Literature DB >> 15837174

Enhancing the accuracy, the efficiency and the scope of free energy simulations.

Tomas Rodinger1, Régis Pomès.   

Abstract

Many different methods exist for computing free energy changes from molecular simulations. Recent advances have led to improvements in the theoretical framework underlying these calculations, as well as in the accuracy and sampling efficiency of the algorithms. Novel methods combining the advantages afforded by various existing approaches offer promising strategies and open up new perspectives to help elucidate the physical basis of important biological processes.

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Year:  2005        PMID: 15837174     DOI: 10.1016/j.sbi.2005.03.001

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  17 in total

1.  Calculating pH-dependent free energy of proteins by using Monte Carlo protonation probabilities of ionizable residues.

Authors:  Qiang Huang; Andreas Herrmann
Journal:  Protein Cell       Date:  2012-03-31       Impact factor: 14.870

2.  Prediction of SAMPL3 host-guest binding affinities: evaluating the accuracy of generalized force-fields.

Authors:  Hari S Muddana; Michael K Gilson
Journal:  J Comput Aided Mol Des       Date:  2012-01-25       Impact factor: 3.686

Review 3.  Identification of HIV inhibitors guided by free energy perturbation calculations.

Authors:  Orlando Acevedo; Zandrea Ambrose; Patrick T Flaherty; Hadega Aamer; Prashi Jain; Somisetti V Sambasivarao
Journal:  Curr Pharm Des       Date:  2012       Impact factor: 3.116

4.  Probing a model of a GPCR/ligand complex in an explicit membrane environment: the human cholecystokinin-1 receptor.

Authors:  Jérôme Hénin; Bernard Maigret; Mounir Tarek; Chantal Escrieut; Daniel Fourmy; Christophe Chipot
Journal:  Biophys J       Date:  2005-12-02       Impact factor: 4.033

5.  Predicting absolute ligand binding free energies to a simple model site.

Authors:  David L Mobley; Alan P Graves; John D Chodera; Andrea C McReynolds; Brian K Shoichet; Ken A Dill
Journal:  J Mol Biol       Date:  2007-06-08       Impact factor: 5.469

6.  Application of a polarizable force field to calculations of relative protein-ligand binding affinities.

Authors:  Oleg Khoruzhii; Alexander G Donchev; Nikolay Galkin; Alexei Illarionov; Mikhail Olevanov; Vladimir Ozrin; Cary Queen; Vladimir Tarasov
Journal:  Proc Natl Acad Sci U S A       Date:  2008-07-24       Impact factor: 11.205

7.  Topography of funneled landscapes determines the thermodynamics and kinetics of protein folding.

Authors:  Jin Wang; Ronaldo J Oliveira; Xiakun Chu; Paul C Whitford; Jorge Chahine; Wei Han; Erkang Wang; José N Onuchic; Vitor B P Leite
Journal:  Proc Natl Acad Sci U S A       Date:  2012-09-10       Impact factor: 11.205

Review 8.  Fluorescence spectroscopy and molecular dynamics simulations in studies on the mechanism of membrane destabilization by antimicrobial peptides.

Authors:  Gianfranco Bocchinfuso; Sara Bobone; Claudia Mazzuca; Antonio Palleschi; Lorenzo Stella
Journal:  Cell Mol Life Sci       Date:  2011-05-17       Impact factor: 9.261

9.  Calculation of Host-Guest Binding Affinities Using a Quantum-Mechanical Energy Model.

Authors:  Hari S Muddana; Michael K Gilson
Journal:  J Chem Theory Comput       Date:  2012-05-11       Impact factor: 6.006

10.  An efficient protocol for obtaining accurate hydration free energies using quantum chemistry and reweighting from molecular dynamics simulations.

Authors:  Frank C Pickard; Gerhard König; Andrew C Simmonett; Yihan Shao; Bernard R Brooks
Journal:  Bioorg Med Chem       Date:  2016-08-22       Impact factor: 3.641

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