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Items: 1 to 20 of 126

1.

Blind prediction of SAMPL4 cucurbit[7]uril binding affinities with the mining minima method.

Muddana HS, Yin J, Sapra NV, Fenley AT, Gilson MK.

J Comput Aided Mol Des. 2014 Apr;28(4):463-74. doi: 10.1007/s10822-014-9726-2. Epub 2014 Feb 8.

2.

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.

3.

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.

4.

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
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.

Blind prediction of binding affinities for charged supramolecular host-guest systems: achievements and shortcomings of DFT-D3.

Sure R, Antony J, Grimme S.

J Phys Chem B. 2014 Mar 27;118(12):3431-40. doi: 10.1021/jp411616b. Epub 2014 Mar 17.

PMID:
24588346
7.

MM/GBSA and LIE estimates of host-guest affinities: dependence on charges and solvation model.

Genheden S.

J Comput Aided Mol Des. 2011 Nov;25(11):1085-93. doi: 10.1007/s10822-011-9486-1. Epub 2011 Nov 19.

PMID:
22101362
8.

Grid inhomogeneous solvation theory: hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril.

Nguyen CN, Young TK, Gilson MK.

J Chem Phys. 2012 Jul 28;137(4):044101. doi: 10.1063/1.4733951. Erratum in: J Chem Phys. 2012 Oct 14;137(14):149901.

9.

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.

10.

Force-field and quantum-mechanical binding study of selected SAMPL3 host-guest complexes.

Hamaguchi N, Fusti-Molnar L, Wlodek S.

J Comput Aided Mol Des. 2012 May;26(5):577-82. doi: 10.1007/s10822-012-9553-2. Epub 2012 Feb 25.

PMID:
22366954
11.

Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations.

Misini Ignjatović M, Caldararu O, Dong G, Muñoz-Gutierrez C, Adasme-Carreño F, Ryde U.

J Comput Aided Mol Des. 2016 Sep;30(9):707-730. Epub 2016 Aug 26.

12.

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.

13.

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.

14.

Estimates of ligand-binding affinities supported by quantum mechanical methods.

Söderhjelm P, Kongsted J, Genheden S, Ryde U.

Interdiscip Sci. 2010 Mar;2(1):21-37. doi: 10.1007/s12539-010-0083-0. Epub 2010 Jan 28.

PMID:
20640794
15.

Correlating solution binding and ESI-MS stabilities by incorporating solvation effects in a confined cucurbit[8]uril system.

Rauwald U, Biedermann F, Deroo S, Robinson CV, Scherman OA.

J Phys Chem B. 2010 Jul 8;114(26):8606-15. doi: 10.1021/jp102933h.

PMID:
20550146
16.

Comparison of Methods To Reweight from Classical Molecular Simulations to QM/MM Potentials.

Dybeck EC, König G, Brooks BR, Shirts MR.

J Chem Theory Comput. 2016 Apr 12;12(4):1466-80. doi: 10.1021/acs.jctc.5b01188. Epub 2016 Mar 23.

PMID:
26928941
17.

A QM/MM study of the binding of RAPTA ligands to cathepsin B.

Ciancetta A, Genheden S, Ryde U.

J Comput Aided Mol Des. 2011 Aug;25(8):729-42. doi: 10.1007/s10822-011-9448-7. Epub 2011 Jun 24.

PMID:
21701919
18.

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
19.

Host-guest complexes with protein-ligand-like affinities: computational analysis and design.

Moghaddam S, Inoue Y, Gilson MK.

J Am Chem Soc. 2009 Mar 25;131(11):4012-21. doi: 10.1021/ja808175m.

20.

Quantum mechanical binding free energy calculation for phosphopeptide inhibitors of the Lck SH2 domain.

Anisimov VM, Cavasotto CN.

J Comput Chem. 2011 Jul 30;32(10):2254-63. doi: 10.1002/jcc.21808. Epub 2011 Apr 11.

PMID:
21484840

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