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Glen M Hocky - Publications

Affiliations: 
2018- Chemistry New York University, New York, NY, United States 
Area:
Theoretical and Computational Chemistry, Chemical Physics, Biophysics
Website:
http://hockygroup.hosting.nyu.edu/
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40 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Wellawatte GP, Hocky GM, White AD. Neural potentials of proteins extrapolate beyond training data. The Journal of Chemical Physics. 159. PMID 37642255 DOI: 10.1063/5.0147240  0.578
2023 Singh Y, Hocky GM, Nolen BJ. Molecular dynamics simulations support a multistep pathway for activation of branched actin filament nucleation by Arp2/3 complex. The Journal of Biological Chemistry. 299: 105169. PMID 37595874 DOI: 10.1016/j.jbc.2023.105169  0.395
2023 Sasmal S, McCullagh M, Hocky GM. Reaction Coordinates for Conformational Transitions Using Linear Discriminant Analysis on Positions. Journal of Chemical Theory and Computation. PMID 37130367 DOI: 10.1021/acs.jctc.3c00051  0.668
2023 White AD, Hocky GM, Gandhi HA, Ansari M, Cox S, Wellawatte GP, Sasmal S, Yang Z, Liu K, Singh Y, Peña Ccoa WJ. Assessment of chemistry knowledge in large language models that generate code. Digital Discovery. 2: 368-376. PMID 37065678 DOI: 10.1039/d2dd00087c  0.543
2022 Hocky GM, White AD. Natural language processing models that automate programming will transform chemistry research and teaching. Digital Discovery. 1: 79-83. PMID 35515080 DOI: 10.1039/d1dd00009h  0.531
2022 Klem H, Hocky GM, McCullagh M. Size-and-Shape Space Gaussian Mixture Models for Structural Clustering of Molecular Dynamics Trajectories. Journal of Chemical Theory and Computation. PMID 35483073 DOI: 10.1021/acs.jctc.1c01290  0.677
2021 Bashirzadeh Y, Redford SA, Lorpaiboon C, Groaz A, Moghimianavval H, Litschel T, Schwille P, Hocky GM, Dinner AR, Liu AP. Actin crosslinker competition and sorting drive emergent GUV size-dependent actin network architecture. Communications Biology. 4: 1136. PMID 34584211 DOI: 10.1038/s42003-021-02653-6  0.625
2021 Qiu Y, Nguyen M, Hocky GM, Dinner AR, Vaikuntanathan S. A strong nonequilibrium bound for sorting of cross-linkers on growing biopolymers. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34518221 DOI: 10.1073/pnas.2102881118  0.771
2021 Hocky GM, Sindelar CV, Cao W, Voth GA, De La Cruz EM. Structural basis of fast- and slow-severing actin-cofilactin boundaries. The Journal of Biological Chemistry. 100337. PMID 33508320 DOI: 10.1016/j.jbc.2021.100337  0.736
2020 Calio PB, Hocky GM, Voth GA. A Minimal Experimental Bias on the Hydrogen Bond Greatly Improves Ab Initio Molecular Dynamics Simulations of Water. Journal of Chemical Theory and Computation. PMID 32786913 DOI: 10.1021/Acs.Jctc.0C00558  0.566
2020 Hartmann MJ, Singh Y, Vanden-Eijnden E, Hocky GM. Infinite switch simulated tempering in force (FISST). The Journal of Chemical Physics. 152: 244120. PMID 32610977 DOI: 10.1063/5.0009280  0.336
2020 Hueckel T, Hocky GM, Palacci J, Sacanna S. Ionic solids from common colloids. Nature. 580: 487-490. PMID 32322078 DOI: 10.1038/S41586-020-2205-0  0.626
2020 Lake PT, Davidson RB, Klem H, Hocky GM, McCullagh M. Residue-Level Allostery Propagates Through the Effective Coarse-Grained Hessian. Journal of Chemical Theory and Computation. PMID 32251581 DOI: 10.1021/Acs.Jctc.9B01149  0.704
2019 Schroeder CM, Valenzuela JR, Natividad IM, Hocky GM, Malik HS. A burst of genetic innovation in Drosophila actin-related proteins for testis-specific function. Molecular Biology and Evolution. PMID 31697328 DOI: 10.1093/Molbev/Msz262  0.419
2019 Bonomi M, Bussi G, Camilloni C, Tribello GA, Banáš P, Barducci A, Bernetti M, Bolhuis PG, Bottaro S, Branduardi D, Capelli R, Carloni P, Ceriotti M, Cesari A, Chen H, ... ... Hocky GM, et al. Promoting transparency and reproducibility in enhanced molecular simulations Nature Methods. 16: 670-673. PMID 31363226 DOI: 10.1038/S41592-019-0506-8  0.706
2019 Freedman SL, Suarez C, Winkelman JD, Kovar DR, Voth GA, Dinner AR, Hocky GM. Mechanical and kinetic factors drive sorting of F-actin cross-linkers on bundles. Proceedings of the National Academy of Sciences of the United States of America. PMID 31346091 DOI: 10.1073/Pnas.1820814116  0.78
2019 Schramm AC, Hocky GM, Voth GA, Martiel JL, De La Cruz EM. Plastic Deformation and Fragmentation of Strained Actin Filaments. Biophysical Journal. PMID 31301801 DOI: 10.1016/J.Bpj.2019.06.018  0.763
2018 Katkar HH, Davtyan A, Durumeric AEP, Hocky GM, Schramm AC, De La Cruz EM, Voth GA. Insights into the Cooperative Nature of ATP Hydrolysis in Actin Filaments. Biophysical Journal. PMID 30249402 DOI: 10.1016/J.Bpj.2018.08.034  0.757
2018 Freedman SL, Hocky GM, Banerjee S, Dinner AR. Nonequilibrium phase diagrams for actomyosin networks. Soft Matter. PMID 30204203 DOI: 10.1039/C8Sm00741A  0.764
2017 Zimmermann D, Homa KE, Hocky GM, Pollard LW, De La Cruz EM, Voth GA, Trybus KM, Kovar DR. Mechanoregulated inhibition of formin facilitates contractile actomyosin ring assembly. Nature Communications. 8: 703. PMID 28951543 DOI: 10.1038/S41467-017-00445-3  0.786
2017 Elam WA, Cao W, Kang H, Huehn A, Hocky GM, Prochniewicz E, Schramm AC, Negrón K, Garcia J, Bonello TT, Gunning PW, Thomas DD, Voth GA, Sindelar CV, De La Cruz EM. Phosphomimetic S3D-Cofilin Binds But Only Weakly Severs Actin Filaments. The Journal of Biological Chemistry. PMID 28939776 DOI: 10.1074/Jbc.M117.808378  0.767
2017 Hocky GM, Dannenhoffer-Lafage T, Voth GA. Coarse-grained Directed Simulation. Journal of Chemical Theory and Computation. PMID 28800392 DOI: 10.1021/Acs.Jctc.7B00690  0.617
2017 Freedman SL, Banerjee S, Hocky GM, Dinner AR. A Versatile Framework for Simulating the Dynamic Mechanical Structure of Cytoskeletal Networks. Biophysical Journal. 113: 448-460. PMID 28746855 DOI: 10.1016/J.Bpj.2017.06.003  0.767
2017 Schramm AC, Hocky GM, Voth GA, Blanchoin L, Martiel JL, De La Cruz EM. Actin Filament Strain Promotes Severing and Cofilin Dissociation. Biophysical Journal. 112: 2624-2633. PMID 28636918 DOI: 10.1016/J.Bpj.2017.05.016  0.774
2017 Christensen JR, Hocky GM, Homa KE, Morganthaler AN, Hitchcock-DeGregori SE, Voth GA, Kovar DR. Competition between Tropomyosin, Fimbrin, and ADF/Cofilin drives their sorting to distinct actin filament networks. Elife. 6. PMID 28282023 DOI: 10.7554/Elife.23152  0.751
2017 White AD, Knight C, Hocky GM, Voth GA. Communication: Improved ab initio molecular dynamics by minimally biasing with experimental data. The Journal of Chemical Physics. 146: 041102. PMID 28147531 DOI: 10.1063/1.4974837  0.704
2017 Christensen JR, Hocky GM, Homa KE, Morganthaler AN, Hitchcock-DeGregori SE, Voth GA, Kovar DR. Author response: Competition between Tropomyosin, Fimbrin, and ADF/Cofilin drives their sorting to distinct actin filament networks Elife. DOI: 10.7554/Elife.23152.024  0.729
2017 Hocky GM, Christensen JR, Kovar DR, Voth GA. Modeling the Cooperativity of Tropomyosin Binding to Actin Filaments Biophysical Journal. 112: 431a. DOI: 10.1016/J.Bpj.2016.11.2301  0.767
2016 Winkelman JD, Suarez C, Hocky GM, Harker AJ, Morganthaler AN, Christensen JR, Voth GA, Bartles JR, Kovar DR. Fascin- and α-Actinin-Bundled Networks Contain Intrinsic Structural Features that Drive Protein Sorting. Current Biology : Cb. PMID 27666967 DOI: 10.1016/J.Cub.2016.07.080  0.761
2016 Hocky GM, Baker JL, Bradley MJ, Sinitskiy AV, De La Cruz EM, Voth GA. Cations Stiffen Actin Filaments by Adhering a Key Structural Element to Adjacent Subunits. The Journal of Physical Chemistry. B. PMID 27146246 DOI: 10.1021/Acs.Jpcb.6B02741  0.79
2016 Li Y, Christensen JR, Homa KE, Hocky GM, Fok A, Sees JA, Voth GA, Kovar DR. The F-actin bundler α-actinin Ain1 is tailored for ring assembly and constriction during cytokinesis in fission yeast. Molecular Biology of the Cell. PMID 27075176 DOI: 10.1091/Mbc.E16-01-0010  0.764
2016 Hocky GM, Baker JL, Bradley MJ, Sinitskiy AV, De La Cruz EM, Voth GA. Specific Cation Binding Stiffens Actin Filaments by Adhering D-Loops to Adjacent Monomers Biophysical Journal. 110: 125a. DOI: 10.1016/J.Bpj.2015.11.721  0.809
2015 Dama JF, Hocky GM, Sun R, Voth GA. Exploring Valleys without Climbing Every Peak: More Efficient and Forgiving Metabasin Metadynamics via Robust On-the-Fly Bias Domain Restriction. Journal of Chemical Theory and Computation. PMID 26587809 DOI: 10.1021/Acs.Jctc.5B00907  0.617
2014 Hocky GM, Berthier L, Reichman DR. Equilibrium ultrastable glasses produced by random pinning. The Journal of Chemical Physics. 141: 224503. PMID 25494756 DOI: 10.1063/1.4903200  0.661
2014 Hocky GM, Coslovich D, Ikeda A, Reichman DR. Correlation of local order with particle mobility in supercooled liquids is highly system dependent. Physical Review Letters. 113: 157801. PMID 25375744 DOI: 10.1103/Physrevlett.113.157801  0.663
2014 Hocky GM, Berthier L, Kob W, Reichman DR. Crossovers in the dynamics of supercooled liquids probed by an amorphous wall. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 89: 052311. PMID 25353804 DOI: 10.1103/Physreve.89.052311  0.646
2013 Hocky GM, Reichman DR. A small subset of normal modes mimics the properties of dynamical heterogeneity in a model supercooled liquid. The Journal of Chemical Physics. 138: 12A537. PMID 23556788 DOI: 10.1063/1.4790799  0.654
2012 Hocky GM, Markland TE, Reichman DR. Growing point-to-set length scale correlates with growing relaxation times in model supercooled liquids. Physical Review Letters. 108: 225506. PMID 23003622 DOI: 10.1103/Physrevlett.108.225506  0.746
2010 DeBartolo J, Hocky G, Wilde M, Xu J, Freed KF, Sosnick TR. Protein structure prediction enhanced with evolutionary diversity: SPEED. Protein Science : a Publication of the Protein Society. 19: 520-34. PMID 20066664 DOI: 10.1002/Pro.330  0.635
2008 Gong H, Hocky G, Freed KF. Influence of nonlinear electrostatics on transfer energies between liquid phases: Charge burial is far less expensive than Born model Proceedings of the National Academy of Sciences of the United States of America. 105: 11146-11151. PMID 18678891 DOI: 10.1073/Pnas.0804506105  0.466
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