Brooks BR - Search Results

1

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.

2

Probing the "annealing" mechanism of GroEL minichaperone using molecular dynamics simulations.

Stan G, Brooks BR, Thirumalai D. Stan G, et al. Among authors: brooks br. J Mol Biol. 2005 Jul 22;350(4):817-29. doi: 10.1016/j.jmb.2005.05.012. J Mol Biol. 2005. PMID: 15967467

3

Development of small molecules designed to modulate protein-protein interactions.

Che Y, Brooks BR, Marshall GR. Che Y, et al. Among authors: brooks br. J Comput Aided Mol Des. 2006 Feb;20(2):109-30. doi: 10.1007/s10822-006-9040-8. Epub 2006 Apr 19. J Comput Aided Mol Des. 2006. PMID: 16622794

4

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.

5

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.

6

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.

7

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.

8

Computational scheme for pH-dependent binding free energy calculation with explicit solvent.

Lee J, Miller BT, Brooks BR. Lee J, et al. Among authors: brooks br. Protein Sci. 2016 Jan;25(1):231-43. doi: 10.1002/pro.2755. Epub 2015 Aug 20. Protein Sci. 2016. PMID: 26189656 Free PMC article.

9

Enhanced Sampling in Free Energy Calculations: Combining SGLD with the Bennett's Acceptance Ratio and Enveloping Distribution Sampling Methods.

König G, Miller BT, Boresch S, Wu X, Brooks BR. König G, et al. Among authors: brooks br. J Chem Theory Comput. 2012 Oct 9;8(10):3650-62. doi: 10.1021/ct300116r. Epub 2012 Jul 3. J Chem Theory Comput. 2012. PMID: 26593010 Free PMC article.

10

Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical Method.

König G, Mei Y, Pickard FC 4th, Simmonett AC, Miller BT, Herbert JM, Woodcock HL, Brooks BR, Shao Y. König G, et al. Among authors: brooks br. J Chem Theory Comput. 2016 Jan 12;12(1):332-44. doi: 10.1021/acs.jctc.5b00874. Epub 2015 Dec 11. J Chem Theory Comput. 2016. PMID: 26613419 Free PMC article.

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