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Items: 1 to 20 of 154

1.

Predicting binding affinities of host-guest systems in the SAMPL3 blind challenge: the performance of relative free energy calculations.

König G, Brooks BR.

J Comput Aided Mol Des. 2012 May;26(5):543-50. doi: 10.1007/s10822-011-9525-y. Epub 2011 Dec 24.

2.

Thermodynamic integration to predict host-guest binding affinities.

Lawrenz M, Wereszczynski J, Ortiz-Sánchez JM, Nichols SE, McCammon JA.

J Comput Aided Mol Des. 2012 May;26(5):569-76. doi: 10.1007/s10822-012-9542-5. Epub 2012 Feb 16.

3.

Comparison of thermodynamic integration and Bennett acceptance ratio for calculating relative protein-ligand binding free energies.

de Ruiter A, Boresch S, Oostenbrink C.

J Comput Chem. 2013 May 5;34(12):1024-34. doi: 10.1002/jcc.23229. Epub 2013 Jan 19.

PMID:
23335287
4.

Prediction of hydration free energies for aliphatic and aromatic chloro derivatives using molecular dynamics simulations with the OPLS-AA force field.

Beckstein O, Iorga BI.

J Comput Aided Mol Des. 2012 May;26(5):635-45. doi: 10.1007/s10822-011-9527-9. Epub 2011 Dec 21.

PMID:
22187140
5.

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

Muddana HS, Gilson MK.

J Comput Aided Mol Des. 2012 May;26(5):517-25. doi: 10.1007/s10822-012-9544-3. Epub 2012 Jan 25.

6.

Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM).

Gallicchio E, Levy RM.

J Comput Aided Mol Des. 2012 May;26(5):505-16. doi: 10.1007/s10822-012-9552-3. Epub 2012 Feb 22.

7.
8.

Efficiency of alchemical free energy simulations. II. Improvements for thermodynamic integration.

Bruckner S, Boresch S.

J Comput Chem. 2011 May;32(7):1320-33. doi: 10.1002/jcc.21712. Epub 2010 Dec 31.

PMID:
21425289
10.

Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4.

König G, Pickard FC 4th, Mei Y, Brooks BR.

J Comput Aided Mol Des. 2014 Mar;28(3):245-57. doi: 10.1007/s10822-014-9708-4. Epub 2014 Feb 7.

11.

Blind prediction of host-guest binding affinities: a new SAMPL3 challenge.

Muddana HS, Varnado CD, Bielawski CW, Urbach AR, Isaacs L, Geballe MT, Gilson MK.

J Comput Aided Mol Des. 2012 May;26(5):475-87. doi: 10.1007/s10822-012-9554-1. Epub 2012 Feb 25.

12.

The SAMPL4 host-guest blind prediction challenge: an overview.

Muddana HS, Fenley AT, Mobley DL, Gilson MK.

J Comput Aided Mol Des. 2014 Apr;28(4):305-17. doi: 10.1007/s10822-014-9735-1. Epub 2014 Mar 6. Review.

14.

Calculation of solvation free energies of charged solutes using mixed cluster/continuum models.

Bryantsev VS, Diallo MS, Goddard WA 3rd.

J Phys Chem B. 2008 Aug 14;112(32):9709-19. doi: 10.1021/jp802665d. Epub 2008 Jul 23.

PMID:
18646800
15.

Computation of relative binding free energy for an inhibitor and its analogs binding with Erk kinase using thermodynamic integration MD simulation.

Wu KW, Chen PC, Wang J, Sun YC.

J Comput Aided Mol Des. 2012 Oct;26(10):1159-69. doi: 10.1007/s10822-012-9606-6. Epub 2012 Sep 18.

PMID:
22986633
16.

Prediction of SAMPL4 host-guest binding affinities using funnel metadynamics.

Hsiao YW, Söderhjelm P.

J Comput Aided Mol Des. 2014 Apr;28(4):443-54. doi: 10.1007/s10822-014-9724-4. Epub 2014 Feb 18.

PMID:
24535628
17.

Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies.

Mikulskis P, Cioloboc D, Andrejić M, Khare S, Brorsson J, Genheden S, Mata RA, Söderhjelm P, Ryde U.

J Comput Aided Mol Des. 2014 Apr;28(4):375-400. doi: 10.1007/s10822-014-9739-x. Epub 2014 Apr 4.

PMID:
24700414
18.

Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials.

Wang J, Deng Y, Roux B.

Biophys J. 2006 Oct 15;91(8):2798-814. Epub 2006 Jul 14.

19.

Calculating binding free energies of host-guest systems using the AMOEBA polarizable force field.

Bell DR, Qi R, Jing Z, Xiang JY, Mejias C, Schnieders MJ, Ponder JW, Ren P.

Phys Chem Chem Phys. 2016 Jun 2. [Epub ahead of print]

PMID:
27254477
20.

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

Muddana HS, Gilson MK.

J Chem Theory Comput. 2012 Jun 12;8(6):2023-2033. Epub 2012 May 11.

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