affinities (free energy simulations, continuum electrostatics, linear interaction energy approximations, and empirical solvation models) are reviewed together with recent applications to biological systems. The decomposability of the binding free energy into physically meaningful components is examined and results obtained for these components are presented. Some of these components, such as the direct interactions, the translational / rotational entropy loss, and the desolvation free energy are well recognized. Recent calculations have shown that the translational / rotational entropy loss is not as large as some theoretical calculations have previously suggested because of substantial residual movements in the bound complex. Recent work also points to the importance of contributions that are often neglected in binding affinity calculations, such as the protein reorganization energy and, for flexible ligands, the ligand reorganization energy. Future work should concentrate on the improvement of the energy functions and simulation protocols for the achievement of more precise and accurate predictions.

Keywords: Molecular mechanics; free energy; molecular dynamics; surface area

Document Type: Review Article

DOI: http://dx.doi.org/10.2174/1385272023373491

Publication date: December 1, 2002

ben/coc/2002/00000006/00000014/art00006
dcterms_title,dcterms_description,pub_keyword
6
5
20
40
5

Access Key

Free Content
Free content
New Content
New content
Open Access Content
Open access content
Subscribed Content
Subscribed content
Free Trial Content
Free trial content
Cookie Policy
X
Cookie Policy
ingentaconnect website makes use of cookies so as to keep track of data that you have filled in. I am Happy with this Find out more