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Items: 1 to 20 of 109

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.

Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge.

Lee J, Tofoleanu F, Pickard FC 4th, König G, Huang J, Damjanović A, Baek M, Seok C, Brooks BR.

J Comput Aided Mol Des. 2017 Jan;31(1):71-85. doi: 10.1007/s10822-016-9968-2. Epub 2016 Sep 27.

4.

Absolute binding free energies for octa-acids and guests in SAMPL5 : Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge.

Tofoleanu F, Lee J, Pickard Iv FC, König G, Huang J, Baek M, Seok C, Brooks BR.

J Comput Aided Mol Des. 2017 Jan;31(1):107-118. doi: 10.1007/s10822-016-9965-5. Epub 2016 Sep 30.

PMID:
27696242
5.

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
6.

On the fly estimation of host-guest binding free energies using the movable type method: participation in the SAMPL5 blind challenge.

Bansal N, Zheng Z, Cerutti DS, Merz KM.

J Comput Aided Mol Des. 2017 Jan;31(1):47-60. doi: 10.1007/s10822-016-9980-6. Epub 2016 Oct 3.

PMID:
27699553
7.

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
8.

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.

9.

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.

10.

The SAMPL5 host-guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method.

Yin J, Henriksen NM, Slochower DR, Gilson MK.

J Comput Aided Mol Des. 2017 Jan;31(1):133-145. doi: 10.1007/s10822-016-9970-8. Epub 2016 Sep 16.

11.
12.

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
13.

Binding free energies in the SAMPL5 octa-acid host-guest challenge calculated with DFT-D3 and CCSD(T).

Caldararu O, Olsson MA, Riplinger C, Neese F, Ryde U.

J Comput Aided Mol Des. 2017 Jan;31(1):87-106. doi: 10.1007/s10822-016-9957-5. Epub 2016 Sep 6.

15.

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.

16.

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.

17.

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
18.

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.

19.

Blinded predictions of host-guest standard free energies of binding in the SAMPL5 challenge.

Bosisio S, Mey ASJS, Michel J.

J Comput Aided Mol Des. 2017 Jan;31(1):61-70. doi: 10.1007/s10822-016-9933-0. Epub 2016 Aug 8.

PMID:
27503495

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