| Year |
Citation |
Score |
| 2025 |
Zang S, Paul S, Leung CW, Chen MS, Hueckel T, Hocky GM, Sacanna S. Direct observation and control of non-classical crystallization pathways in binary colloidal systems. Nature Communications. 16: 3645. PMID 40240410 DOI: 10.1038/s41467-025-58959-0 |
0.593 |
|
| 2025 |
Sasmal S, McCullagh M, Hocky GM. Improved data-driven collective variables for biased sampling through iteration on biased data. Biorxiv : the Preprint Server For Biology. PMID 40196594 DOI: 10.1101/2025.03.25.644418 |
0.666 |
|
| 2025 |
Tribello GA, Bonomi M, Bussi G, Camilloni C, Armstrong BI, Arsiccio A, Aureli S, Ballabio F, Bernetti M, Bonati L, Brookes SGH, Brotzakis ZF, Capelli R, Ceriotti M, Chan KT, ... ... Hocky GM, et al. PLUMED Tutorials: A collaborative, community-driven learning ecosystem. The Journal of Chemical Physics. 162. PMID 40035582 DOI: 10.1063/5.0251501 |
0.751 |
|
| 2025 |
Fitzmaurice DR, Amador A, Starr T, Hocky GM, Rojas ER. β-barrel proteins dictate the effect of core oligosaccharide composition on outer membrane mechanics. Biophysical Journal. PMID 39863924 DOI: 10.1016/j.bpj.2025.01.017 |
0.673 |
|
| 2024 |
Shu T, Mitra G, Alberts J, Viana MP, Levy ED, Hocky GM, Holt LJ. Mesoscale molecular assembly is favored by the active, crowded cytoplasm. Prx Life. 2. PMID 40162127 DOI: 10.1103/prxlife.2.033001 |
0.667 |
|
| 2024 |
Vizcarra CL, Trainor RF, Ringer McDonald A, Richardson CT, Potoyan D, Nash JA, Lundgren B, Luchko T, Hocky GM, Foley JJ, Atherton TJ, Stokes GY. An interdisciplinary effort to integrate coding into science courses. Nature Computational Science. PMID 39438741 DOI: 10.1038/s43588-024-00708-2 |
0.17 |
|
| 2024 |
Ccoa WJP, Mukadum F, Ramon A, Stirnemann G, Hocky GM. A direct computational assessment of vinculin-actin unbinding kinetics reveals catch bonding behavior. Biorxiv : the Preprint Server For Biology. PMID 39415985 DOI: 10.1101/2024.10.10.617580 |
0.681 |
|
| 2024 |
Fitzmaurice D, Amador A, Starr T, Hocky GM, Rojas ER. β-barrel proteins dictate the effect of core oligosaccharide composition on outer membrane mechanics. Biorxiv : the Preprint Server For Biology. PMID 39282359 DOI: 10.1101/2024.09.02.610904 |
0.695 |
|
| 2024 |
Xie Y, Shu T, Liu T, Spindler MC, Mahamid J, Hocky GM, Gresham D, Holt LJ. Polysome collapse and RNA condensation fluidize the cytoplasm. Molecular Cell. 84: 2698-2716.e9. PMID 39059370 DOI: 10.1016/j.molcel.2024.06.024 |
0.717 |
|
| 2024 |
Mazzaferro N, Sasmal S, Cossio P, Hocky GM. Good Rates From Bad Coordinates: The Exponential Average Time-dependent Rate Approach. Journal of Chemical Theory and Computation. PMID 38954555 DOI: 10.1021/acs.jctc.4c00425 |
0.338 |
|
| 2024 |
Zang S, Hauser AW, Paul S, Hocky GM, Sacanna S. Enabling three-dimensional real-space analysis of ionic colloidal crystallization. Nature Materials. PMID 38831129 DOI: 10.1038/s41563-024-01917-w |
0.61 |
|
| 2024 |
Sasmal S, Pal T, Hocky GM, McCullagh M. Quantifying Unbiased Conformational Ensembles from Biased Simulations Using ShapeGMM. Journal of Chemical Theory and Computation. PMID 38662196 DOI: 10.1021/acs.jctc.4c00223 |
0.735 |
|
| 2024 |
Homa KE, Hocky GM, Suarez C, Kovar DR. Arp2/3 complex- and formin-mediated actin cytoskeleton networks facilitate actin binding protein sorting in fission yeast. European Journal of Cell Biology. 103: 151404. PMID 38493594 DOI: 10.1016/j.ejcb.2024.151404 |
0.665 |
|
| 2024 |
Mukadum F, Peña Ccoa WJ, Hocky GM. Molecular simulation approaches to probing the effects of mechanical forces in the actin cytoskeleton. Cytoskeleton (Hoboken, N.J.). PMID 38334204 DOI: 10.1002/cm.21837 |
0.419 |
|
| 2024 |
Liu K, Rotskoff GM, Vanden-Eijnden E, Hocky GM. Computing equilibrium free energies through a nonequilibrium quench. The Journal of Chemical Physics. 160. PMID 38240301 DOI: 10.1063/5.0176700 |
0.777 |
|
| 2024 |
Singh Y, Hocky GM. Improved Prediction of Molecular Response to Pulling by Combining Force Tempering with Replica Exchange Methods. The Journal of Physical Chemistry. B. 128: 706-715. PMID 38230998 DOI: 10.1021/acs.jpcb.3c07081 |
0.732 |
|
| 2023 |
Mukadum F, Ccoa WJP, Hocky GM. Molecular simulation approaches to probing the effects of mechanical forces in the actin cytoskeleton. Arxiv. PMID 38045481 |
0.42 |
|
| 2023 |
Singh Y, Hocky GM. Improved prediction of molecular response to pulling by combining force tempering with replica exchange methods. Arxiv. PMID 37904741 |
0.732 |
|
| 2023 |
Shu T, Mitra G, Alberts J, Viana MP, Levy ED, Hocky GM, Holt LJ. Mesoscale molecular assembly is favored by the active, crowded cytoplasm. Biorxiv : the Preprint Server For Biology. PMID 37781612 DOI: 10.1101/2023.09.19.558334 |
0.788 |
|
| 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 |
0.622 |
|
| 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 |
0.755 |
|
| 2023 |
Mitra G, Chang C, McMullen A, Puchall D, Brujic J, Hocky GM. A coarse-grained simulation model for colloidal self-assembly explicit mobile binders. Soft Matter. 19: 4223-4236. PMID 37255223 DOI: 10.1039/d3sm00196b |
0.777 |
|
| 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 |
0.7 |
|
| 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 |
0.739 |
|
| 2022 |
Cossio P, Hocky GM. Catching actin proteins in action. Nature. 611: 241-243. PMID 36289412 DOI: 10.1038/d41586-022-03343-x |
0.353 |
|
| 2022 |
Ding B, Narvaez-Ortiz HY, Singh Y, Hocky GM, Chowdhury S, Nolen BJ. Structure of Arp2/3 complex at a branched actin filament junction resolved by single-particle cryo-electron microscopy. Proceedings of the National Academy of Sciences of the United States of America. 119: e2202723119. PMID 35622886 DOI: 10.1073/pnas.2202723119 |
0.799 |
|
| 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 |
0.575 |
|
| 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 |
0.709 |
|
| 2022 |
Peña Ccoa WJ, Hocky GM. Assessing models of force-dependent unbinding rates via infrequent metadynamics. The Journal of Chemical Physics. 156: 125102. PMID 35364872 DOI: 10.1063/5.0081078 |
0.356 |
|
| 2021 |
Gomez D, Peña Ccoa WJ, Singh Y, Rojas E, Hocky GM. Molecular Paradigms for Biological Mechanosensing. The Journal of Physical Chemistry. B. PMID 34709040 DOI: 10.1021/acs.jpcb.1c06330 |
0.788 |
|
| 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 |
0.792 |
|
| 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 |
0.782 |
|
| 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 |
0.742 |
|
| 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 |
0.608 |
|
| 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 |
0.79 |
|
| 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 |
0.664 |
|
| 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 |
0.731 |
|
| 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 |
0.475 |
|
| 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 |
0.783 |
|
| 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 |
0.791 |
|
| 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 |
0.766 |
|
| 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 |
0.764 |
|
| 2018 |
Freedman SL, Hocky GM, Banerjee S, Dinner AR. Nonequilibrium phase diagrams for actomyosin networks. Soft Matter. PMID 30204203 DOI: 10.1039/C8Sm00741A |
0.781 |
|
| 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 |
0.799 |
|
| 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 |
0.763 |
|
| 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 |
0.664 |
|
| 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 |
0.777 |
|
| 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 |
0.775 |
|
| 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 |
0.752 |
|
| 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 |
0.73 |
|
| 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 |
0.731 |
|
| 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 |
0.766 |
|
| 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 |
0.801 |
|
| 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 |
0.765 |
|
| 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 |
0.815 |
|
| 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 |
0.658 |
|
| 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 |
0.687 |
|
| 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 |
0.681 |
|
| 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 |
0.669 |
|
| 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 |
0.678 |
|
| 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 |
0.766 |
|
| 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 |
0.734 |
|
| 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 |
0.32 |
|
| 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 |
0.536 |
|
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