Brooks BR - Search Results

1

Multi-phase Boltzmann weighting: accounting for local inhomogeneity in molecular simulations of water-octanol partition coefficients in the SAMPL6 challenge.

Krämer A, Hudson PS, Jones MR, Brooks BR. Krämer A, et al. Among authors: brooks br. J Comput Aided Mol Des. 2020 May;34(5):471-483. doi: 10.1007/s10822-020-00285-2. Epub 2020 Feb 14. J Comput Aided Mol Des. 2020. PMID: 32060677 Free PMC article.

2

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

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

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

Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challenge.

König G, Pickard FC 4th, Huang J, Simmonett AC, Tofoleanu F, Lee J, Dral PO, Prasad S, Jones M, Shao Y, Thiel W, Brooks BR. König G, et al. Among authors: brooks br. J Comput Aided Mol Des. 2016 Nov;30(11):989-1006. doi: 10.1007/s10822-016-9936-x. Epub 2016 Aug 30. J Comput Aided Mol Des. 2016. PMID: 27577746

6

Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pK _a corrections.

Pickard FC 4th, König G, Tofoleanu F, Lee J, Simmonett AC, Shao Y, Ponder JW, Brooks BR. Pickard FC 4th, et al. Among authors: brooks br. J Comput Aided Mol Des. 2016 Nov;30(11):1087-1100. doi: 10.1007/s10822-016-9955-7. Epub 2016 Sep 19. J Comput Aided Mol Des. 2016. PMID: 27646286

7

Partition coefficients for the SAMPL5 challenge using transfer free energies.

Jones MR, Brooks BR, Wilson AK. Jones MR, et al. Among authors: brooks br. J Comput Aided Mol Des. 2016 Nov;30(11):1129-1138. doi: 10.1007/s10822-016-9964-6. Epub 2016 Sep 19. J Comput Aided Mol Des. 2016. PMID: 27646287 Free PMC article.

8

An efficient protocol for obtaining accurate hydration free energies using quantum chemistry and reweighting from molecular dynamics simulations.

Pickard FC 4th, König G, Simmonett AC, Shao Y, Brooks BR. Pickard FC 4th, et al. Among authors: brooks br. Bioorg Med Chem. 2016 Oct 15;24(20):4988-4997. doi: 10.1016/j.bmc.2016.08.031. Epub 2016 Aug 22. Bioorg Med Chem. 2016. PMID: 27667551 Free PMC article.

9

Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge.

Lee J, Tofoleanu F, Pickard FC 4th, König G, Huang J, Damjanović A, Baek M, Seok C, Brooks BR. Lee J, et al. Among authors: brooks br. J Comput Aided Mol Des. 2017 Jan;31(1):71-85. doi: 10.1007/s10822-016-9968-2. Epub 2016 Sep 27. J Comput Aided Mol Des. 2017. PMID: 27677749 Free PMC article.

10

Absolute binding free energies for octa-acids and guests in SAMPL5 : Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge.

Tofoleanu F, Lee J, Pickard Iv FC, König G, Huang J, Baek M, Seok C, Brooks BR. Tofoleanu F, et al. Among authors: brooks br. J Comput Aided Mol Des. 2017 Jan;31(1):107-118. doi: 10.1007/s10822-016-9965-5. Epub 2016 Sep 30. J Comput Aided Mol Des. 2017. PMID: 27696242 Free PMC article.

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