He P - Search Results

1

Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis.

Xia J, Flynn WF, Gallicchio E, Zhang BW, He P, Tan Z, Levy RM. Xia J, et al. Among authors: he p. J Comput Chem. 2015 Sep 5;36(23):1772-85. doi: 10.1002/jcc.23996. Epub 2015 Jul 7. J Comput Chem. 2015. PMID: 26149645 Free PMC article.

2

Simulating Replica Exchange: Markov State Models, Proposal Schemes, and the Infinite Swapping Limit.

Zhang BW, Dai W, Gallicchio E, He P, Xia J, Tan Z, Levy RM. Zhang BW, et al. Among authors: he p. J Phys Chem B. 2016 Aug 25;120(33):8289-301. doi: 10.1021/acs.jpcb.6b02015. Epub 2016 Apr 29. J Phys Chem B. 2016. PMID: 27079355 Free PMC article.

3

Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge.

Gallicchio E, Deng N, He P, Wickstrom L, Perryman AL, Santiago DN, Forli S, Olson AJ, Levy RM. Gallicchio E, et al. Among authors: he p. J Comput Aided Mol Des. 2014 Apr;28(4):475-90. doi: 10.1007/s10822-014-9711-9. Epub 2014 Feb 7. J Comput Aided Mol Des. 2014. PMID: 24504704 Free PMC article.

4

Large scale affinity calculations of cyclodextrin host-guest complexes: Understanding the role of reorganization in the molecular recognition process.

Wickstrom L, He P, Gallicchio E, Levy RM. Wickstrom L, et al. Among authors: he p. J Chem Theory Comput. 2013 Jul 9;9(7):3136-3150. doi: 10.1021/ct400003r. J Chem Theory Comput. 2013. PMID: 25147485 Free PMC article.

5

Distinguishing binders from false positives by free energy calculations: fragment screening against the flap site of HIV protease.

Deng N, Forli S, He P, Perryman A, Wickstrom L, Vijayan RS, Tiefenbrunn T, Stout D, Gallicchio E, Olson AJ, Levy RM. Deng N, et al. Among authors: he p. J Phys Chem B. 2015 Jan 22;119(3):976-88. doi: 10.1021/jp506376z. Epub 2014 Sep 17. J Phys Chem B. 2015. PMID: 25189630 Free PMC article.

6

Parameterization of an effective potential for protein-ligand binding from host-guest affinity data.

Wickstrom L, Deng N, He P, Mentes A, Nguyen C, Gilson MK, Kurtzman T, Gallicchio E, Levy RM. Wickstrom L, et al. Among authors: he p. J Mol Recognit. 2016 Jan;29(1):10-21. doi: 10.1002/jmr.2489. Epub 2015 Aug 10. J Mol Recognit. 2016. PMID: 26256816 Free PMC article.

7

Structural propensities of kinase family proteins from a Potts model of residue co-variation.

Haldane A, Flynn WF, He P, Vijayan RS, Levy RM. Haldane A, et al. Among authors: he p. Protein Sci. 2016 Aug;25(8):1378-84. doi: 10.1002/pro.2954. Epub 2016 Jun 26. Protein Sci. 2016. PMID: 27241634 Free PMC article.

8

Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015.

Deng N, Flynn WF, Xia J, Vijayan RS, Zhang B, He P, Mentes A, Gallicchio E, Levy RM. Deng N, et al. Among authors: he p. J Comput Aided Mol Des. 2016 Sep;30(9):743-751. doi: 10.1007/s10822-016-9952-x. Epub 2016 Aug 25. J Comput Aided Mol Des. 2016. PMID: 27562018 Free PMC article.

9

Coevolutionary Landscape of Kinase Family Proteins: Sequence Probabilities and Functional Motifs.

Haldane A, Flynn WF, He P, Levy RM. Haldane A, et al. Among authors: he p. Biophys J. 2018 Jan 9;114(1):21-31. doi: 10.1016/j.bpj.2017.10.028. Biophys J. 2018. PMID: 29320688 Free PMC article.

10

Conformational Free Energy Changes via an Alchemical Path without Reaction Coordinates.

He P, Zhang BW, Arasteh S, Wang L, Abel R, Levy RM. He P, et al. J Phys Chem Lett. 2018 Aug 2;9(15):4428-4435. doi: 10.1021/acs.jpclett.8b01851. Epub 2018 Jul 24. J Phys Chem Lett. 2018. PMID: 30024165 Free PMC article.

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