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Cited In for PubMed (Select 17334987)


Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics.

Tao P, Sodt AJ, Shao Y, König G, Brooks BR.

J Chem Theory Comput. 2014 Oct 14;10(10):4198-4207. Epub 2014 Aug 15.


Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies.

Sodt AJ, Mei Y, König G, Tao P, Steele RP, Brooks BR, Shao Y.

J Phys Chem A. 2015 Mar 5;119(9):1511-23. doi: 10.1021/jp5072296. Epub 2014 Oct 30.


Computational study of Gleevec and G6G reveals molecular determinants of kinase inhibitor selectivity.

Lin YL, Meng Y, Huang L, Roux B.

J Am Chem Soc. 2014 Oct 22;136(42):14753-62. doi: 10.1021/ja504146x. Epub 2014 Oct 7.


Perturbation of long-range water dynamics as the mechanism for the antifreeze activity of antifreeze glycoprotein.

Mallajosyula SS, Vanommeslaeghe K, MacKerell AD Jr.

J Phys Chem B. 2014 Oct 9;118(40):11696-706. doi: 10.1021/jp508128d. Epub 2014 Aug 26.


Web-based computational chemistry education with CHARMMing I: Lessons and tutorial.

Miller BT, Singh RP, Schalk V, Pevzner Y, Sun J, Miller CS, Boresch S, Ichiye T, Brooks BR, Woodcock HL 3rd.

PLoS Comput Biol. 2014 Jul 24;10(7):e1003719. doi: 10.1371/journal.pcbi.1003719. eCollection 2014 Jul.


Theory of Adaptive Optimization for Umbrella Sampling.

Park S, Im W.

J Chem Theory Comput. 2014 Jul 8;10(7):2719-2728. Epub 2014 Jun 12.


Identification and Characterization of Noncovalent Interactions That Drive Binding and Specificity in DD-Peptidases and β-Lactamases.

Hargis JC, Vankayala SL, White JK, Woodcock HL.

J Chem Theory Comput. 2014 Feb 11;10(2):855-864. Epub 2014 Jan 10.


Electrostatics, hydration, and proton transfer dynamics in the membrane domain of respiratory complex I.

Kaila VR, Wikström M, Hummer G.

Proc Natl Acad Sci U S A. 2014 May 13;111(19):6988-93. doi: 10.1073/pnas.1319156111. Epub 2014 Apr 28.


Can molecular dynamics and QM/MM solve the penicillin binding protein protonation puzzle?

Hargis JC, White JK, Chen Y, Woodcock HL.

J Chem Inf Model. 2014 May 27;54(5):1412-24. doi: 10.1021/ci5000517. Epub 2014 May 9.


Contradictions in X-ray structures of intermediates in the photocycle of photoactive yellow protein.

Kaila VR, Schotte F, Cho HS, Hummer G, Anfinrud PA.

Nat Chem. 2014 Apr;6(4):258-9. doi: 10.1038/nchem.1898. No abstract available.


Conformational properties of α- or β-(1→6)-linked oligosaccharides: Hamiltonian replica exchange MD simulations and NMR experiments.

Patel DS, Pendrill R, Mallajosyula SS, Widmalm G, MacKerell AD Jr.

J Phys Chem B. 2014 Mar 20;118(11):2851-71. doi: 10.1021/jp412051v. Epub 2014 Mar 5.


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.


Calcium inhibition of ribonuclease H1 two-metal ion catalysis.

Rosta E, Yang W, Hummer G.

J Am Chem Soc. 2014 Feb 26;136(8):3137-44. doi: 10.1021/ja411408x. Epub 2014 Feb 18.


An extensible interface for QM/MM molecular dynamics simulations with AMBER.

Götz AW, Clark MA, Walker RC.

J Comput Chem. 2014 Jan 15;35(2):95-108. doi: 10.1002/jcc.23444. Epub 2013 Oct 9.


How does catalase release nitric oxide? A computational structure-activity relationship study.

Vankayala SL, Hargis JC, Woodcock HL.

J Chem Inf Model. 2013 Nov 25;53(11):2951-61. doi: 10.1021/ci400395c. Epub 2013 Oct 28.


Computational analysis of the binding specificity of Gleevec to Abl, c-Kit, Lck, and c-Src tyrosine kinases.

Lin YL, Roux B.

J Am Chem Soc. 2013 Oct 2;135(39):14741-53. doi: 10.1021/ja405939x. Epub 2013 Sep 20.


Catalytic mechanism of α-phosphate attack in dUTPase is revealed by X-ray crystallographic snapshots of distinct intermediates, 31P-NMR spectroscopy and reaction path modelling.

Barabás O, Németh V, Bodor A, Perczel A, Rosta E, Kele Z, Zagyva I, Szabadka Z, Grolmusz VI, Wilmanns M, Vértessy BG.

Nucleic Acids Res. 2013 Dec;41(22):10542-55. doi: 10.1093/nar/gkt756. Epub 2013 Aug 27.


Conformational determinants of the activity of antiproliferative factor glycopeptide.

Mallajosyula SS, Adams KM, Barchi JJ, MacKerell AD.

J Chem Inf Model. 2013 May 24;53(5):1127-37. doi: 10.1021/ci400147s. Epub 2013 May 15.


Comparison of Three Chain-of-States Methods: Nudged Elastic Band and Replica Path with Restraints or Constraints.

Tao P, Hodošček M, Larkin JD, Shao Y, Brooks BR.

J Chem Theory Comput. 2012;8(12):5035-5051. Epub 2012 Sep 27.

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