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Items: 1 to 20 of 37

1.

Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations.

Mobley DL, Bayly CI, Cooper MD, Shirts MR, Dill KA.

J Chem Theory Comput. 2009 Feb 10;5(2):350-358.

2.

DOCK 6: combining techniques to model RNA-small molecule complexes.

Lang PT, Brozell SR, Mukherjee S, Pettersen EF, Meng EC, Thomas V, Rizzo RC, Case DA, James TL, Kuntz ID.

RNA. 2009 Jun;15(6):1219-30. doi: 10.1261/rna.1563609. Epub 2009 Apr 15.

3.

Are mixed explicit/implicit solvation models reliable for studying phosphate hydrolysis? A comparative study of continuum, explicit and mixed solvation models.

Kamerlin SC, Haranczyk M, Warshel A.

Chemphyschem. 2009 May 11;10(7):1125-34. doi: 10.1002/cphc.200800753.

PMID:
19301306
4.

Predictions of hydration free energies from all-atom molecular dynamics simulations.

Mobley DL, Bayly CI, Cooper MD, Dill KA.

J Phys Chem B. 2009 Apr 9;113(14):4533-7. doi: 10.1021/jp806838b.

5.

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.

6.
7.

Accelerating QM/MM free energy calculations: representing the surroundings by an updated mean charge distribution.

Rosta E, Haranczyk M, Chu ZT, Warshel A.

J Phys Chem B. 2008 May 8;112(18):5680-92. doi: 10.1021/jp711496y. Epub 2008 Apr 16.

8.

Predicting small-molecule solvation free energies: an informal blind test for computational chemistry.

Nicholls A, Mobley DL, Guthrie JP, Chodera JD, Bayly CI, Cooper MD, Pande VS.

J Med Chem. 2008 Feb 28;51(4):769-79. doi: 10.1021/jm070549+. Epub 2008 Jan 24.

PMID:
18215013
9.

A synthetic host-guest system achieves avidin-biotin affinity by overcoming enthalpy-entropy compensation.

Rekharsky MV, Mori T, Yang C, Ko YH, Selvapalam N, Kim H, Sobransingh D, Kaifer AE, Liu S, Isaacs L, Chen W, Moghaddam S, Gilson MK, Kim K, Inoue Y.

Proc Natl Acad Sci U S A. 2007 Dec 26;104(52):20737-42. Epub 2007 Dec 19.

10.

Accurate and efficient corrections for missing dispersion interactions in molecular simulations.

Shirts MR, Mobley DL, Chodera JD, Pande VS.

J Phys Chem B. 2007 Nov 15;111(45):13052-63. Epub 2007 Oct 19.

PMID:
17949030
11.

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

Mobley DL, Graves AP, Chodera JD, McReynolds AC, Shoichet BK, Dill KA.

J Mol Biol. 2007 Aug 24;371(4):1118-34. Epub 2007 Jun 8.

12.

Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent.

Mobley DL, Dumont E, Chodera JD, Dill KA.

J Phys Chem B. 2007 Mar 8;111(9):2242-54. Epub 2007 Feb 10. Erratum in: J Phys Chem B. 2011 Feb 10;115(5):1329-32.

PMID:
17291029
14.

Development and validation of a modular, extensible docking program: DOCK 5.

Moustakas DT, Lang PT, Pegg S, Pettersen E, Kuntz ID, Brooijmans N, Rizzo RC.

J Comput Aided Mol Des. 2006 Oct-Nov;20(10-11):601-19. Epub 2006 Dec 6.

PMID:
17149653
15.

FEP-guided selection of bicyclic heterocycles in lead optimization for non-nucleoside inhibitors of HIV-1 reverse transcriptase.

Kim JT, Hamilton AD, Bailey CM, Domaoal RA, Wang L, Anderson KS, Jorgensen WL.

J Am Chem Soc. 2006 Dec 6;128(48):15372-3. Erratum in: J Am Chem Soc. 2007 Mar 14;129(10):3027. Domoal, Robert A [corrected to Domaoal, Robert A].

PMID:
17131993
16.

Modeling electrostatic effects in proteins.

Warshel A, Sharma PK, Kato M, Parson WW.

Biochim Biophys Acta. 2006 Nov;1764(11):1647-76. Epub 2006 Aug 25. Review.

PMID:
17049320
17.
18.

Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics.

Jayachandran G, Shirts MR, Park S, Pande VS.

J Chem Phys. 2006 Aug 28;125(8):084901.

PMID:
16965051
19.

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.

20.

Automatic atom type and bond type perception in molecular mechanical calculations.

Wang J, Wang W, Kollman PA, Case DA.

J Mol Graph Model. 2006 Oct;25(2):247-60. Epub 2006 Feb 3.

PMID:
16458552

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