| Conformational analysis of the DFG-out kinase motif and biochemical profiling of structurally validated type II inhibitors RSK Vijayan, P He, V Modi, KC Duong-Ly, H Ma, JR Peterson, ... Journal of medicinal chemistry 58 (1), 466-479, 2015 | 209 | 2015 |
| A multiscale coarse-grained model of the SARS-CoV-2 virion A Yu, AJ Pak, P He, V Monje-Galvan, L Casalino, Z Gaieb, AC Dommer, ... Biophysical journal 120 (6), 1097-1104, 2021 | 152 | 2021 |
| Large scale affinity calculations of cyclodextrin host–guest complexes: Understanding the role of reorganization in the molecular recognition process L Wickstrom, P He, E Gallicchio, RM Levy Journal of chemical theory and computation 9 (7), 3136-3150, 2013 | 94 | 2013 |
| Distinguishing binders from false positives by free energy calculations: fragment screening against the flap site of HIV protease N Deng, S Forli, P He, A Perryman, L Wickstrom, RSK Vijayan, ... The Journal of Physical Chemistry B 119 (3), 976-988, 2015 | 66 | 2015 |
| Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge E Gallicchio, N Deng, P He, L Wickstrom, AL Perryman, DN Santiago, ... Journal of computer-aided molecular design 28, 475-490, 2014 | 66 | 2014 |
| Structural propensities of kinase family proteins from a Potts model of residue co‐variation A Haldane, WF Flynn, P He, RSK Vijayan, RM Levy Protein Science 25 (8), 1378-1384, 2016 | 59 | 2016 |
| Simulating replica exchange: Markov state models, proposal schemes, and the infinite swapping limit BW Zhang, W Dai, E Gallicchio, P He, J Xia, Z Tan, RM Levy The Journal of Physical Chemistry B 120 (33), 8289-8301, 2016 | 50 | 2016 |
| The transition between active and inactive conformations of Abl kinase studied by rock climbing and Milestoning B Narayan, A Fathizadeh, C Templeton, P He, S Arasteh, R Elber, ... Biochimica et Biophysica Acta (BBA)-General Subjects 1864 (4), 129508, 2020 | 29 | 2020 |
| Parameterization of an effective potential for protein–ligand binding from host–guest affinity data L Wickstrom, N Deng, P He, A Mentes, C Nguyen, MK Gilson, T Kurtzman, ... Journal of Molecular Recognition 29 (1), 10-21, 2016 | 28 | 2016 |
| Large‐scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis J Xia, WF Flynn, E Gallicchio, BW Zhang, P He, Z Tan, RM Levy Journal of computational chemistry 36 (23), 1772-1785, 2015 | 26 | 2015 |
| BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge E Gallicchio, H Chen, H Chen, M Fitzgerald, Y Gao, P He, M Kalyanikar, ... Journal of computer-aided molecular design 29, 315-325, 2015 | 24 | 2015 |
| Coevolutionary landscape of kinase family proteins: sequence probabilities and functional motifs A Haldane, WF Flynn, P He, RM Levy Biophysical journal 114 (1), 21-31, 2018 | 20 | 2018 |
| Large scale free energy calculations for blind predictions of protein–ligand binding: the D3R Grand Challenge 2015 N Deng, WF Flynn, J Xia, RSK Vijayan, B Zhang, P He, A Mentes, ... Journal of computer-aided molecular design 30, 743-751, 2016 | 20 | 2016 |
| Conformational free energy changes via an alchemical path without reaction coordinates P He, BW Zhang, S Arasteh, L Wang, R Abel, RM Levy The journal of physical chemistry letters 9 (15), 4428-4435, 2018 | 13 | 2018 |
| Ligand selectivity in the recognition of protoberberine alkaloids by hybrid-2 human telomeric G-quadruplex: binding free energy calculation, fluorescence binding, and NMR … N Deng, J Xia, L Wickstrom, C Lin, K Wang, P He, Y Yin, D Yang Molecules 24 (8), 1574, 2019 | 12 | 2019 |
| A framework for flexible and scalable replica-exchange on production distributed CI BK Radak, M Romanus, E Gallicchio, TS Lee, O Weidner, NJ Deng, P He, ... Proceedings of the Conference on Extreme Science and Engineering Discovery …, 2013 | 9 | 2013 |
| Role of displacing confined solvent in the conformational equilibrium of β-cyclodextrin P He, S Sarkar, E Gallicchio, T Kurtzman, L Wickstrom The Journal of Physical Chemistry B 123 (40), 8378-8386, 2019 | 8 | 2019 |
| Synthesis, characterization, and simulation of four-armed megamolecules S Zhou, P He, S Dhindwal, VL Grum-Tokars, Y Li, K Parker, JA Modica, ... Biomacromolecules 22 (6), 2363-2372, 2021 | 6 | 2021 |
| A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion (preprint) A Yu, AJ Pak, P He, V Monje-Galvan, L Casalino, Z Gaieb, AC Dommer, ... | 3 | 2020 |
| Modeling Synthesized Protein Megamolecules: Structure, Dynamics, and Functions P He, J Zuchniarz, S Zhou, J Modica, S Dhindwal, Y Li, GA Voth, ... Biophysical Journal 118 (3), 517a, 2020 | | 2020 |
Emilio GallicchioCUNY Brooklyn CollegeVerified email at brooklyn.cuny.edu
