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Items: 1 to 20 of 107

1.

The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations.

Rizzi A, Jensen T, Slochower DR, Aldeghi M, Gapsys V, Ntekoumes D, Bosisio S, Papadourakis M, Henriksen NM, de Groot BL, Cournia Z, Dickson A, Michel J, Gilson MK, Shirts MR, Mobley DL, Chodera JD.

J Comput Aided Mol Des. 2020 Jan 27. doi: 10.1007/s10822-020-00290-5. [Epub ahead of print]

PMID:
31984465
2.

Overview of the SAMPL6 host-guest binding affinity prediction challenge.

Rizzi A, Murkli S, McNeill JN, Yao W, Sullivan M, Gilson MK, Chiu MW, Isaacs L, Gibb BC, Mobley DL, Chodera JD.

J Comput Aided Mol Des. 2018 Oct;32(10):937-963. doi: 10.1007/s10822-018-0170-6. Epub 2018 Nov 10.

3.

Detailed potential of mean force studies on host-guest systems from the SAMPL6 challenge.

Song LF, Bansal N, Zheng Z, Merz KM Jr.

J Comput Aided Mol Des. 2018 Oct;32(10):1013-1026. doi: 10.1007/s10822-018-0153-7. Epub 2018 Aug 24.

PMID:
30143917
4.

SAMPL6 host-guest challenge: binding free energies via a multistep approach.

Eken Y, Patel P, Díaz T, Jones MR, Wilson AK.

J Comput Aided Mol Des. 2018 Oct;32(10):1097-1115. doi: 10.1007/s10822-018-0159-1. Epub 2018 Sep 17.

PMID:
30225724
5.

Converging free energies of binding in cucurbit[7]uril and octa-acid host-guest systems from SAMPL4 using expanded ensemble simulations.

Monroe JI, Shirts MR.

J Comput Aided Mol Des. 2014 Apr;28(4):401-15. doi: 10.1007/s10822-014-9716-4. Epub 2014 Mar 8.

PMID:
24610238
6.

Prediction of octanol-water partition coefficients for the SAMPL6-[Formula: see text] molecules using molecular dynamics simulations with OPLS-AA, AMBER and CHARMM force fields.

Fan S, Iorga BI, Beckstein O.

J Comput Aided Mol Des. 2020 Jan 20. doi: 10.1007/s10822-019-00267-z. [Epub ahead of print]

PMID:
31960254
7.

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.

8.

Prediction of CB[8] host-guest binding free energies in SAMPL6 using the double-decoupling method.

Han K, Hudson PS, Jones MR, Nishikawa N, Tofoleanu F, Brooks BR.

J Comput Aided Mol Des. 2018 Oct;32(10):1059-1073. doi: 10.1007/s10822-018-0144-8. Epub 2018 Aug 6.

9.

Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host-guest challenges.

Nishikawa N, Han K, Wu X, Tofoleanu F, Brooks BR.

J Comput Aided Mol Des. 2018 Oct;32(10):1075-1086. doi: 10.1007/s10822-018-0166-2. Epub 2018 Oct 15.

10.

Absolute binding free energies for the SAMPL6 cucurbit[8]uril host-guest challenge via the AMOEBA polarizable force field.

Laury ML, Wang Z, Gordon AS, Ponder JW.

J Comput Aided Mol Des. 2018 Oct;32(10):1087-1095. doi: 10.1007/s10822-018-0147-5. Epub 2018 Oct 15.

11.

Blinded predictions of standard binding free energies: lessons learned from the SAMPL6 challenge.

Papadourakis M, Bosisio S, Michel J.

J Comput Aided Mol Des. 2018 Oct;32(10):1047-1058. doi: 10.1007/s10822-018-0154-6. Epub 2018 Aug 29.

PMID:
30159717
12.

Binding free energies in the SAMPL6 octa-acid host-guest challenge calculated with MM and QM methods.

Caldararu O, Olsson MA, Misini Ignjatović M, Wang M, Ryde U.

J Comput Aided Mol Des. 2018 Oct;32(10):1027-1046. doi: 10.1007/s10822-018-0158-2. Epub 2018 Sep 10.

PMID:
30203229
13.

Binding Thermodynamics of Host-Guest Systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative.

Slochower DR, Henriksen NM, Wang LP, Chodera JD, Mobley DL, Gilson MK.

J Chem Theory Comput. 2019 Nov 12;15(11):6225-6242. doi: 10.1021/acs.jctc.9b00748. Epub 2019 Oct 25.

PMID:
31603667
14.

Predicting ligand binding affinity using on- and off-rates for the SAMPL6 SAMPLing challenge.

Dixon T, Lotz SD, Dickson A.

J Comput Aided Mol Des. 2018 Oct;32(10):1001-1012. doi: 10.1007/s10822-018-0149-3. Epub 2018 Aug 23.

PMID:
30141102
15.

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.

16.

SAMPL6 blind predictions of water-octanol partition coefficients using nonequilibrium alchemical approaches.

Procacci P, Guarnieri G.

J Comput Aided Mol Des. 2019 Oct 17. doi: 10.1007/s10822-019-00233-9. [Epub ahead of print]

PMID:
31624982
17.

Evaluating Force Field Performance in Thermodynamic Calculations of Cyclodextrin Host-Guest Binding: Water Models, Partial Charges, and Host Force Field Parameters.

Henriksen NM, Gilson MK.

J Chem Theory Comput. 2017 Sep 12;13(9):4253-4269. doi: 10.1021/acs.jctc.7b00359. Epub 2017 Aug 4.

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.

SAMPL6 host-guest blind predictions using a non equilibrium alchemical approach.

Procacci P, Guarrasi M, Guarnieri G.

J Comput Aided Mol Des. 2018 Oct;32(10):965-982. doi: 10.1007/s10822-018-0151-9. Epub 2018 Aug 20.

PMID:
30128927
20.

Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary tale.

Hudson PS, Han K, Woodcock HL, Brooks BR.

J Comput Aided Mol Des. 2018 Oct;32(10):983-999. doi: 10.1007/s10822-018-0165-3. Epub 2018 Oct 1.

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