List of Publications

At Michigan State University (since 2003)
  165. Andriy Kryshtafovych, John Moult, Wendy M. Billings, Dennis Della Corte, Krzysztof Fidelis, Sohee Kwon, Kliment Olechnovic, Chaok Seok, Ceslovas Venclovas, Jonghun Won, CASP-COVID participants (Michael Feig, Lim Heo, et al.): Modeling SARS-CoV-2 proteins in the CASP-commons experiment Proteins (2021) 89, 1987-1996 Abstract PDF
  164. Natalia Ostrowska, Michael Feig, Joanna Trylska: Crowding affects structural dynamics and contributes to membrane association of the NS3/4A complex Biophysical Journal (2021) 120, 3795-3806 Abstract PDF
  163. Elise Rivett, Lim Heo, Michael Feig, Eric 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 (2021) 56, 640-668 Abstract PDF
  162. Michael Feig: Virtual Issue on Protein Crowding and Stability Journal of Physical Chemistry B (2021) 125, 10649-10651 Abstract PDF
  161. Kento Kasahara, Suyong Re, Grzeogorz Nawrocki, Hiraku Oshima, Chiemi Mishima-Tsumagari, Yukako Yabuki, Mutsuko Kukimoto-Niino, Isseki Yu, Mikako Shirouzu, Michael Feig, Yuji Sugita: Reduced Efficacy of Src Kinase Inhibitor in Crowded Protein Solution Nature Communications (2021) 12, 4099 Abstract PDF
  160. Lim Heo, Giacomo Janson, Michael Feig: Physics-Based Protein Structure Refinement in the Era of Artifical Intelligence Proteins (2021) 89, 1870-1887 Abstract PDF
  159. Lim Heo, Collin F. Arbour, Giacomo Janson, Michael Feig: Improved Sampling Strategies for Protein Model Refinement Based on Molecular Dynamics Simulation Journal of Chemical Theory and Computation (2021) 17, 1931-1943 Abstract PDF
  158. Bercem Dutagaci, Grzegorz Nawrocki, Joyce Goodluck, Ali Akbar Ashkarran, Charles G. Hoogstraten, Lisa J. Lapidus, Michael Feig: Charge-driven condensation of RNA and proteins suggests broad role of phase separation in cytoplasmic environments eLife (2021) 10, e64004 Abstract PDF
  157. 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 Journal of Computational Chemistry (2021) 42, 231-241 Abstract PDF
  156. Agnieszka Popielec, Natalia Ostrowska, Monika Wojciechowska, Michael Feig, Joanna Trylska: Crowded environment affects the activity and inhibition of the NS3/4A protease Biochimie (2020) 176, 169-180 Abstract PDF
  155. Lim Heo, Michael Feig: Modeling of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Proteins by Machine Learning and Physics-Based Refinement bioRxiv (2020) 2020.03.25.008904, Abstract PDF
  154. Toshinobu Shida, Yuji O. Kamatari, Takao Yoda, Yoshiki Yamaguchi, Michael Feig, Yumiko Ohhashi, Yuji Sugita, Kazuo Kuwata, Motomasa Tanaka: Short disordered protein segment regulates cross-species transmission of a yeast prion Nature Chemical Biology (2020) 16, 756-765 Abstract PDF
  153. Michael Rigby, Yun Ding, Mark Farrugia, Michael Feig, Giuseppe Cortese, Heather Mitchell, Corinna Burger, Luigi Puglielli: Differential regularion of the endoplasmic reticulum acetyltransferases ATase1/NAT8B and ATase2/NAT8 adjusts secretory pathway efficiency for neuronal function Journal of Neurochemistry (2020) 154, 404-423 Abstract PDF
  152. Yuji Sugita, Michael Feig: All-atom Molecular Dynamics Simulation of Proteins in Crowded Environments In-cell NMR Spectroscopy: From Molecular Sciences to Cell Biology, eds. Yutaka Ito, Volker Dötsch, Masahiro Shirakawa, Royal Society of Chemistry (2020) Chapter 14, 228-248 Abstract PDF
  151. Xiping Gong, Mara Chiricotto, Xiaorong Liu, Erik Nordquist, Michael Feig, Charles L. Brooks, Jianhan Chen: Accelerating GBMV2/SA Implicit Solvent Model Using Graphic Processing Units Journal of Computational Chemistry (2020) 41, 830-838 Abstract PDF
  150. Lim Heo, Michael Feig: High-accuracy protein structures by combining machine-learning with physics-based refinement Proteins (2020) 88, 637-642 Abstract PDF
  149. Grzegorz Nawrocki, Wonpil Im, Yuji Sugita, Michael Feig: Clustering and Dynamics of Crowded Proteins near Membranes and Their Influence on Membrane Bending Proceedings of the National Academy of Sciences, USA (2019) 116, 24562-24567 Abstract PDF
  148. Natalia Ostrowska, Michael Feig, Joanna Trylska: Modeling crowded environment in molecular simulations Frontiers in Molecular Biosciences (2019) 6, 86 Abstract PDF
  147. Michael Feig, Yuji Sugita: Whole-Cell Models and Simulations in Molecular Detail Annual Reviews of Cell and Developmental Biology (2019) 35, 191-211 Abstract PDF
  146. Maciej Jasinski, Joanna Miszkiewicz, Michael Feig, Joanna Trylska: Thermal Stability of Peptide Nucleic Acid Complexes Journal of Physical Chemisty B (2019) 123, 8168-8177 Abstract PDF
  145. Lim Heo, Collin F. Arbour, Michael Feig: Driven to Near-Experimental Accuracy by Refinement via Molecular Dynamics Simulations Proteins (2019) 87, 1263-1275 Abstract PDF
  144. Rebecca L. Newcomer, Jason R. Schrad, Eddie B. Gilcrease, Sherwood R. Casjens, Michael 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 (2019) 8, e45345 Abstract PDF
  143. 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 Journal of Chemical Information and Modeling (2019) 59, 1147-1162 Abstract PDF
  142. Grzegorz Nawrocki, Alp Karaboga, Yuji Sugita, Michael Feig: Effect of Protein-Protein Interactions and Solvent Viscosity on the Rotational Diffusion of Proteins in Crowded Environments Physical Chemistry Chemical Physics (2019) 21, 876-883 Abstract PDF
  141. Asli Yildirim, Nathalie Brenner, Robert Sutherland, Michael Feig: Role of Protein Interactions in Stabilizing Canonical DNA Features in Simulations of DNA in Crowded Environments BMC Biophysics (2018) 11, 8 Abstract PDF
  140. Lim Heo, Michael Feig: Experimental Accuracy in Protein Structure Refinement via Molecular Dynamics Simulations Proceedings of the National Academy of Sciences, USA (2018) 115, 13276-13281 Abstract PDF
  139. Jaie Woodard, Kinshuk R. Srivastava, Gil Rahamim, Asaf Grupi, Steven Hogan, David J. Witalka, Grzegorz Nawrocki, Elisha Haas, Michael Feig, Lisa J. Lapidus: Intramolecular Diffusion in α-Synuclein: It Depends on How you Measure It Biophysical Journal (2018) 115, 1190-1199 Abstract PDF data:bj2018synuclein_trajectory.tgz
  138. Maciej Jasinski, Michael Feig, Joanna Trylska: Improved Force Fields for Peptide Nucleic Acids with Optimized Backbone Torsion Parameters Journal of Chemical Theory and Computation (2018) 14, 3603-3620 Abstract PDF
  137. Bercem Dutagaci, Lim Heo, Michael Feig: Structure Refinement of Membrane Proteins via Molecular Dynamics Simulations Proteins (2018) 86, 738-750 Abstract PDF
  136. Asli Yildirim, Michael Feig: High-Resolution 3D Models of Caulobacter crescentus Chromosome Reveal Genome Structural Variability and Organization Nucleic Acids Research (2018) 46, 3937-3952 Abstract PDF
  135. Lim Heo, Michael Feig: PREFMD: A web server for protein structure refinement via molecular dynamics simulations Bioinformatics (2018) 34, 1063-1065 Abstract PDF
  134. Isseki Yu, Michael Feig, Yuji Sugita: High-Performance Data Analysis on the Big Trajectory Data of Cellular Scale All-atom Molecular Dynamics Simulations Journal of Physics, Conference Series (2018) 1036, 012009 Abstract PDF
  133. Michael Feig, Grzegorz Nawrocki, Isseki Yu, Po-hung Wang, Yuji Sugita: Challenges and opportunities in connecting simulations with experiments via molecular dynamics of cellular environments Journal of Physics, Conference Series (2018) 1036, 012010 Abstract PDF
  132. Lim Heo, Michael Feig: What makes it difficult to refine protein models further via molecular dynamics simulations? Proteins (2018) 86, 177-188 Abstract PDF
  131. Bercem Dutagaci, Michael Feig: Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane Model Journal of Chemical Information and Modeling (2017) 57, 3032-3042 Abstract PDF
  130. Grzegorz Nawrocki, Po-hung Wang, Isseki Yu, Yuji Sugita, Michael Feig: Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation Journal of Physical Chemistry B (2017) 121, 11072-11084 Abstract PDF
  129. Sabyasachi Halder, Daniel Parrell, Douglas Whitten, Michael Feig, Lee Kroos: Interaction of intramembrane metalloprotease SpoIVFB with substrate Pro-σK Proceedings of the National Academy of Sciences, USA (2017) 114, E10677-E10686 Abstract PDF
  128. Yuji Sugita, Isseki Yu, Michael Feig: Molecular Dynamics Simulations of Biomolecules in Cellular Environments Molecular Science (2017) 11, A0094 Abstract PDF
  127. Parimal Kar, Michael Feig: Hybrid All-Atom/Coarse-Grained Simulations of Proteins by Direct Coupling of CHARMM and PRIMO force Fields Journal of Chemical Theory and Computation (2017) 13, 5753-5765 Abstract PDF
  126. Michael Feig, Isseki Yu, Po-hung Wang, Grzegorz Nawrocki, Yuji Sugita: Crowding and Interactions in Cellular Environments at an Atomistic Level from Computer Simulations Journal of Physical Chemistry B (2017) 121, 8009-8025 Abstract PDF
  125. Bercem Dutagaci, Kitiyaporn Wittayanarakul, Takaharu Mori, Michael Feig: Discrimination of Native-like States of Membrane Proteins with Implicit Membrane-Based Scoring Functions Journal of Chemical Theory and Computation (2017) 13, 3049-3059 Abstract PDF
  124. Michael Feig: Computational structure refinement: Almost there, yet still so far to go WIREs Computational Molecular Science (2017) 7, e1307 Abstract PDF
  123. Beibei Wang, Rachel E. Sexton, Michael Feig: Kinetics of Nucleotide Entry via Secondary Pore into RNA Polymerase II Active Site Provides Mechanism for Efficiency and Fidelity BBA Gene Regulatory Mechanisms (2017) 1860, 482-490 Abstract PDF
  122. Po-hung Wang, Isseki Yu, Michael Feig, Yuji Sugita: Influence of Protein Crowder Size on Hydration Structure and Dynamics in Macromolecular Crowding Chemical Physics Letters (2017) 671, 63-70 Abstract PDF
  121. 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 Journal of Computational Chemistry (2017) 38, 1308-1320 Abstract PDF
  120. Jing Huang, Sarah Rauscher, Grzegorz Nawrocki, Ting Ran, Michael Feig, Bert L. de Groot, Helmut Grubmüller, Alexander D. MacKerell Jr.: CHARMM36m: An Improved Force Field for Folded and Intrinsically Disordered Proteins Nature Methods (2017) 14, 71-73 Abstract PDF
  119. Takaharu Mori, Naoyuki Miyashita, Wonpil Im, Michael Feig, Yuji Sugita: Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms BBA - Biomembranes (2016) 1858, 1635-1651 Abstract PDF
  118. Tadashi Ando, Isseki Yu, Michael Feig, Yuji Sugita: Thermodynamics of macromolecular association in heterogeneous crwoding environments: Theoretical and simulation studies with a simplified model Journal of Physical Chemistry B (2016) 120, 11856-11865 Abstract PDF
  117. Isseki Yu, Takaharu Mori, Tadashi Ando, Ryuhei Harada, Jaewoon Jung, Yuji Sugita, Michael Feig: Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm eLife (2016) 5, e19274 Abstract PDF
  116. Patrick O. Ochieng, Neil A. White, Michael Feig, Charles Hoogstraten: Intrinsic base-pairing rearrangement in the hairpin ribozyme directs RNA conformational sampling and tertiary interface formation Journal of Physical Chemistry B (2016) 120, 10885-10898 Abstract PDF
  115. 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 Computational Biology (2016) 12, e1005159 Abstract PDF
  114. Michael Feig: Local protein structure refinement via molecular dynamics simulation with locPREFMD Journal of Chemical Information and Modeling (2016) 56, 1304-1312 Abstract PDF
  113. Sundari Chodavarapu, A. Daniel Jones, Michael Feig, Jon M. Kaguni: DnaC traps DnaB as an open ring and remodels the domain that binds primase Nucleic Acids Research (2016) 44, 210-220 Abstract PDF
  112. Michael Feig, Vahid Mirjalili: Protein structure refinement via molecular dynamics simulations: What works and what does not? Proteins (2016) 84 (Suppl 1), 282-292 Abstract PDF
  111. Mark Ferrugia, Beibei Wang, Michael Feig, Robert P. Hausinger: Activation of Klebsiella aerogenes urease uses a nickel-transfer tunnel in UreD as revealed by mutagenesis and computational studies Biochemistry (2015) 54, 6392-6401 Abstract PDF
  110. Melissa D. Lehti-Shiu, Sahra Uygun, Gaurav D. Moghe, Nicholas Panchy, Liang Fang, David E. Hufnagel, Hannah L. Jasicki, Michael Feig, Shin-Han Shiu: Molecular Evidence for Functional Divergence and Decay of a Transcription Factor Derived from Whole-Genome Duplication in Arabidposis thaliana Plant Physiology (2015) 168, 1717-1734 Abstract PDF
  109. Satyaki Sengupta, Raj Lingnurkar, Timothy S. Carey, Monica Pomaville, Parimal Kar, Michael Feig, Catherine A. Wilson, Jason G. Knott, David N. Arnosti, R. William Henry: The Evolutionarily Conserved C-terminal Domains in the Mammalian Retinoblastoma Tumor Suppressor Family Serve as Dual Regulators of Protein Stability and Transcriptional Potency Journal of Biological Chemistry (2015) 290, 14462-14475 Abstract PDF
  108. Hasan H. Ince, F. Aylin Sungur Konuklar, Ilke Ugur, Maryam Sayadi, Michael Feig, Viktorya Aviyente: Role of the n+1 amino acid residue on the deamidation of asparagine in pentapeptides Molecular Physics (2015) 113, 3839-3848 Abstract PDF
  107. Jaewoon Jong, Takakaru Mori, Chigusa Kobayashi, Yasuhiro Matsunaga, Takao Yoda, Michael Feig, Yuji Sugita: GENESIS: A hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations WIREs Computational Molecular Science (2015) 5, 310-323 Abstract PDF
  106. Michael Feig, Ryuhei Harada, Takaharu Mori, Isseki Yu, Koichi Takahashi, Yuji Sugita: Complete Atomistic Model of a Bacterial Cytoplasm Integrates Physics, Biochemistry, and Systems Biology Journal of Molecular Graphics and Modeling (2015) 58, 1-9 Abstract PDF
  105. Vahid Mirjalil, Michael Feig: Interactions of Amino Acid Side-Chain Analogs within Membrane Environments Journal of Physical Chemistry B (2015) 119, 2877-2885 Abstract PDF
  104. Beibei Wang, Kristopher Opron, Zachary F. Burton, Robert I. Cukier, Michael Feig: Five checkpoints maintaining the fidelity of transcription by RNA polymersases in structural and energetic detail Nucleic Acids Research (2015) 43, 1133-1146 Abstract PDF
  103. Vahid Mirjalili, Michael Feig: Density-biased sampling: A robust computational method for studying pore formation in membranes Journal of Chemical Theory and Computation (2015) 11, 343-350 Abstract PDF
  102. Asli Yildirim, Monika Sharma, Bradley Varner, Liang Fang, Michael Feig: Conformational Preferences of DNA in Cellular Environments Journal of Physical Chemistry B (2014) 118, 10874-10881 Abstract PDF
  101. Parimal Kar, Michael Feig: Recent Advances in Transferable Coarse-Grained Modeling of Proteins Advances in Protein Chemistry & Structural Biology: Biomolecular Modelling and Simulations (2014) 10, 3459-3472 Abstract PDF
  100. Parimal Kar, Srinivasa Murthy Gopal, Yi-Ming Cheng, Afra Panahi, Michael Feig: Transferring the PRIMO Coarse-Grained Force Field to the Membrane Environment: Simulation of Proteins and Helix-Helix Association Journal of Chemical Theory and Computation (2014) 10, 3459-3472 Abstract PDF
  99. Liang Fang, Hyun Ju Cho, Christina Chan, Michael Feig: Binding site multiplicity with fatty acid ligands: Implications for the regulation of PKR kinase autophosphorylation with palmitate Proteins (2014) 82, 2429-2442 Abstract PDF
  98. Monika Sharma, Alexander V. Predeus, Nicholas Kovacs, Michael Feig: Differential mismatch recognition specificities of eukaryotic MutS homologs, MutSα and MutSβ Biophysical Journal (2014) 106, 375-382 Abstract PDF
  96. Vahid Mirjalili, Kennan Noyes, Michael Feig: Physics Based Protein Structure Refinement through Multiple Molecular Dynamics Trajectories and Structure Averaging Proteins (2014) 82 (Supplement S2), 196-207 Abstract PDF
  95. Michael Feig, Yuji Sugita: Reaching New Levels of Realism in Modeling Biological Macromolecules in Cellular Environments Journal of Molecular Graphics and Modeling (2013) 45, 144-156 Abstract PDF
  94. Beibei Wang, Michael Feig, Robert Cukier, Zachary Burton: Computational simulation strategies for analysis of multi-subunit RNA polymerases Chemical Reviews (2013) 113, 8546-8566 Abstract PDF
  93. Cheol Choi, Suyong Re, Mohammad Rashid, Hui Li, Michael Feig, Yuji Sugita: Solvent Electronic Polarization Effects on Na+-Na+ and Cl--CL- pair associations in aqueous solution Journal of Physical Chemistry B (2013) 117, 9273-9279 Abstract PDF
  92. Parimal Kar, Srinivasa Murthy Gopal, Yi-Ming Cheng, Alexander Predeus, Michael Feig: PRIMO: A transferable coarse-grained force field for proteins Journal of Chemical Theory and Computation (2013) 9, 3769-3788 Abstract PDF
  91. Beibei Wang, Alexander Predeus, Zachary Burton, Michael Feig: Energetic and Structural Details of Trigger Loop Closing Transition in RNA Polymerase II Biophysical Journal (2013) 105, 767-775 Abstract PDF
  90. Monika Sharma, Alexander Predeus, Shayantani Mukherjee, Michael Feig: DNA Bending Propensity in the Presence of Base Mismatches: Implications for DNA Repair Journal of Physical Chemistry B (2013) 117, 6194-6205 Abstract PDF
  89. Afra Panahi, Michael Feig: Dynamic Heterogeneous Dielectric Generalized Born (DHDGB): An implicit membrane model with a dynamically varying bilayer thickness Journal of Chemical Theory and Computation (2013) 9, 1709-1719 Abstract PDF
  88. Ryuhei Harada, Naoya Tochio, Takanori Kigawa, Yuji Sugita, Michael Feig: Reduced Native State Stability in Crowded Cellular Environment Due to Protein-Protein Interactions Journal of the American Chemical Society (2013) 135, 3696-3701 Abstract PDF
  87. Vahid Mirjalili, Michael Feig: Protein structure refinement through structure selection and averaging from molecular dynamics ensembles Journal of Chemical Theory and Computation (2013) 9, 1294-1303 Abstract PDF
  86. Manik Kumer Ghosh, Suyong Re, Michael Feig, Yuji Sugita, Cheol Ho Choi: Interionic Hydration Structures of NaCl in aqueous solution: A Combined Study of Quantum Mechanical Cluster Calculations and QM/EFP-MD Simulations Journal of Physical Chemistry B (2013) 117, 289-295 Abstract PDF
  85. Maryam Sayadi, Michael Feig: Role of Conformational Sampling of Ser16 and Thr17-phosphorylated Phospholamban in Interactions with SERCA BBA Biomembranes (2013) 1828, 577-585 Abstract PDF
  84. Robert Best, Jeetain Mittal, Michael Feig, Alexander MacKerell: Inclusion of many-body effects in the additive CHARMM protein CMAP potential results in enhanced cooperativity of alpha-helix and beta-hairpin formation Biophysical Journal (2012) 103, 1045-1051 Abstract PDF
  83. Robert Best, Xiao Zhu, Jihyun Shim, Pedro Lopes, Jeetain Mittal, Michael Feig, Alexander MacKerell: Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone phi, psi, and side-chain chi1 and chi2 Dihedral Angles Journal of Chemical Theory and Computation (2012) 8, 3257-3273 Abstract PDF
  82. Cheol Ho Choi, Suyong Re, Michael Feig, Yuji Sugita: Quantum mechanical/effective fragment potential molecular dynamics (QM/EFP-MD) study on intra-molecular proton transfer of glycine in water Chemical Physics Letters (2012) 539-540, 218-221 Abstract PDF
  81. Ryuhei Harada, Yuji Sugita, Michael Feig: Protein crowding affects hydration structure and dynamics Journal of the American Chemical Society (2012) 134, 4842-4849 Abstract PDF
  80. Alexander Predeus, Seref Gul, Srinivasa Gopal, Michael Feig: Conformational Sampling of Peptides in the Presence of Protein Crowders from AA/CG-Multiscale Simulations Journal of Physical Chemistry B (2012) 116, 8610-8620 Abstract PDF
  79. Michael Feig, Yuji Sugita: Variable interactions between protein crowders and biomolecular solutes are important in understanding cellular crowding Journal of Physical Chemistry B (2012) 116, 599-605 Abstract PDF
  78. Yiming Cheng, Srinivasa Gopal, Sean Law, Michael Feig: Molecular dynamics trajectory compression with a coarse-grained model IEEE/ACM Transactions in Computational Biology and Bioinformatics (2012) 6, 476-486 Abstract PDF
  77. Sean Law, Michael Feig: Base-flipping mechanism in DNA mismatch recognition by MutS Biophysical Journal (2011) 101, 2223-2231 Abstract PDF
  76. Daisuke Imamura, Ritsuko Kuwana, Lee Kroos, Michael Feig, Hiromu Takamatsu, Kazuhito Watabe: Substrate Specificity of SpoIIGA, a Signal-transducing Aspartic Protease in Bacilli Journal of Biochemistry (2011) 149, 665-671 Abstract PDF
  75. Hyunju Cho, Shayantani Mukherjee, Pratheeba Palasuberniam, Lisa Pillow, Betul Bilgin, Catherine Nezich, Patrick Walton, Michael Feig, Christina Chan: Molecular mechanism by which palmitate inhibts PKR autophosphorylation Biochemistry (2011) 50, 1110-1119 Abstract PDF
  74. Adam Jaskierny, Afra Panahi, Michael Feig: Effect of flanking residues on the conformational sampling of the internal fusion peptide from Ebola virus Proteins (2011) 79, 1109-1117 Abstract PDF
  72. Michael Feig, Zachary F. Burton: RNA Polymerase II with Open and Closed Trigger Loops: Active Site Dynamics and Nucleic Acid Translocation Biophysical Journal (2010) 99, 2577-2586 Abstract PDF
  71. Michael Feig, Srinivasa Gopal, Kangasabai Vadivel, Andrew Stumpff-Kane: Conformational sampling in structure prediction and refinement with atomistic and coarse-grained models in: Multiscale approaches to protein modeling: Structure prediction, dynamics, thermodynamics and macromolecular assemblies, ed. A. Kolinski, Springer (2010) ,
  70. Michael Feig: Biomolecular Solvation in Theory and Experiment Modeling Solvent Environments: Applications to simulations of biomolecuels, ed. M. Feig, Wiley-VCH (2010) ,
  69. Michael Feig: Molecular Simulation Methods: Standard Practices and Modern Challenges Computational Modeling in Lignocellulosic Biofuel Production, eds. Mark R. Nimlos and Michael Crowley, ACS (2010) ,
  68. Weili Yang, Michael Pollard, Y. Beisson-Li, F. Beisson, Michael Feig, John Ohlrogge: A distinct type of glycerol-3-phosphate acyltransferease with sn-2 preference and phosphatase activity producing 2-monoacylglycerol PNAS (2010) 107, 12040-12045 Abstract PDF
  67. Steve Seibold, Badri Nath Singh, Chunfen Zhang, Maria Kireeva, Celine Domecq, Annie Bouchard, Anthnoy Nazione, Michael Feig, Robert Cukier, Benoit Coulombe, Mikhail Kashlev, Michael Hampsey, Zachary Burton: Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms (2010) 1799, 575-587 Abstract PDF
  66. Michael Feig, Kahsay Gebreyohannes, Victoria McGuffin: Conformational Sampling of S- and R-Warfarin in Polar Solvents: Implications for Stereoselective Complex Formation Journal of Molecular Structure: THEOCHEM (2010) 949, 41-51 Abstract PDF
  65. Afra Panahi, Michael Feig: Conformational Sampling of Influenza Fusion Peptide in Membrane Bilayers as a Function of Termini and Protonation States Journal of Physical Chemistry B (2010) 114, 1407-1416 Abstract PDF
  64. Maryam Sayadi, Seiichiro Tanizaki, Michael Feig: Effect of membrane thickness on conformational sampling of phospholamban from computer simulations Biophysical Journal (2010) 98, 805-814 Abstract PDF
  63. Srinivasa M. Gopal, Shayantani Mukherjee, Yi-Ming Cheng, Michael Feig: PRIMO/PRIMONA: A coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy Proteins (2010) 78, 1266-1281 Abstract PDF
  62. Michael Feig, Zachary F. Burton: RNA Polymerase II Flexibility During Translocation From Normal Mode Analysis Proteins (2010) 78, 434-446 Abstract PDF
  61. B. R. Brooks, C. L. Brooks III, A. D. MacKerell, Jr., L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, M. Karplus: CHARMM: The Biomolecular Simulation Program Journal of Computational Chemistry (2009) 30, 1545-1614 Abstract PDF
  60. Shayantani Mukherjee, Michael Feig: Conformational change in MSH2-MSH6 upon binding DNA coupled to ATPase activity Biophysical Journal (2009) 96, L63-L65 Abstract PDF
  59. Maria I. Zavodszky, Andrew W. Stumpff-Kane, David J. Lee, Michael Feig: Scoring Confidence Index: Statistical Evaluation of Ligand Binding Mode Predictions Journal of Computer-Aided Molecular Design (2009) 23, 289-299 Abstract PDF
  58. Shayantani Mukherjee, Sean Law, Michael Feig: Deciphering the mismatch recognition cycle in MutS and MSH2-MSH6 using normal mode analysis Biophysical Journal (2009) 96, 1707-1720 Abstract PDF
  57. Michael Feig, Seiichiro Tanizaki, Maryam Sayadi: Implicit solvent simulations of biomolecules in cellular environments Annual Reviews in Computational Chemistry, Elsevier, Oxford (2008) 4,
  56. Michael Feig: Implicit Membrane Models for Membrane Protein Simulation Methods in Molecular Biology: Molecular Modeling of Proteins edited by Andreas Kukol, Humana Press (2008) 443, 181-198
  55. Michael Feig, Seiichiro Tanizaki, Jana Chocholousova, Maryam Sayadi, Jacob Clifford, Brian Connelly, Shayantani Mukherjee, Sean Law: Simulating Biomolecules in Cellular Environments From Computational Biophysics to Systems Biology (CBSB08) Proceedings, John von Neumann Institute for Computing (NIC) Series, ed. Ulrich Hansmann et al. (2008) 40, 23-30
  54. Sean Law, Michael Feig: Application of a Novel Biasing Potential to Study DNA Translocation and DNA Base Flipping From Computational Biophysics to Systems Biology (CBSB08) Proceedings, John von Neumann Institute for Computing (NIC) Series, ed. Ulrich Hansmann et al. (2008) 40, 285-288
  53. Michael Feig: Is Alanine Dipeptide a Good Model for Representing the Torsional Preferences of Protein Backbones? Journal of Chemical Theory and Computation (2008) 4, 1555-1564 Abstract PDF
  52. Imamura Daisuke, Ruanbao Zhou, Michael Feig, Lee Kroos: Evidence that the Bacillus subtilis SpoIIGA protein is a novel type of signal-transducing aspartic protease Journal of Biological Chemistry (2008) 283, 15287-15299 Abstract PDF
  50. 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 Journal of Computational Chemistry (2008) 29, 673-685 Abstract PDF
  49. Andrew Stumpff-Kane, Katarzyna Maksimiak, Michael S. Lee, Michael Feig: Sampling of near-native protein conformations during protein structure refinement using a coarse-grained model, normal modes, and molecular dynamics simulations Proteins (2008) 70, 1345-1356 Abstract PDF
  48. Seiichiro Tanizaki, Jacob W. Clifford, Brian D. Connelly, Michael Feig: Conformational Sampling of Peptides in Cellular Environments Biophysical Journal (2008) 94, 747-759 Abstract PDF
  47. Yongcheng Zhou, Michael Feig, Guowei Wei: Highly Accurate Biomolecular Electrostatics in Continuum Dieletric Environments Journal of Computational Chemistry (2008) 29, 87-97 Abstract PDF
  46. Michael Feig: Kinetics from Implicit Solvent Simulations of Biomolecules as a Function of Viscosity Journal of Chemical Theory and Computation (2007) 3, 1734-1748 Abstract PDF
  45. Gabriela Montero-Moran, Meng Li, Erika Rendon-Huerta, Fabrice Jourdan, David Lowe, Andrew Stumpff-Kane, Michael Feig, Claudio Scazzocchio, Robert Hausinger: Purification and Characterization of the FeII- and alpha-Ketoglutarate-Dependent Xanthine Hydroxylase from Aspergillus nidulans Biochemistry (2007) 46, 5293-5304 Abstract PDF
  44. Michael Feig, Seiichiro Tanizaki: Development of a Heterogeneous Dielectric Generalized Born Model for the Implicit Modeling of Membrane Environments Modelling Molecular Structure and Reactivity in Biological Systems edited by Kevin J. Naidoo, John Brady, Martin J. Field, Jiali Gao, and Michael Hann, Proceedings of WATOC 2005, Royal Society of Chemistry (2006) , 141-150
  43. Gauri W. Jawdekar, Andrej Hanzlowsky, Stacy L. Hovde, Blanka Jelencic, Michael Feig, James H. Geiger, and Ronald W. Henry: The unorthodox SNAP50 zinc finger domain contributes to co-operative promoter recognition by human SNAPc Journal of Biological Chemistry (2006) 281, 31050-31060 Abstract PDF
  42. Jana Chocholousova, Michael Feig: Implicit Solvent Simulations of DNA and DNA-Protein Complexes: Agreement with Explicit Solvent vs. Experiment Journal of Physical Chemistry B (2006) 110, 17240-17251 Abstract PDF
  41. Tina A. Müller, Maria I. Zavodszky, Michael Feig, Leslie A. Kuhn, Robert P. Hausinger: Structural Basis for the Enantiospecificities of R- and S-Specific Phenoxypropionate/α-Ketoglutarate Dioxygenases Protein Science (2006) 15, 1356-1368 Abstract PDF
  40. Jerzy Jankun, Ansari M. Aleem, Sylvia Malgorzewicz, Maria Szkudlarek, Maria I. Zavodszky, David L. DeWitt, Michael Feig, Steven H. Selman, Ewa Skrzypczak-Jankun: Synthetic curcuminoids modulate the arachidonic acid metabolism of human P-12-LOX and reduce sprout formation of human endothelial cells Molecular Cancer Therapeutics (2006) 5, 1371-1382 Abstract PDF
  39. Seiichiro Tanizaki, Michael Feig: Molecular Dynamics Simulations of Large Integral Membrane Proteins with an Implicit Membrane Model Journal of Physical Chemistry B (2006) 110, 548-556 Abstract PDF
  38. Andrew Stumpff-Kane, Michael Feig: A Correlation-Based Method for the Enhancement of Scoring Functions on Funnel-Shaped Energy Landscapes Proteins (2006) 63, 155-164 Abstract PDF
  37. Jana Chocholousova, Michael Feig: Balancing an Accurate Representation of the Molecular Surface in Generalized Born Formalisms with Integrator Stability in Molecular Dynamics Simulations Journal of Computational Chemistry (2006) 27, 719-729 Abstract PDF
  36. Yong C. Zhou, Shan Zhao, Michael Feig, Guo W. Wei: High order matched interface and boundary method for elliptic equations with discontinuous coefficients and singular sources Journal of Computational Physics (2006) 213, 1-30 Abstract PDF
  35. Michael Feig, Jana Chocholousova, Seiichiro Tanizaki: Extending the Horizon: Towards the Efficient Modeling of Large Biomolecular Complexes in Atomic Detail Theoretical Chemistry Accounts (2006) 116, 194-205 Abstract PDF
  34. Xue Q. Gong, Chunfen Zhang, Michael Feig, Zachary F. Burton: Dynamic Error Correction and Regulation of Downstream Bubble Opening by Human RNA Polymerase II Molecular Cell (2005) 18, 461-470 Abstract PDF
  33. Zachary F. Burton, Michael Feig, Xue Qian Gong, Chunfen Zhang, Yuri A. Nedialkov, Yalin Xiong: NTP-driven translocation and regulation of downstream template opening by multi-subunit RNA polymerases Biochemistry And Cell Biology (2005) 83, 486-496 Abstract PDF
  32. Seiichiro Tanizaki, Michael Feig: A generalized Born formalism for heterogeneous dielectric environments: Application to the implicit modeling of biological membranes Journal of Chemical Physics (2005) 122, 124706 Abstract PDF
  29. Michael Feig, Charles L. Brooks III: Recent advances in the development and application of implicit solvent models in biomolecule simulations Current Opinion in Structural Biology (2004) 14, 217-224 Abstract PDF
  28. Timothy F. Henshaw, Michael Feig, Robert P. Hausinger: Aberrant activity of the DNA repair enzyme AlkB Journal of Inorganic Biochemistry (2004) 98, 856-861 Abstract PDF
Postdoctoral Training at the Scripps Research Institute (1999-2003)
  97. Kenneth A. Taylor, Michael Feig, Charles L. Brooks III, Patricia M. Fagnant, Susan Lowey, Kathleen M. Trybus: Role of the Essential Light Chain in the Activation of Smooth Muscle Myosin by Regulatory Light Chain Phosphorylation Journal of Structural Biology (2014) 185, 375-382 Abstract PDF
  51. Mark A. Olson, Michael Feig, Charles L. Brooks III: Prediction of Protein Loop Conformations Using Multiscale Modeling Methods with Physical Energy Scoring Functions Journal of Computational Chemistry (2008) 29, 820-831 Abstract PDF
  31. Florence Tama, Michael Feig, Jun Liu, Charles L. Brooks III, Kenneth A. Taylor: The Requirement for Mechanical Coupling Between Head and S2 Domains in Smooth Muscle Myosin ATPase Regulation and its Implications for Dimeric Motor Function Journal of Molecular Biology (2005) 345, 837-854 Abstract PDF
  30. 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 Journal of Computational Chemistry (2004) 25, 1400-1415 Abstract PDF
  27. Alexander D. MacKerell jr., Michael Feig, Charles L. Brooks III: Improved treatment of the protein backbone in empiricial force fields Journal of the American Chemical Society (2004) 126, 698-699 Abstract PDF
  26. Michael Feig, John Karanicolas, Charles L. Brooks III: MMTSB Tool Set: Enhanced Sampling and Multiscale Modeling Methods for Applications in Structural Biology Journal of Molecular Graphics and Modeling (2004) 22, 377-395 Abstract PDF
  25. Michael Feig, Wonpil Im, Charles L. Brooks III: Implicit solvation based on generalized Born theory in different dielectric environments Journal of Chemical Physics (2004) 120, 903-911 Abstract PDF
  24. 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 Journal of Computational Chemistry (2004) 25, 265-284 Abstract PDF
  23. Wonpil Im, Michael Feig, Charles L. Brooks III: An implicit membrane generalized Born theory for the study of structure, stability, and interactions of membrane proteins Biophysical Journal (2003) 85, 2900-2918 Abstract PDF
  22. Michael Feig, Alexander D. MacKerell jr., Charles L. Brooks III: The force field influence on the observation of pi-helical protein structures in molecular dynamics simulations Journal of Physical Chemistry B (2003) 107, 2831-2836 Abstract PDF
  21. Michael S. Lee, Michael Feig, Freddie R. Salsbury jr., Charles L. Brooks III: A New Analytical Approximation to the Standard Molecular Volume Definition And Its Application to Generalized Born Calculations Journal of Computational Chemistry (2003) 24, 1348-1356 Abstract PDF
  19. Michael Feig, Charles L. Brooks III: Evaluating CASP4 Predictions with Physical Energy Functions Proteins (2002) 49, 232-245 Abstract PDF
  18. Andras Fiser, Michael Feig, Charles L. Brooks III, Andrej Sali: Evolution and Physics in Comparative Protein Structure Modeling Accounts of Chemical Research (2002) 35, 413-421 Abstract PDF
  15. Michael Feig, Piotr Rotkiewicz, Andrzej Kolinski, Jeffrey Skolnick, Charles L. Brooks III: Accurate Reconstruction of All-Atom Protein Representations from Side-Chain-Based Low-Resolution Models Proteins (2000) 41, 86-97 Abstract PDF
Graduate Studies at the University of Houston (1994-1999)
  20. John F. Marko, Michael Feig, B. Montgomery Pettitt: Microscopic DNA fluctuations are in accord with macroscopic DNA stretching elasticity without strong dependence on force field choice NATO ASI Series: Metal Ligand Interactions: Molecular-, Nano-, Micro-systems in Complex Environments (2003) 116, 193-204 Abstract PDF
  17. Vladimir Makarov, B. Montgomery Pettitt, Michael Feig: Solvation and Hydration of Proteins and Nucleic Acids: A Theoretical View of Simulation and Experiment Accounts of Chemical Research (2002) 35, 376-384 Abstract PDF
  16. Michael Feig, Martin Zacharias, B. Montgomery Pettitt: Conformations of an Adenine Bulge in a DNA Octamer And Its Influence on DNA Structure from Molecular Dynamics Simulations Biophysical Journal (2001) 81, 352-370 Abstract PDF
  14. Matin Abdullah, Michael Feig, Lennart Johnsson, Montgomery Pettitt: SimDB: A Problem Solving Environment for Molecular Dynamics Simulation and Analysis First European Grid Forum Workshop, Proceedings of ISThmus 2000: Research and Development for the Information Society (2000) , 321-329
  12. Olle Larsson, Michael Feig, Lennart Johnsson: Some Metacomputing Experiences for Scientific Applications Parallel Processing Letters (1999) 9, 243-252 Abstract PDF
  11. Michael Feig, B. Montgomery Pettitt: Sodium and Chlorine Ions as Part of the DNA Solvation Shell Biophysical Journal (1999) 77, 1769-1781 Abstract PDF
  10. Michael Feig, B. Montgomery Pettitt: Modeling High Resolution Hydration Patterns in Correlation with DNA Sequence and Conformation Journal of Molecular Biology (1999) 286, 1075-1095 Abstract PDF
  9. Michael Feig, Matin Abdullah, Lennart Johnsson, B. Montgomery Pettitt: Large Scale Distributed Data Repository: Design of a Molecular Dynamics Trajectory Database Future Generation Computer Systems (1999) 16, 101-110 Abstract PDF
  8. Michael Feig, B. Montgomery Pettitt: A molecular simulation picture of DNA hydration around A- and B-DNA Biopolymers (Nucleic Acid Sciences) (1998) 48, 199-209 Abstract PDF
  7. Michael Feig, B. Montgomery Pettitt: Crystallographic water sites from a theoretical perspective Structure (1998) 6, 1351-1354 Abstract PDF
  6. Vladimir A. Makarov, Michael Feig, B. Kim Andrews, B. Montgomery Pettitt: Diffusion of Solvent around Biomolecular Solutes. A Molecular Dynamics Simulations Study Biophysical Journal (1998) 75, 150-158 Abstract PDF
  5. Michael Feig, B. Montgomery Pettitt: Structural Equilibrium of DNA Represented with Different Force Fields Biophysical Journal (1998) 75, 134-149 Abstract PDF
  4. Michael Feig, B. Montgomery Pettitt: Experiment vs. force fields: DNA conformation from molecular dynamics simulations Journal of Physical Chemistry B (1997) 101, 7361-7363 Abstract PDF
Books and Theses
  73. Michael Feig (ed.): Modeling solvent environments: Applications to simulations of biomolecules Wiley-VCH, Weinheim (2010)
  13. Michael Feig: Molecular Dynamics Simulations of DNA Ph.D. Thesis, Department of Chemistry, University of Houston (1999)
  3. Michael Feig: Einführung in GNU Hanser Verlag, München (1996)
  2. Michael Feig: Präparation und Charakterisierung wasserstoffpassivierter Siliziumoberflächen Diplom-Arbeit, Institut für Festkörperphysik, Technische Universität Berlin (1994)
  1. Michael Feig: UNIX von Anfang an Fischer Verlag, Frankfurt/Main (1993)