Michael F Feig (Michael Feig)

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 63

Top Topics

Machine Learning

Single Molecule

Molecular Dynamics

Top Venues

PLoS computational biology

bioRxiv : the preprint server for biology

The journal of physical chemistry. B

This page only lists publications with an associated author ORCID identifier.

Publications

Giacomo Janson, Michael F Feig
Transferable deep generative modeling of intrinsically disordered protein conformations. bioRxiv : the preprint server for biology (2024)
Guowu Lin, Christopher O Barnes, Simon Weiss, Bercem Dutagaci, Chenxi Qiu, Michael F Feig, Jihnu Song, Artem Lyubimov, Aina E Cohen, Craig D Kaplan, Guillermo Calero
Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser. Proceedings of the National Academy of Sciences of the United States of America 121 (36) (2024)
Guangkuan Zhao, Alexis D Richaud, Robert Thomas Williamson, Michael F Feig, Stéphane P Roche
De Novo Synthesis and Structural Elucidation of CDR-H3 Loop Mimics. ACS chemical biology 19 (7) (2024)
Giacomo Janson, Michael F Feig
Transferable deep generative modeling of intrinsically disordered protein conformations. PLoS computational biology 20 (5) (2024)
Luis E Coronas, Thong Van, Antonio Iorio, Lisa J Lapidus, Michael F Feig, Fabio Sterpone
Stability and deformation of biomolecular condensates under the action of shear flow. The Journal of chemical physics 160 (21) (2024)
Giacomo Janson, Michael F Feig
Transferable deep generative modeling of intrinsically disordered protein conformations. PLoS computational biology 20 (5) (2024)
Guowu Lin, Christopher O Barnes, Simon Weiss, Bercem Dutagaci, Chenxi Qiu, Michael F Feig, Jihnu Song, Artem Lyubimov, Aina E Cohen, Craig D Kaplan, Guillermo Calero
Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser. Proceedings of the National Academy of Sciences of the United States of America 121 (36) (2024)
Guangkuan Zhao, Alexis D Richaud, Robert Thomas Williamson, Michael F Feig, Stéphane P Roche
De Novo Synthesis and Structural Elucidation of CDR-H3 Loop Mimics. ACS chemical biology 19 (7) (2024)
Guangkuan Zhao, Alexis D Richaud, Robert Thomas Williamson, Michael F Feig, Stéphane P Roche
De Novo Synthesis and Structural Elucidation of CDR-H3 Loop Mimics. ACS chemical biology (2024)
Giacomo Janson, Michael F Feig
Transferable deep generative modeling of intrinsically disordered protein conformations. bioRxiv : the preprint server for biology (2024)
Giacomo Janson, Michael F Feig
Transferable deep generative modeling of intrinsically disordered protein conformations. bioRxiv : the preprint server for biology (2024)
Giacomo Janson, Michael F Feig
Transferable deep generative modeling of intrinsically disordered protein conformations. PLoS computational biology 20 (5) (2024)
Giacomo Janson, Michael F Feig
Transferable deep generative modeling of intrinsically disordered protein conformations. PLoS computational biology 20 (5) (2024)
Giacomo Janson, Michael F Feig
Transferable deep generative modeling of intrinsically disordered protein conformations. bioRxiv : the preprint server for biology (2024)
Giacomo Janson, Michael F Feig
Transferable deep generative modeling of intrinsically disordered protein conformations. PLoS computational biology 20 (5) (2024)
Guowu Lin, Christopher O Barnes, Simon Weiss, Bercem Dutagaci, Chenxi Qiu, Michael F Feig, Jihnu Song, Artem Lyubimov, Aina E Cohen, Craig D Kaplan, Guillermo Calero
Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser. Proceedings of the National Academy of Sciences of the United States of America 121 (36) (2024)
Guangkuan Zhao, Alexis D Richaud, Robert Thomas Williamson, Michael F Feig, Stéphane P Roche
De Novo Synthesis and Structural Elucidation of CDR-H3 Loop Mimics. ACS chemical biology 19 (7) (2024)
Giacomo Janson, Michael F Feig
Transferable deep generative modeling of intrinsically disordered protein conformations. bioRxiv : the preprint server for biology (2024)
Samuel N Snyder, Alexander Jussupow, Michael F Feig, Andrea M Potocny, Markus Sutter, Cheryl A Kerfeld, Karen L Mulfort, Lisa M Utschig
In Vitro Encapsulation of Functionally Active Abiotic Photosensitizers Inside a Bacterial Microcompartment Shell. The journal of physical chemistry letters 15 (31) (2024)
Giacomo Janson, Michael F Feig
Transferable deep generative modeling of intrinsically disordered protein conformations. PLoS computational biology 20 (5) (2024)
Wonmuk Hwang, Steven L Austin, Arnaud Blondel, Eric D Boittier, Stefan Boresch, Matthias Buck, Joshua Buckner, Amedeo Caflisch, Hao-Ting Chang, Xi Cheng, Yeol Kyo Choi, Jhih-Wei Chu, Michael F Crowley, Qiang Cui, Ana Damjanovic, Yuqing Deng, Michael Devereux, Xinqiang Ding, Michael F Feig, Jiali Gao, David R Glowacki, James E Gonzales, Mehdi Bagerhi Hamaneh, Edward D Harder, Ryan L Hayes, Jing Huang, Yandong Huang, Phillip S Hudson, Wonpil Im, Shahidul M Islam, Wei Jiang, Michael R Jones, Silvan Käser, Fiona L Kearns, Nathan R Kern, Jeffery B Klauda, Themis Lazaridis, Jinhyuk Lee, Justin A Lemkul, Xiaorong Liu, Yun Lyna Luo, Alexander D MacKerell, Dan Thomas Major, Markus Meuwly, Kwangho Nam, Lennart Nilsson, Victor Ovchinnikov, Emanuele Paci, Soohyung Park, Richard W Pastor, Amanda R Pittman, Carol Beth Post, Samarjeet Prasad, Jingzhi Pu, John Z H Zhang, Thenmalarchelvi Rathinavelan, Daniel R Roe, Benoı T Roux, Christopher N Rowley, Jana Shen, Andrew C Simmonett, Alexander J Sodt, Kai Töpfer, Meenu Upadhyay, Arjan van der Vaart, Luis Itza Vazquez-Salazar, Richard M Venable, Luke C Warrensford, H Lee Woodcock, Yujin Wu, Charles L Brooks Iii, Bernard R Brooks, Martin Karplus
CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed. The journal of physical chemistry. B (2024)
Samuel N Snyder, Alexander Jussupow, Michael F Feig, Andrea M Potocny, Markus Sutter, Cheryl A Kerfeld, Karen L Mulfort, Lisa M Utschig
In Vitro Encapsulation of Functionally Active Abiotic Photosensitizers Inside a Bacterial Microcompartment Shell. The journal of physical chemistry letters (2024)
Guangkuan Zhao, Alexis D Richaud, Robert Thomas Williamson, Michael F Feig, Stéphane P Roche
De Novo Synthesis and Structural Elucidation of CDR-H3 Loop Mimics. ACS chemical biology 19 (7) (2024)
Giacomo Janson, Michael F Feig
Transferable deep generative modeling of intrinsically disordered protein conformations. bioRxiv : the preprint server for biology (2024)
Giacomo Janson, Michael F Feig
Transferable deep generative modeling of intrinsically disordered protein conformations. bioRxiv : the preprint server for biology (2024)
Giacomo Janson, Gilberto Valdés-García, Lim Heo, Michael F Feig
Direct generation of protein conformational ensembles via machine learning. Nature communications 14 (1) (2023)
Natalia Ostrowska, Michael F Feig, Joanna Trylska
Varying molecular interactions explain aspects of crowder-dependent enzyme function of a viral protease. PLoS computational biology 19 (4) (2023)
Giacomo Janson, Gilberto Valdés-García, Lim Heo, Michael F Feig
Direct generation of protein conformational ensembles via machine learning. Nature communications 14 (1) (2023)
Natalia Ostrowska, Michael F Feig, Joanna Trylska
Varying molecular interactions explain aspects of crowder-dependent enzyme function of a viral protease. PLoS computational biology 19 (4) (2023)
Giacomo Janson, Gilberto Valdés-García, Lim Heo, Michael F Feig
Direct generation of protein conformational ensembles via machine learning. Nature communications 14 (1) (2023)
Natalia Ostrowska, Michael F Feig, Joanna Trylska
Varying molecular interactions explain aspects of crowder-dependent enzyme function of a viral protease. PLoS computational biology 19 (4) (2023)
Giacomo Janson, Gilberto Valdés-García, Lim Heo, Michael F Feig
Direct generation of protein conformational ensembles via machine learning. Nature communications 14 (1) (2023)
Natalia Ostrowska, Michael F Feig, Joanna Trylska
Varying molecular interactions explain aspects of crowder-dependent enzyme function of a viral protease. PLoS computational biology 19 (4) (2023)
Gilberto Valdes-Garcia, Lim Heo, Lisa J Lapidus, Michael F Feig
Modeling Concentration-dependent Phase Separation Processes Involving Peptides and RNA via Residue-Based Coarse-Graining. Journal of chemical theory and computation (2023)
Natalia Ostrowska, Michael F Feig, Joanna Trylska
Varying molecular interactions explain aspects of crowder-dependent enzyme function of a viral protease. PLoS computational biology 19 (4) (2023)
Bercem Dutagaci, Bingbing Duan, Chenxi Qiu, Craig D Kaplan, Michael F Feig
Characterization of RNA polymerase II trigger loop mutations using molecular dynamics simulations and machine learning. PLoS computational biology 19 (3) (2023)
Lim Heo, Kasun Gamage, Gilberto Valdes-Garcia, Lisa J Lapidus, Michael F Feig
Characterizing Transient Protein-Protein Interactions by Trp-Cys Quenching and Computer Simulations. The journal of physical chemistry letters 13 (43) (2022)
Peter K Walhout, Zhe He, Bercem Dutagaci, Grzegorz Nawrocki, Michael F Feig
Molecular Dynamics Simulations of Rhodamine B Zwitterion Diffusion in Polyelectrolyte Solutions. The journal of physical chemistry. B 126 (48) (2022)
Lim Heo, Michael F Feig
Multi-state modeling of G-protein coupled receptors at experimental accuracy. Proteins 90 (11) (2022)
Lim Heo, Collin F Arbour, Giacomo Janson, Michael F Feig
Improved Sampling Strategies for Protein Model Refinement Based on Molecular Dynamics Simulation. Journal of chemical theory and computation 17 (3) (2021)
Kento Kasahara, Suyong Re, Grzegorz Nawrocki, Hiraku Oshima, Chiemi Mishima-Tsumagari, Yukako Miyata-Yabuki, Mutsuko Kukimoto-Niino, Isseki Yu, Mikako Shirouzu, Michael F Feig, Yuji Sugita
Reduced efficacy of a Src kinase inhibitor in crowded protein solution. Nature communications 12 (1) (2021)
Elise D Rivett, Lim Heo, Michael F Feig, Eric L Hegg
Biosynthesis and trafficking of heme o and heme a: new structural insights and their implications for reaction mechanisms and prenylated heme transfer. Critical reviews in biochemistry and molecular biology 56 (6) (2021)
Michael F Feig
Virtual Issue on Protein Crowding and Stability. The journal of physical chemistry. B 125 (38) (2021)
Lim Heo, Giacomo Janson, Michael F Feig
Physics-based protein structure refinement in the era of artificial intelligence. Proteins 89 (12) (2021)
Bercem Dutagaci, Grzegorz Nawrocki, Joyce Goodluck, Ali Akbar Ashkarran, Charles G Hoogstraten, Lisa J Lapidus, Michael F Feig
Charge-driven condensation of RNA and proteins suggests broad role of phase separation in cytoplasmic environments. eLife 10 (2021)
Maciej Jasiński, Joanna Miszkiewicz, Michael F Feig, Joanna Trylska
Thermal Stability of Peptide Nucleic Acid Complexes. The journal of physical chemistry. B 123 (39) (2019)
Lim Heo, Collin F Arbour, Michael F Feig
Driven to near-experimental accuracy by refinement via molecular dynamics simulations. Proteins 87 (12) (2019)
Lim Heo, Michael F Feig
High-accuracy protein structures by combining machine-learning with physics-based refinement. Proteins 88 (5) (2019)
Grzegorz Nawrocki, Wonpil Im, Yuji Sugita, Michael F Feig
Clustering and dynamics of crowded proteins near membranes and their influence on membrane bending. Proceedings of the National Academy of Sciences of the United States of America 116 (49) (2019)
Rebecca L Newcomer, Jason R Schrad, Eddie B Gilcrease, Sherwood R Casjens, Michael F Feig, Carolyn M Teschke, Andrei T Alexandrescu, Kristin N Parent
The phage L capsid decoration protein has a novel OB-fold and an unusual capsid binding strategy. eLife 8 (2019)
Lim Heo, Michael F Feig
Experimental accuracy in protein structure refinement via molecular dynamics simulations. Proceedings of the National Academy of Sciences of the United States of America 115 (52) (2018)
Maciej Jasiński, Michael F Feig, Joanna Trylska
Improved Force Fields for Peptide Nucleic Acids with Optimized Backbone Torsion Parameters. Journal of chemical theory and computation 14 (7) (2018)
Asli Yildirim, Nathalie Brenner, Robert Sutherland, Michael F Feig
Role of protein interactions in stabilizing canonical DNA features in simulations of DNA in crowded environments. BMC biophysics 11 (2018)
Bercem Dutagaci, Lim Heo, Michael F Feig
Structure refinement of membrane proteins via molecular dynamics simulations. Proteins 86 (7) (2018)
Stephanie A Brocke, Alexandra Degen, Alexander D MacKerell, Bercem Dutagaci, Michael F Feig
Prediction of Membrane Permeation of Drug Molecules by Combining an Implicit Membrane Model with Machine Learning. Journal of chemical information and modeling 59 (3) (2018)
Parimal Kar, Michael F Feig
Hybrid All-Atom/Coarse-Grained Simulations of Proteins by Direct Coupling of CHARMM and PRIMO Force Fields. Journal of chemical theory and computation 13 (11) (2017)
Bercem Dutagaci, Michael F Feig
Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane Model. Journal of chemical information and modeling 57 (12) (2017)
Bercem Dutagaci, Kitiyaporn Wittayanarakul, Takaharu Mori, Michael F Feig
Discrimination of Native-like States of Membrane Proteins with Implicit Membrane-based Scoring Functions. Journal of chemical theory and computation 13 (6) (2017)
Lim Heo, Michael F Feig
What makes it difficult to refine protein models further via molecular dynamics simulations? Proteins (2017)
Michael F Feig, Isseki Yu, Po-Hung Wang, Grzegorz Nawrocki, Yuji Sugita
Crowding in Cellular Environments at an Atomistic Level from Computer Simulations. The journal of physical chemistry. B 121 (34) (2017)
Grzegorz Nawrocki, Po-Hung Wang, Isseki Yu, Yuji Sugita, Michael F Feig
Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation. The journal of physical chemistry. B 121 (49) (2017)
Isseki Yu, Takaharu Mori, Tadashi Ando, Ryuhei Harada, Jaewoon Jung, Yuji Sugita, Michael F Feig
Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm. eLife 5 (2016)
Jing Huang, Sarah Rauscher, Grzegorz Nawrocki, Ting Ran, Michael F Feig, Bert L de Groot, Helmut Grubmüller, Alexander D MacKerell
CHARMM36m: an improved force field for folded and intrinsically disordered proteins. Nature methods 14 (1) (2016)