At Michigan State University (since 2003) |
2021
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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
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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
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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
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162. |
Michael Feig: Virtual Issue on Protein Crowding and Stability Journal of Physical Chemistry B (2021) 125, 10649-10651
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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
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160. |
Lim Heo, Giacomo Janson, Michael Feig: Physics-Based Protein Structure Refinement in the Era of Artifical Intelligence Proteins (2021) 89, 1870-1887
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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
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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
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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
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2020
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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
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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,
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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
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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
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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
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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
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150. |
Lim Heo, Michael Feig: High-accuracy protein structures by combining machine-learning with physics-based refinement Proteins (2020) 88, 637-642
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2019
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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
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148. |
Natalia Ostrowska, Michael Feig, Joanna Trylska: Modeling crowded environment in molecular simulations Frontiers in Molecular Biosciences (2019) 6, 86
Abstract
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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
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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
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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
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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
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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
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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
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2018
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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
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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
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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
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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
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137. |
Bercem Dutagaci, Lim Heo, Michael Feig: Structure Refinement of Membrane Proteins via Molecular Dynamics Simulations Proteins (2018) 86, 738-750
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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
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135. |
Lim Heo, Michael Feig: PREFMD: A web server for protein structure refinement via molecular dynamics simulations Bioinformatics (2018) 34, 1063-1065
Abstract
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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
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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
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132. |
Lim Heo, Michael Feig: What makes it difficult to refine protein models further via molecular dynamics simulations? Proteins (2018) 86, 177-188
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2017
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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
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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
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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
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128. |
Yuji Sugita, Isseki Yu, Michael Feig: Molecular Dynamics Simulations of Biomolecules in Cellular Environments Molecular Science (2017) 11, A0094
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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
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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
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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
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124. |
Michael Feig: Computational structure refinement: Almost there, yet still so far to go WIREs Computational Molecular Science (2017) 7, e1307
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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
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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
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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
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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
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2016
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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
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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
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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
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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
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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
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114. |
Michael Feig: Local protein structure refinement via molecular dynamics simulation with locPREFMD Journal of Chemical Information and Modeling (2016) 56, 1304-1312
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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
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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
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2015
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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
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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
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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
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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
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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
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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
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105. |
Vahid Mirjalil, Michael Feig: Interactions of Amino Acid Side-Chain Analogs within Membrane Environments Journal of Physical Chemistry B (2015) 119, 2877-2885
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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
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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
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2014
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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
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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
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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
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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
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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
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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
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2013
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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2012
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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
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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
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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
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81. |
Ryuhei Harada, Yuji Sugita, Michael Feig: Protein crowding affects hydration structure and dynamics Journal of the American Chemical Society (2012) 134, 4842-4849
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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
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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
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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
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2011
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77. |
Sean Law, Michael Feig: Base-flipping mechanism in DNA mismatch recognition by MutS Biophysical Journal (2011) 101, 2223-2231
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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
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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
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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
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2010
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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
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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) ,
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70. |
Michael Feig: Biomolecular Solvation in Theory and Experiment Modeling Solvent Environments: Applications to simulations of biomolecuels, ed. M. Feig, Wiley-VCH (2010) ,
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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) ,
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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
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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
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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
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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
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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
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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
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62. |
Michael Feig, Zachary F. Burton: RNA Polymerase II Flexibility During Translocation From Normal Mode Analysis Proteins (2010) 78, 434-446
Abstract
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2009
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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
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60. |
Shayantani Mukherjee, Michael Feig: Conformational change in MSH2-MSH6 upon binding DNA coupled to ATPase activity Biophysical Journal (2009) 96, L63-L65
Abstract
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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
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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
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2008
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57. |
Michael Feig, Seiichiro Tanizaki, Maryam Sayadi: Implicit solvent simulations of biomolecules in cellular environments Annual Reviews in Computational Chemistry, Elsevier, Oxford (2008) 4,
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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
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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
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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
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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
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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
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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
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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
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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
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47. |
Yongcheng Zhou, Michael Feig, Guowei Wei: Highly Accurate Biomolecular Electrostatics in Continuum Dieletric Environments Journal of Computational Chemistry (2008) 29, 87-97
Abstract
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2007
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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
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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
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2006
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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2005
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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
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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
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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
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2004
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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
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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
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Postdoctoral Training at the Scripps Research Institute (1999-2003) |
2014
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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
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2008
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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
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2005
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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
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2004
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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
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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
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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
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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
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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
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2003
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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
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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
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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
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2002
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19. |
Michael Feig, Charles L. Brooks III: Evaluating CASP4 Predictions with Physical Energy Functions Proteins (2002) 49, 232-245
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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
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2000
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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
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Graduate Studies at the University of Houston (1994-1999) |
2003
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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
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2002
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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
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2001
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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
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2000
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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
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1999
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12. |
Olle Larsson, Michael Feig, Lennart Johnsson: Some Metacomputing Experiences for Scientific Applications Parallel Processing Letters (1999) 9, 243-252
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11. |
Michael Feig, B. Montgomery Pettitt: Sodium and Chlorine Ions as Part of the DNA Solvation Shell Biophysical Journal (1999) 77, 1769-1781
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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
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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
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1998
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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
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7. |
Michael Feig, B. Montgomery Pettitt: Crystallographic water sites from a theoretical perspective Structure (1998) 6, 1351-1354
Abstract
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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
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5. |
Michael Feig, B. Montgomery Pettitt: Structural Equilibrium of DNA Represented with Different Force Fields Biophysical Journal (1998) 75, 134-149
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1997
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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
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Books and Theses |
2010
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73. |
Michael Feig (ed.): Modeling solvent environments: Applications to simulations of biomolecules Wiley-VCH, Weinheim (2010)
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1999
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13. |
Michael Feig: Molecular Dynamics Simulations of DNA Ph.D. Thesis, Department of Chemistry, University of Houston (1999)
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1996
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3. |
Michael Feig: Einführung in GNU Hanser Verlag, München (1996)
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1994
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2. |
Michael Feig: Präparation und Charakterisierung wasserstoffpassivierter Siliziumoberflächen Diplom-Arbeit, Institut für Festkörperphysik, Technische Universität Berlin (1994)
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1993
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1. |
Michael Feig: UNIX von Anfang an Fischer Verlag, Frankfurt/Main (1993)
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