Michael Feig

Publication Activity (10 Years)

Years Active: 1999-2023
Publications (10 Years): 10

Top Topics

Machine Learning

Protein Structure

Amino Acid Sequences

Top Venues

J. Comput. Chem.

J. Chem. Inf. Model.

PLoS Comput. Biol.

Publications

Natalia Ostrowska, Michael Feig, Joanna Trylska
Varying molecular interactions explain aspects of crowder-dependent enzyme function of a viral protease. PLoS Comput. Biol. 19 (4) (2023)
Bercem Dutagaci, Bingbing Duan, Chenxi Qiu, Craig D. Kaplan, Michael Feig
Characterization of RNA polymerase II trigger loop mutations using molecular dynamics simulations and machine learning. PLoS Comput. Biol. 19 (3) (2023)
Jaewoon Jung, Chigusa Kobayashi, Kento Kasahara, Cheng Tan, Akiyoshi Kuroda, Kazuo Minami, Shigeru Ishiduki, Tatsuo Nishiki, Hikaru Inoue, Yutaka Ishikawa, Michael Feig, Yuji Sugita
New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems. J. Comput. Chem. 42 (4) (2021)
Xiping Gong, Mara Chiricotto, Xiaorong Liu, Erik Nordquist, Michael Feig, Charles L. Brooks III, Jianhan Chen
Accelerating the Generalized Born with Molecular Volume and Solvent Accessible Surface Area Implicit Solvent Model Using Graphics Processing Units. J. Comput. Chem. 41 (8) (2020)
Stephanie A. Brocke, Alexandra Degen, Alexander D. MacKerell Jr., Bercem Dutagaci, Michael Feig
Prediction of Membrane Permeation of Drug Molecules by Combining an Implicit Membrane Model with Machine Learning. J. Chem. Inf. Model. 59 (3) (2019)
Lim Heo, Michael Feig
PREFMD: a web server for protein structure refinement via molecular dynamics simulations. Bioinform. 34 (6) (2018)
Bercem Dutagaci, Michael Feig
Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane Model. J. Chem. Inf. Model. 57 (12) (2017)
Bercem Dutagaci, Maryam Sayadi, Michael Feig
Heterogeneous dielectric generalized Born model with a van der Waals term provides improved association energetics of membrane-embedded transmembrane helices. J. Comput. Chem. 38 (16) (2017)
Beibei Wang, Joshua Francis, Monika Sharma, Sean M. Law, Alexander V. Predeus, Michael Feig
Long-Range Signaling in MutS and MSH Homologs via Switching of Dynamic Communication Pathways. PLoS Comput. Biol. 12 (10) (2016)
Michael Feig
Local Protein Structure Refinement via Molecular Dynamics Simulations with locPREFMD. J. Chem. Inf. Model. 56 (7) (2016)
Yi-Ming Cheng, Srinivasa Murthy Gopal, Sean M. Law, Michael Feig
Molecular Dynamics Trajectory Compression with a Coarse-Grained Model. IEEE ACM Trans. Comput. Biol. Bioinform. 9 (2) (2012)
Maria I. Zavodszky, Andrew W. Stumpff-Kane, David J. Lee, Michael Feig
Scoring confidence index: statistical evaluation of ligand binding mode predictions. J. Comput. Aided Mol. Des. 23 (5) (2009)
Bernard R. Brooks, Charles L. Brooks III, Alexander D. MacKerell Jr., Lennart Nilsson, Robert J. Petrella, Benoît Roux, Y. Won, G. Archontis, Christian Bartels, Stefan Boresch, Amedeo Caflisch, Leo S. D. Caves, Qiang Cui, Aaron R. Dinner, Michael Feig, S. Fischer, Jiali Gao, Milan Hodoscek, Wonpil Im, Krzysztof Kuczera, Themis Lazaridis, J. Ma, V. Ovchinnikov, Emanuele Paci, Richard W. Pastor, C. B. Post, J. Z. Pu, Michael Schaefer, Bruce Tidor, Richard M. Venable, H. Lee Woodcock III, X. Wu, W. Yang, Darrin M. York, Martin Karplus
CHARMM: The biomolecular simulation program. J. Comput. Chem. 30 (10) (2009)
Yongcheng Zhou, Michael Feig, Guo-Wei Wei
Highly accurate biomolecular electrostatics in continuum dielectric environments. J. Comput. Chem. 29 (1) (2008)
Mark A. Olson, Michael Feig, Charles L. Brooks III
Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions. J. Comput. Chem. 29 (5) (2008)
Kitiyaporn Wittayanarakul, Supot Hannongbua, Michael Feig
Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors. J. Comput. Chem. 29 (5) (2008)
Kitiyaporn Wittayanarakul, Supot Hannongbua, Michael Feig
On the correlation between drug-resistant pattern of HIV-1 protease inhibitors and binding free energy and structural changes. BMC Syst. Biol. 1 (S-1) (2007)
Yongcheng Zhou, Shan Zhao, Michael Feig, Guo-Wei Wei
High order matched interface and boundary method for elliptic equations with discontinuous coefficients and singular sources. J. Comput. Phys. 213 (1) (2006)
Jana Chocholousová, Michael Feig
Balancing an accurate representation of the molecular surface in generalized born formalisms with integrator stability in molecular dynamics simulations. J. Comput. Chem. 27 (6) (2006)
Michael Feig, Alexey Onufriev, Michael S. Lee, Wonpil Im, David A. Case, Charles L. Brooks III
Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. J. Comput. Chem. 25 (2) (2004)
Alexander D. MacKerell Jr., Michael Feig, Charles L. Brooks III
Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J. Comput. Chem. 25 (11) (2004)
Michael S. Lee, Michael Feig, Freddie R. Salsbury Jr., Charles L. Brooks III
New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations. J. Comput. Chem. 24 (11) (2003)
Michael S. Lee, Michael Feig, Freddie R. Salsbury Jr., Charles L. Brooks III
New analytic approximation to the standard molecular volume definition and its application to generalized born calculations - Erratum. J. Comput. Chem. 24 (14) (2003)
Michael Feig, Matin Abdullah, S. Lennart Johnsson, B. Montgomery Pettitt
Large scale distributed data repository: design of a molecular dynamics trajectory database. Future Gener. Comput. Syst. 16 (1) (1999)
Olle Larsson, Michael Feig, S. Lennart Johnsson
Some Metacomputing Experiences for Scientific Applications. Parallel Process. Lett. 9 (2) (1999)