IMR Press / FBS / Volume 5 / Issue 2 / DOI: 10.2741/S384

Frontiers in Bioscience-Scholar (FBS) is published by IMR Press from Volume 13 Issue 1 (2021). Previous articles were published by another publisher on a subscription basis, and they are hosted by IMR Press on as a courtesy and upon agreement with Frontiers in Bioscience.

A statistical mechanics handbook for protein-ligand binding simulation
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1 Drug Discovery and Development, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
2 Department of Physics, University of Rome "La Sapienza" and CNISM Unit 1, Ple A. Moro 5, 00185 Rome, Italy

*Author to whom correspondence should be addressed.

Academic Editor: Indrajit Chowdhury

Front. Biosci. (Schol Ed) 2013, 5(2), 478–495;
Published: 1 January 2013
(This article belongs to the Special Issue Recent progress in reproductive biology)

In this work, the fundamental elements of statistical mechanics underlying the simulation of the protein-ligand binding process, such as statistical ensembles and the concept of microscopic estimators of macroscopic observables and free energy, are summarized in a self consistent fashion. Particular attention is then devoted to the introduction of some mathematical tools that are used in atomistic simulations aimed at estimating binding affinities and free energy profiles, and to the illustration of the origins of the difficulties encountered in this endeavor.

Statistical mechanics
free energy
activated processes
collective variables
protein-ligand binding
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