Brooks BR - Search Results

1

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

Tao P, Sodt AJ, Shao Y, König G, Brooks BR. Tao P, et al. Among authors: brooks br. J Chem Theory Comput. 2014 Oct 14;10(10):4198-4207. doi: 10.1021/ct500342h. Epub 2014 Aug 15. J Chem Theory Comput. 2014. PMID: 25328492 Free PMC article.

2

Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit.

Woodcock HL, Zheng W, Ghysels A, Shao Y, Kong J, Brooks BR. Woodcock HL, et al. Among authors: brooks br. J Chem Phys. 2008 Dec 7;129(21):214109. doi: 10.1063/1.3013558. J Chem Phys. 2008. PMID: 19063546 Free PMC article.

3

Predicting binding affinities of host-guest systems in the SAMPL3 blind challenge: the performance of relative free energy calculations.

König G, Brooks BR. König G, et al. Among authors: brooks br. J Comput Aided Mol Des. 2012 May;26(5):543-50. doi: 10.1007/s10822-011-9525-y. Epub 2011 Dec 24. J Comput Aided Mol Des. 2012. PMID: 22198474 Free PMC article.

4

Maintain rigid structures in Verlet based cartesian molecular dynamics simulations.

Tao P, Wu X, Brooks BR. Tao P, et al. Among authors: brooks br. J Chem Phys. 2012 Oct 7;137(13):134110. doi: 10.1063/1.4756796. J Chem Phys. 2012. PMID: 23039588 Free PMC article.

5

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. Tao P, et al. Among authors: brooks br. J Chem Theory Comput. 2012;8(12):5035-5051. doi: 10.1021/ct3006248. Epub 2012 Sep 27. J Chem Theory Comput. 2012. PMID: 23526888 Free PMC article.

6

Generating reservoir conformations for replica exchange through the use of the conformational space annealing method.

Okur A, Miller BT, Joo K, Lee J, Brooks BR. Okur A, et al. Among authors: brooks br. J Chem Theory Comput. 2013 Feb 1;9(2):1115-1124. doi: 10.1021/ct300996m. J Chem Theory Comput. 2013. PMID: 23585739 Free PMC article.

7

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. König G, et al. Among authors: brooks br. J Comput Aided Mol Des. 2014 Mar;28(3):245-57. doi: 10.1007/s10822-014-9708-4. Epub 2014 Feb 7. J Comput Aided Mol Des. 2014. PMID: 24504703 Free PMC article.

8

Constant pH Molecular Dynamics in Explicit Solvent with Enveloping Distribution Sampling and Hamiltonian Exchange.

Lee J, Miller BT, Damjanović A, Brooks BR. Lee J, et al. Among authors: brooks br. J Chem Theory Comput. 2014 Jul 8;10(7):2738-2750. doi: 10.1021/ct500175m. Epub 2014 Jun 3. J Chem Theory Comput. 2014. PMID: 25061443 Free PMC article.

9

Correcting for the free energy costs of bond or angle constraints in molecular dynamics simulations.

König G, Brooks BR. König G, et al. Among authors: brooks br. Biochim Biophys Acta. 2015 May;1850(5):932-943. doi: 10.1016/j.bbagen.2014.09.001. Epub 2014 Sep 16. Biochim Biophys Acta. 2015. PMID: 25218695 Free PMC article.

10

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. Sodt AJ, et al. Among authors: brooks br. J Phys Chem A. 2015 Mar 5;119(9):1511-23. doi: 10.1021/jp5072296. Epub 2014 Oct 30. J Phys Chem A. 2015. PMID: 25321186 Free PMC article.

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