| Year |
Citation |
Score |
| 2021 |
Ostrowska N, Feig M, Trylska J. Crowding affects structural dynamics and contributes to membrane association of the NS3/4A complex. Biophysical Journal. PMID 34270995 DOI: 10.1016/j.bpj.2021.07.008 |
0.313 |
|
| 2021 |
Ostrowska N, Feig M, Trylska J. Crowding affects structural dynamics and contributes to membrane association of the NS3/4A complex. Biophysical Journal. PMID 34270995 DOI: 10.1016/j.bpj.2021.07.008 |
0.313 |
|
| 2021 |
Heo L, Arbour CF, Janson G, Feig M. Improved Sampling Strategies for Protein Model Refinement Based on Molecular Dynamics Simulation. Journal of Chemical Theory and Computation. PMID 33562962 DOI: 10.1021/acs.jctc.0c01238 |
0.325 |
|
| 2020 |
Shida T, Kamatari YO, Yoda T, Yamaguchi Y, Feig M, Ohhashi Y, Sugita Y, Kuwata K, Tanaka M. Short disordered protein segment regulates cross-species transmission of a yeast prion. Nature Chemical Biology. PMID 32284601 DOI: 10.1038/S41589-020-0516-Y |
0.349 |
|
| 2020 |
Yu I, Feig M, Sugita Y. All-Atom Molecular Dynamics Simulation of the Altered Protein-Protein Interaction with Metabolites and Ions in the Cytoplasm Biophysical Journal. 118: 217a. DOI: 10.1016/J.Bpj.2019.11.1288 |
0.367 |
|
| 2019 |
Gong X, Chiricotto M, Liu X, Nordquist E, Feig M, Brooks CL, Chen J. Accelerating the Generalized Born with Molecular Volume and Solvent Accessible Surface Area Implicit Solvent Model Using Graphics Processing Units. Journal of Computational Chemistry. PMID 31875339 DOI: 10.1002/Jcc.26133 |
0.712 |
|
| 2019 |
Nawrocki G, Im W, Sugita Y, Feig M. Clustering and dynamics of crowded proteins near membranes and their influence on membrane bending. Proceedings of the National Academy of Sciences of the United States of America. PMID 31740611 DOI: 10.1073/Pnas.1910771116 |
0.369 |
|
| 2019 |
Heo L, Feig M. High-Accuracy Protein Structures by Combining Machine-Learning with Physics-Based Refinement. Proteins. PMID 31693199 DOI: 10.1002/Prot.25847 |
0.365 |
|
| 2019 |
Ostrowska N, Feig M, Trylska J. Modeling Crowded Environment in Molecular Simulations. Frontiers in Molecular Biosciences. 6: 86. PMID 31572730 DOI: 10.3389/Fmolb.2019.00086 |
0.409 |
|
| 2019 |
Feig M, Sugita Y. Whole-Cell Models and Simulations in Molecular Detail. Annual Review of Cell and Developmental Biology. PMID 31299173 DOI: 10.1146/Annurev-Cellbio-100617-062542 |
0.359 |
|
| 2019 |
Heo L, Arbour CF, Feig M. Driven to Near-Experimental Accuracy by Refinement via Molecular Dynamics Simulations. Proteins. PMID 31197841 DOI: 10.1002/Prot.25759 |
0.422 |
|
| 2019 |
Newcomer RL, Schrad JR, Gilcrease EB, Casjens SR, Feig M, Teschke CM, Alexandrescu AT, Parent KN. The phage L capsid decoration protein has a novel OB-fold and an unusual capsid binding strategy. Elife. 8. PMID 30945633 DOI: 10.7554/Elife.45345 |
0.345 |
|
| 2019 |
Nawrocki G, Karaboga A, Sugita Y, Feig M. Effect of protein-protein interactions and solvent viscosity on the rotational diffusion of proteins in crowded environments. Physical Chemistry Chemical Physics : Pccp. 21: 876-883. PMID 30560249 DOI: 10.1039/C8Cp06142D |
0.313 |
|
| 2018 |
Yildirim A, Brenner N, Sutherland R, Feig M. Role of protein interactions in stabilizing canonical DNA features in simulations of DNA in crowded environments. Bmc Biophysics. 11: 8. PMID 30555686 DOI: 10.1186/S13628-018-0048-Y |
0.436 |
|
| 2018 |
Brocke S, Degen A, MacKerell AD, Dutagaci B, Feig M. Prediction of Membrane Permeation of Drug Molecules by Combining an Implicit Membrane Model with Machine Learning. Journal of Chemical Information and Modeling. PMID 30540459 DOI: 10.1021/Acs.Jcim.8B00648 |
0.326 |
|
| 2018 |
Heo L, Feig M. Experimental accuracy in protein structure refinement via molecular dynamics simulations. Proceedings of the National Academy of Sciences of the United States of America. PMID 30530696 DOI: 10.1073/Pnas.1811364115 |
0.431 |
|
| 2018 |
Jasiński M, Feig M, Trylska J. Improved Force Fields for Peptide Nucleic Acids with Optimized Backbone Torsion Parameters. Journal of Chemical Theory and Computation. PMID 29791152 DOI: 10.1021/Acs.Jctc.8B00291 |
0.389 |
|
| 2018 |
Dutagaci B, Heo L, Feig M. Structure Refinement of Membrane Proteins via Molecular Dynamics Simulations. Proteins. PMID 29675899 DOI: 10.1002/Prot.25508 |
0.424 |
|
| 2018 |
Yildirim A, Feig M. High-resolution 3D models of Caulobacter crescentus chromosome reveal genome structural variability and organization. Nucleic Acids Research. PMID 29529244 DOI: 10.1093/Nar/Gky141 |
0.334 |
|
| 2018 |
Feig M, Heo L. Protein Structure Refinement via Molecular Dynamics Simulations Biophysical Journal. 114: 575a. DOI: 10.1016/J.Bpj.2017.11.3143 |
0.425 |
|
| 2018 |
Nawrocki G, Wang P, Yu I, Sugita Y, Feig M. Protein Diffusion in a Dense Solution Studied by All-Atom Molecular Dynamics Simulations Biophysical Journal. 114: 233a-234a. DOI: 10.1016/J.Bpj.2017.11.1300 |
0.356 |
|
| 2018 |
Yu I, Mori T, Ando T, Harada R, Jung J, Sugita Y, Feig M. Dynamics and Interactions of Proteins and Metabolites in Cellular Crowding Environments: All-Atom Molecular Dynamics Study of Proteins and Metabolites in Cellular Crowding Environments: All-atom Molecular Dynamics Study Biophysical Journal. 114: 190a. DOI: 10.1016/J.Bpj.2017.11.1063 |
0.354 |
|
| 2017 |
Feig M. Computational protein structure refinement: Almost there, yet still so far to go. Wiley Interdisciplinary Reviews. Computational Molecular Science. 7. PMID 30613211 DOI: 10.1002/Wcms.1307 |
0.407 |
|
| 2017 |
Dutagaci B, Feig M. Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane Model. Journal of Chemical Information and Modeling. PMID 29155578 DOI: 10.1021/Acs.Jcim.7B00510 |
0.354 |
|
| 2017 |
Nawrocki G, Wang PH, Yu I, Sugita Y, Feig M. Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation. The Journal of Physical Chemistry. B. PMID 29151345 DOI: 10.1021/Acs.Jpcb.7B08785 |
0.304 |
|
| 2017 |
Heo L, Feig M. PREFMD: a web server for protein structure refinement via molecular dynamics simulations. Bioinformatics (Oxford, England). PMID 29126101 DOI: 10.1093/Bioinformatics/Btx726 |
0.41 |
|
| 2017 |
Kar P, Feig M. Hybrid All-Atom/Coarse-Grained Simulations of Proteins by Direct Coupling of CHARMM and PRIMO Force Fields. Journal of Chemical Theory and Computation. PMID 28992696 DOI: 10.1021/Acs.Jctc.7B00840 |
0.447 |
|
| 2017 |
Heo L, Feig M. What makes it difficult to refine protein models further via molecular dynamics simulations? Proteins. PMID 28975670 DOI: 10.1002/Prot.25393 |
0.434 |
|
| 2017 |
Feig M, Yu I, Wang PH, Nawrocki G, Sugita Y. Crowding in Cellular Environments at an Atomistic Level from Computer Simulations. The Journal of Physical Chemistry. B. PMID 28666087 DOI: 10.1021/Acs.Jpcb.7B03570 |
0.423 |
|
| 2017 |
Dutagaci B, Wittayanarakul K, Mori T, Feig M. Discrimination of Native-like States of Membrane Proteins with Implicit Membrane-Based Scoring Functions. Journal of Chemical Theory and Computation. PMID 28475346 DOI: 10.1021/Acs.Jctc.7B00254 |
0.367 |
|
| 2017 |
Wang B, Sexton RE, Feig M. Kinetics of nucleotide entry into RNA polymerase active site provides mechanism for efficiency and fidelity. Biochimica Et Biophysica Acta. PMID 28242207 DOI: 10.1016/J.Bbagrm.2017.02.008 |
0.358 |
|
| 2017 |
Dutagaci B, Sayadi M, Feig M. Heterogeneous dielectric generalized Born model with a van der Waals term provides improved association energetics of membrane-embedded transmembrane helices. Journal of Computational Chemistry. PMID 28160300 DOI: 10.1002/Jcc.24691 |
0.612 |
|
| 2017 |
Sugita Y, Yu I, Feig M. Molecular Dynamics Simulations of Biomolecules in Cellular Environments Molecular Science. 11: A0094. DOI: 10.3175/Molsci.11.A0094 |
0.375 |
|
| 2017 |
Wang P, Yu I, Feig M, Sugita Y. Influence of protein crowder size on hydration structure and dynamics in macromolecular crowding Chemical Physics Letters. 671: 63-70. DOI: 10.1016/J.Cplett.2017.01.012 |
0.395 |
|
| 2017 |
Yildirim A, Ando T, Sugita Y, Feig M. Protein Diffusion Around Bacterial Nucleoid Biophysical Journal. 112: 217a-218a. DOI: 10.1016/J.Bpj.2016.11.1201 |
0.356 |
|
| 2016 |
Huang J, Rauscher S, Nawrocki G, Ran T, Feig M, de Groot BL, Grubmüller H, MacKerell AD. CHARMM36m: an improved force field for folded and intrinsically disordered proteins. Nature Methods. PMID 27819658 DOI: 10.1016/J.Bpj.2016.11.971 |
0.363 |
|
| 2016 |
Yu I, Mori T, Ando T, Harada R, Jung J, Sugita Y, Feig M. Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm. Elife. 5. PMID 27801646 DOI: 10.7554/Elife.19274 |
0.399 |
|
| 2016 |
Ando T, Yu I, Feig M, Sugita Y. Thermodynamics of Macromolecular Association in Heterogeneous Crowding Environments: Theoretical and Simulation Studies with a Simplified Model. The Journal of Physical Chemistry. B. PMID 27797534 DOI: 10.1021/Acs.Jpcb.6B06243 |
0.349 |
|
| 2016 |
Wang B, Francis J, Sharma M, Law SM, Predeus AV, Feig M. Long-Range Signaling in MutS and MSH Homologs via Switching of Dynamic Communication Pathways. Plos Computational Biology. 12: e1005159. PMID 27768684 DOI: 10.1371/Journal.Pcbi.1005159 |
0.778 |
|
| 2016 |
Ochieng PO, White NA, Feig M, Hoogstraten CG. Intrinsic Base-Pair Rearrangement in the Hairpin Ribozyme Directs RNA Conformational Sampling and Tertiary Interface Formation. The Journal of Physical Chemistry. B. PMID 27701852 DOI: 10.1021/Acs.Jpcb.6B05606 |
0.361 |
|
| 2016 |
Feig M. Local Protein Structure Refinement via Molecular Dynamics Simulations with locPREFMD. Journal of Chemical Information and Modeling. PMID 27380201 DOI: 10.1021/Acs.Jcim.6B00222 |
0.433 |
|
| 2016 |
Mori T, Miyashita N, Im W, Feig M, Sugita Y. Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms. Biochimica Et Biophysica Acta. PMID 26766517 DOI: 10.1016/J.Bbamem.2015.12.032 |
0.461 |
|
| 2016 |
Yu I, Mori T, Ando T, Harada R, Jung J, Sugita Y, Feig M. Author response: Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm Elife. DOI: 10.7554/Elife.19274.029 |
0.334 |
|
| 2016 |
Feig M, Wang B, Francis J. Long-Range Allosteric Communication in Muts and Homologs via Molecular Dynamics Simulations Biophysical Journal. 110: 62a. DOI: 10.1016/J.Bpj.2015.11.401 |
0.39 |
|
| 2016 |
Dutagaci B, Sayadi M, Feig M. HDGB Implicit Membrane Model with a van Der Waals Dispersion Term Biophysical Journal. 110: 642a. DOI: 10.1016/J.Bpj.2015.11.3435 |
0.612 |
|
| 2015 |
Jung J, Mori T, Kobayashi C, Matsunaga Y, Yoda T, Feig M, Sugita Y. GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations. Wiley Interdisciplinary Reviews. Computational Molecular Science. 5: 310-323. PMID 26753008 DOI: 10.1002/Wcms.1220 |
0.38 |
|
| 2015 |
Chodavarapu S, Jones AD, Feig M, Kaguni JM. DnaC traps DnaB as an open ring and remodels the domain that binds primase. Nucleic Acids Research. PMID 26420830 DOI: 10.1093/Nar/Gkv961 |
0.347 |
|
| 2015 |
Farrugia MA, Wang B, Feig M, Hausinger RP. Mutational and Computational Evidence That a Nickel-Transfer Tunnel in UreD Is Used for Activation of Klebsiella aerogenes Urease. Biochemistry. PMID 26401965 DOI: 10.1021/Acs.Biochem.5B00942 |
0.314 |
|
| 2015 |
Feig M, Mirjalili V. Protein structure refinement via molecular-dynamics simulations: What works and what does not? Proteins. PMID 26234208 DOI: 10.1002/Prot.24871 |
0.751 |
|
| 2015 |
Feig M, Wang B, Sharma M, Burton Z, Opron K, Cukier R, Predeus A, Kovacs N, Law S, Mukherjee S. 10 How is fidelity maintained in nucleic acids? Two tales in DNA repair and DNA transcription from computer simulations. Journal of Biomolecular Structure & Dynamics. 33: 6-7. PMID 26103221 DOI: 10.1080/07391102.2015.1032625 |
0.774 |
|
| 2015 |
Feig M, Harada R, Mori T, Yu I, Takahashi K, Sugita Y. Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology. Journal of Molecular Graphics & Modelling. 58: 1-9. PMID 25765281 DOI: 10.1016/J.Jmgm.2015.02.004 |
0.332 |
|
| 2015 |
Mirjalili V, Feig M. Interactions of amino acid side-chain analogs within membrane environments. The Journal of Physical Chemistry. B. 119: 2877-85. PMID 25621811 DOI: 10.1021/Jp511712U |
0.731 |
|
| 2015 |
Mirjalili V, Feig M. Density-Biased Sampling: A Robust Computational Method for Studying Pore Formation in Membranes. Journal of Chemical Theory and Computation. 11: 343-350. PMID 25620896 DOI: 10.1021/Ct5009153 |
0.703 |
|
| 2015 |
Wang B, Opron K, Burton ZF, Cukier RI, Feig M. Five checkpoints maintaining the fidelity of transcription by RNA polymerases in structural and energetic details. Nucleic Acids Research. 43: 1133-46. PMID 25550432 DOI: 10.1093/Nar/Gku1370 |
0.373 |
|
| 2015 |
Ince HH, Konuklar FAS, Ugur I, Ozcan A, Sayadi M, Feig M, Aviyente V. Role of the n+1 amino acid residue on the deamidation of asparagine in pentapeptides Molecular Physics. DOI: 10.1080/00268976.2015.1068394 |
0.598 |
|
| 2015 |
Ochieng PO, Wang B, Feig M, Hoogstraten CG. Alternative Base-Pairing and Conformational Sampling in Loop a of the Hairpin Ribozyme Biophysical Journal. 108: 238a. DOI: 10.1016/J.Bpj.2014.11.1318 |
0.387 |
|
| 2014 |
Kar P, Feig M. Recent advances in transferable coarse-grained modeling of proteins. Advances in Protein Chemistry and Structural Biology. 96: 143-80. PMID 25443957 DOI: 10.1016/Bs.Apcsb.2014.06.005 |
0.386 |
|
| 2014 |
Yildirim A, Sharma M, Varner BM, Fang L, Feig M. Conformational preferences of DNA in reduced dielectric environments. The Journal of Physical Chemistry. B. 118: 10874-81. PMID 25166278 DOI: 10.1021/Jp505727W |
0.432 |
|
| 2014 |
Kar P, Gopal SM, Cheng YM, Panahi A, Feig M. Transferring the PRIMO Coarse-Grained Force Field to the Membrane Environment: Simulations of Membrane Proteins and Helix-Helix Association. Journal of Chemical Theory and Computation. 10: 3459-3472. PMID 25136271 DOI: 10.1021/Ct500443V |
0.68 |
|
| 2014 |
Sharma M, Predeus AV, Kovacs N, Feig M. Differential mismatch recognition specificities of eukaryotic MutS homologs, MutSα and MutSβ. Biophysical Journal. 106: 2483-92. PMID 24896128 DOI: 10.1016/J.Bpj.2014.04.026 |
0.392 |
|
| 2014 |
Fang L, Cho HJ, Chan C, Feig M. Binding site multiplicity with fatty acid ligands: implications for the regulation of PKR kinase autophosphorylation with palmitate. Proteins. 82: 2429-42. PMID 24862841 DOI: 10.1002/Prot.24607 |
0.321 |
|
| 2014 |
Taylor KA, Feig M, Brooks CL, Fagnant PM, Lowey S, Trybus KM. Role of the essential light chain in the activation of smooth muscle myosin by regulatory light chain phosphorylation. Journal of Structural Biology. 185: 375-82. PMID 24361582 DOI: 10.1016/J.Bpj.2013.11.4006 |
0.565 |
|
| 2014 |
Mirjalili V, Noyes K, Feig M. Physics-based protein structure refinement through multiple molecular dynamics trajectories and structure averaging. Proteins. 82: 196-207. PMID 23737254 DOI: 10.1002/Prot.24336 |
0.757 |
|
| 2014 |
Yu I, Ando T, Mori T, Jung J, Harada R, Sugita Y, Feig M. 3P058 Dynamics and Interactions of Macromolecules in the Bacterial Cytoplasm : All-atom Molecular Dynamics Study(01C. Protein: Property,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014)) Seibutsu Butsuri. 54: S258. DOI: 10.2142/Biophys.54.S258_4 |
0.339 |
|
| 2014 |
Wang P, Yu I, Feig M, Sugita Y. 2P131 The solvent-accessible surface area of proteins is a key factor for hydration structure and dynamics in crowded environment(07. Water & Hydration & Electrolyte,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014)) Seibutsu Butsuri. 54: S216. DOI: 10.2142/Biophys.54.S216_5 |
0.321 |
|
| 2014 |
Feig M, Asli Y. 1SDP-05 Combining Structure with Genomics(1SDP Protein Dynamics and Function in Cells elucidated by in-cell NMR and High Performance Computing,Symposium,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014)) Seibutsu Butsuri. 54: S123. DOI: 10.2142/Biophys.54.S123_6 |
0.324 |
|
| 2014 |
Feig M, Sharma M, Predeus A, Mukherjee S, Kovacs N. DNA Bending and Discrimination of Mismatches by MutS and Human Homologs Biophysical Journal. 106: 691a-692a. DOI: 10.1016/J.Bpj.2013.11.3825 |
0.343 |
|
| 2014 |
Mirjalili V, Feig M. Interaction Profiles of Amino Acid Side-Chain Analog Pairs within Membrane Environments Biophysical Journal. 106: 499a. DOI: 10.1016/J.Bpj.2013.11.2791 |
0.732 |
|
| 2014 |
Kar P, Feig M. PRIMO-M: An Extension of the Coarse-Grained Force Field Primo to the Membrane Environment Biophysical Journal. 106: 462a. DOI: 10.1016/J.Bpj.2013.11.2619 |
0.426 |
|
| 2013 |
Feig M, Sugita Y. Reaching new levels of realism in modeling biological macromolecules in cellular environments. Journal of Molecular Graphics & Modelling. 45: 144-56. PMID 24036504 DOI: 10.1016/J.Jmgm.2013.08.017 |
0.304 |
|
| 2013 |
Kar P, Gopal SM, Cheng YM, Predeus A, Feig M. PRIMO: A Transferable Coarse-grained Force Field for Proteins. Journal of Chemical Theory and Computation. 9: 3769-3788. PMID 23997693 DOI: 10.1021/Ct400230Y |
0.417 |
|
| 2013 |
Wang B, Feig M, Cukier RI, Burton ZF. Computational simulation strategies for analysis of multisubunit RNA polymerases. Chemical Reviews. 113: 8546-66. PMID 23987500 DOI: 10.1021/Cr400046X |
0.365 |
|
| 2013 |
Wang B, Predeus AV, Burton ZF, Feig M. Energetic and structural details of the trigger-loop closing transition in RNA polymerase II. Biophysical Journal. 105: 767-75. PMID 23931324 DOI: 10.1016/J.Bpj.2013.05.060 |
0.371 |
|
| 2013 |
Sharma M, Predeus AV, Mukherjee S, Feig M. DNA bending propensity in the presence of base mismatches: implications for DNA repair. The Journal of Physical Chemistry. B. 117: 6194-205. PMID 23621762 DOI: 10.1021/Jp403127A |
0.328 |
|
| 2013 |
Panahi A, Feig M. Dynamic Heterogeneous Dielectric Generalized Born (DHDGB): An implicit membrane model with a dynamically varying bilayer thickness. Journal of Chemical Theory and Computation. 9: 1709-1719. PMID 23585740 DOI: 10.1021/Ct300975K |
0.63 |
|
| 2013 |
Mirjalili V, Feig M. Protein Structure Refinement through Structure Selection and Averaging from Molecular Dynamics Ensembles. Journal of Chemical Theory and Computation. 9: 1294-1303. PMID 23526422 DOI: 10.1021/Ct300962X |
0.753 |
|
| 2013 |
Harada R, Tochio N, Kigawa T, Sugita Y, Feig M. Reduced native state stability in crowded cellular environment due to protein-protein interactions. Journal of the American Chemical Society. 135: 3696-701. PMID 23402619 DOI: 10.1021/Ja3126992 |
0.398 |
|
| 2013 |
Ghosh MK, Re S, Feig M, Sugita Y, Choi CH. Interionic hydration structures of NaCl in aqueous solution: a combined study of quantum mechanical cluster calculations and QM/EFP-MD simulations. The Journal of Physical Chemistry. B. 117: 289-95. PMID 23231378 DOI: 10.1021/Jp308731Z |
0.333 |
|
| 2013 |
Sayadi M, Feig M. Role of conformational sampling of Ser16 and Thr17-phosphorylated phospholamban in interactions with SERCA. Biochimica Et Biophysica Acta. 1828: 577-85. PMID 22959711 DOI: 10.1016/J.Bbamem.2012.08.017 |
0.578 |
|
| 2013 |
Yu I, Mori T, Jung J, Harada R, Sugita Y, Feig M. 1P058 All-Atom Molecular Dynamics Simulation of Bacterial Cytoplasm(01C. Protein:Property,Poster) Seibutsu Butsuri. 53: S115. DOI: 10.2142/Biophys.53.S115_4 |
0.359 |
|
| 2013 |
Fang L, Feig M. Multi-Scale Models of Genomic Bacterial DNA Biophysical Journal. 104: 583a. DOI: 10.1016/J.Bpj.2012.11.3241 |
0.403 |
|
| 2013 |
Harada R, Sugita Y, Feig M. Stability of Proteins in Cellular Environments Biophysical Journal. 104: 566a. DOI: 10.1016/J.Bpj.2012.11.3137 |
0.35 |
|
| 2012 |
Best RB, Zhu X, Shim J, Lopes PE, Mittal J, Feig M, Mackerell AD. Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles. Journal of Chemical Theory and Computation. 8: 3257-3273. PMID 23341755 DOI: 10.1021/Ct300400X |
0.421 |
|
| 2012 |
Best RB, Mittal J, Feig M, MacKerell AD. Inclusion of many-body effects in the additive CHARMM protein CMAP potential results in enhanced cooperativity of α-helix and β-hairpin formation. Biophysical Journal. 103: 1045-51. PMID 23009854 DOI: 10.1016/J.Bpj.2012.07.042 |
0.38 |
|
| 2012 |
Predeus AV, Gul S, Gopal SM, Feig M. Conformational sampling of peptides in the presence of protein crowders from AA/CG-multiscale simulations. The Journal of Physical Chemistry. B. 116: 8610-20. PMID 22429139 DOI: 10.1021/Jp300129U |
0.42 |
|
| 2012 |
Harada R, Sugita Y, Feig M. Protein crowding affects hydration structure and dynamics. Journal of the American Chemical Society. 134: 4842-9. PMID 22352398 DOI: 10.1021/Ja211115Q |
0.393 |
|
| 2012 |
Feig M, Sugita Y. Variable interactions between protein crowders and biomolecular solutes are important in understanding cellular crowding. The Journal of Physical Chemistry. B. 116: 599-605. PMID 22117862 DOI: 10.1021/Jp209302E |
0.342 |
|
| 2012 |
Cheng YM, Gopal SM, Law SM, Feig M. Molecular dynamics trajectory compression with a coarse-grained model. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 9: 476-86. PMID 22025759 DOI: 10.1109/Tcbb.2011.141 |
0.776 |
|
| 2012 |
Feig M. 2SD-01 Dynamics and stability of proteins in cellular environments(2SD Supercomputing in Molecular Network to Cellular Dynamics,Symposium,The 50th Annual Meeting of the Biophysical Society of Japan) Seibutsu Butsuri. 52: S12. DOI: 10.2142/Biophys.52.S12_1 |
0.327 |
|
| 2012 |
Choi CH, Re S, Feig M, Sugita Y. Quantum mechanical/effective fragment potential molecular dynamics (QM/EFP-MD) study on intra-molecular proton transfer of glycine in water Chemical Physics Letters. 539: 218-221. DOI: 10.1016/J.Cplett.2012.05.014 |
0.339 |
|
| 2012 |
Cho H, Fang L, Feig M, Chan C. Molecular Mechanism of Activation of IRE1α Cytosolic Domain by Palmitate Biophysical Journal. 102: 627a-628a. DOI: 10.1016/J.Bpj.2011.11.3417 |
0.312 |
|
| 2012 |
Feig M, Sugita Y. Protein-Protein Interactions in Crowded Cellular Environments Biophysical Journal. 102: 473a. DOI: 10.1016/J.Bpj.2011.11.2596 |
0.369 |
|
| 2011 |
Law SM, Feig M. Base-flipping mechanism in postmismatch recognition by MutS. Biophysical Journal. 101: 2223-31. PMID 22067162 DOI: 10.1016/J.Bpj.2011.09.045 |
0.803 |
|
| 2011 |
Jaskierny AJ, Panahi A, Feig M. Effect of flanking residues on the conformational sampling of the internal fusion peptide from Ebola virus. Proteins. 79: 1109-17. PMID 21246633 DOI: 10.1002/Prot.22947 |
0.62 |
|
| 2011 |
Cho H, Mukherjee S, Palasuberniam P, Pillow L, Bilgin B, Nezich C, Walton SP, Feig M, Chan C. Molecular mechanism by which palmitate inhibits PKR autophosphorylation. Biochemistry. 50: 1110-9. PMID 21192654 DOI: 10.1021/Bi101923R |
0.305 |
|
| 2010 |
Feig M, Burton ZF. RNA polymerase II with open and closed trigger loops: active site dynamics and nucleic acid translocation. Biophysical Journal. 99: 2577-86. PMID 20959099 DOI: 10.1016/J.Bpj.2010.08.010 |
0.353 |
|
| 2010 |
Seibold SA, Singh BN, Zhang C, Kireeva M, Domecq C, Bouchard A, Nazione AM, Feig M, Cukier RI, Coulombe B, Kashlev M, Hampsey M, Burton ZF. Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase. Biochimica Et Biophysica Acta. 1799: 575-87. PMID 20478425 DOI: 10.1016/J.Bbagrm.2010.05.002 |
0.336 |
|
| 2010 |
Sayadi M, Tanizaki S, Feig M. Effect of membrane thickness on conformational sampling of phospholamban from computer simulations. Biophysical Journal. 98: 805-14. PMID 20197034 DOI: 10.1016/J.Bpj.2009.11.015 |
0.629 |
|
| 2010 |
Panahi A, Feig M. Conformational sampling of influenza fusion peptide in membrane bilayers as a function of termini and protonation states. The Journal of Physical Chemistry. B. 114: 1407-16. PMID 20043654 DOI: 10.1021/Jp907366G |
0.626 |
|
| 2010 |
Gopal SM, Mukherjee S, Cheng YM, Feig M. PRIMO/PRIMONA: a coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy. Proteins. 78: 1266-81. PMID 19967787 DOI: 10.1002/Prot.22645 |
0.349 |
|
| 2010 |
Feig M, Burton ZF. RNA polymerase II flexibility during translocation from normal mode analysis. Proteins. 78: 434-46. PMID 19714773 DOI: 10.1002/Prot.22560 |
0.311 |
|
| 2010 |
Feig M, Gebreyohannes KG, McGuffin VL. Conformational sampling of S- and R-warfarin in polar solvents: Implications for stereoselective complex formation Journal of Molecular Structure: Theochem. 949: 41-51. DOI: 10.1016/J.Theochem.2010.03.001 |
0.359 |
|
| 2010 |
Law SM, Feig M. DNA Base Flipping: New-Found Insights into the DNA Mismatch Recognition Process in E. Coli Muts Biophysical Journal. 98: 437a. DOI: 10.1016/J.Bpj.2009.12.2372 |
0.803 |
|
| 2010 |
Feig M. Enthalpic Vs. Entropic Effects of Crowded Cellular Environments Biophysical Journal. 98: 4a. DOI: 10.1016/J.Bpj.2009.12.027 |
0.335 |
|
| 2010 |
Gopal SM, Mukherjee S, Cheng YM, Feig M. Erratum: PRIMO/PRIMONA: A coarse-grained model for proteins and nucleic acids that preserves near-atonmistic accuracy preserves near-atomistic accuracy (Proteins (2010) 78 (1266-1281)) Proteins. 78. DOI: 10.1002/Prot.22721 |
0.318 |
|
| 2009 |
Mukherjee S, Feig M. Conformational change in MSH2-MSH6 upon binding DNA coupled to ATPase activity. Biophysical Journal. 96: L63-5. PMID 19486659 DOI: 10.1016/J.Bpj.2009.04.012 |
0.401 |
|
| 2009 |
Brooks BR, Brooks CL, Mackerell AD, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, et al. CHARMM: the biomolecular simulation program. Journal of Computational Chemistry. 30: 1545-614. PMID 19444816 DOI: 10.1002/Jcc.21287 |
0.687 |
|
| 2009 |
Mukherjee S, Law SM, Feig M. Deciphering the mismatch recognition cycle in MutS and MSH2-MSH6 using normal-mode analysis. Biophysical Journal. 96: 1707-20. PMID 19254532 DOI: 10.1016/J.Bpj.2008.10.071 |
0.792 |
|
| 2009 |
Sayadi M, Feig M. Structure And Dynamics Of Phospholamban In The Context Of SERCA Biophysical Journal. 96: 153a. DOI: 10.1016/J.Bpj.2008.12.694 |
0.61 |
|
| 2009 |
Gopal SM, Feig M. PRIMO: A Transferable Coarse-Grained Model for Proteins Biophysical Journal. 96: 573a. DOI: 10.1016/J.Bpj.2008.12.3753 |
0.395 |
|
| 2009 |
Mukherjee S, Law SM, Feig M. Mismatch Recognition Cycle in MutS and MSH2-MSH6 from Normal Mode Analysis and Simulations Biophysical Journal. 96: 342a-343a. DOI: 10.1016/J.Bpj.2008.12.1719 |
0.788 |
|
| 2008 |
Feig M. Is Alanine Dipeptide a Good Model for Representing the Torsional Preferences of Protein Backbones? Journal of Chemical Theory and Computation. 4: 1555-64. PMID 26621437 DOI: 10.1021/Ct800153N |
0.425 |
|
| 2008 |
Feig M. Implicit membrane models for membrane protein simulation. Methods in Molecular Biology (Clifton, N.J.). 443: 181-96. PMID 18446288 DOI: 10.1007/978-1-59745-177-2_10 |
0.396 |
|
| 2008 |
Imamura D, Zhou R, Feig M, Kroos L. Evidence that the Bacillus subtilis SpoIIGA protein is a novel type of signal-transducing aspartic protease. The Journal of Biological Chemistry. 283: 15287-99. PMID 18378688 DOI: 10.1074/Jbc.M708962200 |
0.31 |
|
| 2008 |
Tanizaki S, Clifford J, Connelly BD, Feig M. Conformational sampling of peptides in cellular environments. Biophysical Journal. 94: 747-59. PMID 17905846 DOI: 10.1529/Biophysj.107.116236 |
0.362 |
|
| 2008 |
Stumpff-Kane AW, Maksimiak K, Lee MS, Feig M. Sampling of near-native protein conformations during protein structure refinement using a coarse-grained model, normal modes, and molecular dynamics simulations. Proteins. 70: 1345-56. PMID 17876825 DOI: 10.1002/Prot.21674 |
0.429 |
|
| 2008 |
Olson MA, Feig M, Brooks CL. Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions. Journal of Computational Chemistry. 29: 820-31. PMID 17876760 DOI: 10.1002/Jcc.20827 |
0.663 |
|
| 2008 |
Wittayanarakul K, Hannongbua S, Feig M. 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. 29: 673-85. PMID 17849388 DOI: 10.1002/Jcc.20821 |
0.316 |
|
| 2008 |
Zhou YC, Feig M, Wei GW. Highly accurate biomolecular electrostatics in continuum dielectric environments. Journal of Computational Chemistry. 29: 87-97. PMID 17508411 DOI: 10.1002/Jcc.20769 |
0.331 |
|
| 2008 |
Feig M, Tanizaki S, Sayadi M. Chapter 6 Implicit Solvent Simulations of Biomolecules in Cellular Environments Annual Reports in Computational Chemistry. 4: 107-121. DOI: 10.1016/S1574-1400(08)00006-6 |
0.631 |
|
| 2007 |
Feig M. Kinetics from Implicit Solvent Simulations of Biomolecules as a Function of Viscosity. Journal of Chemical Theory and Computation. 3: 1734-48. PMID 26627618 DOI: 10.1021/Ct7000705 |
0.394 |
|
| 2006 |
Chocholousová J, Feig M. Implicit solvent simulations of DNA and DNA-protein complexes: agreement with explicit solvent vs experiment. The Journal of Physical Chemistry. B. 110: 17240-51. PMID 16928023 DOI: 10.1021/Jp0627675 |
0.446 |
|
| 2006 |
Jawdekar GW, Hanzlowsky A, Hovde SL, Jelencic B, Feig M, Geiger JH, Henry RW. The unorthodox SNAP50 zinc finger domain contributes to cooperative promoter recognition by human SNAPC. The Journal of Biological Chemistry. 281: 31050-60. PMID 16901896 DOI: 10.1074/Jbc.M603810200 |
0.319 |
|
| 2006 |
Chocholousová J, Feig M. Balancing an accurate representation of the molecular surface in generalized born formalisms with integrator stability in molecular dynamics simulations. Journal of Computational Chemistry. 27: 719-29. PMID 16518883 DOI: 10.1002/Jcc.20387 |
0.398 |
|
| 2006 |
Tanizaki S, Feig M. Molecular dynamics simulations of large integral membrane proteins with an implicit membrane model. The Journal of Physical Chemistry. B. 110: 548-56. PMID 16471567 DOI: 10.1021/Jp054694F |
0.428 |
|
| 2006 |
Stumpff-Kane AW, Feig M. A correlation-based method for the enhancement of scoring functions on funnel-shaped energy landscapes. Proteins. 63: 155-64. PMID 16397892 DOI: 10.1002/Prot.20853 |
0.313 |
|
| 2006 |
Feig M, Chocholoušová J, Tanizaki S. Extending the horizon: Towards the efficient modeling of large biomolecular complexes in atomic detail Theoretical Chemistry Accounts. 116: 194-205. DOI: 10.1007/S00214-005-0062-4 |
0.412 |
|
| 2005 |
Tanizaki S, Feig M. A generalized Born formalism for heterogeneous dielectric environments: application to the implicit modeling of biological membranes. The Journal of Chemical Physics. 122: 124706. PMID 15836408 DOI: 10.1063/1.1865992 |
0.423 |
|
| 2005 |
Tama F, Feig M, Liu J, Brooks CL, Taylor KA. 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. 345: 837-54. PMID 15588830 DOI: 10.1016/J.Jmb.2004.10.084 |
0.715 |
|
| 2004 |
Feig M, Im W, Brooks CL. Implicit solvation based on generalized Born theory in different dielectric environments. The Journal of Chemical Physics. 120: 903-11. PMID 15267926 DOI: 10.1063/1.1631258 |
0.601 |
|
| 2004 |
Mackerell AD, Feig M, Brooks CL. 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. 25: 1400-15. PMID 15185334 DOI: 10.1002/Jcc.20065 |
0.653 |
|
| 2004 |
Henshaw TF, Feig M, Hausinger RP. Aberrant activity of the DNA repair enzyme AlkB. Journal of Inorganic Biochemistry. 98: 856-61. PMID 15134932 DOI: 10.1016/J.Jinorgbio.2003.10.021 |
0.303 |
|
| 2004 |
Feig M, Karanicolas J, Brooks CL. MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology. Journal of Molecular Graphics & Modelling. 22: 377-95. PMID 15099834 DOI: 10.1016/J.Jmgm.2003.12.005 |
0.758 |
|
| 2004 |
Feig M, Brooks CL. Recent advances in the development and application of implicit solvent models in biomolecule simulations. Current Opinion in Structural Biology. 14: 217-24. PMID 15093837 DOI: 10.1016/J.Sbi.2004.03.009 |
0.656 |
|
| 2004 |
MacKerell AD, Feig M, Brooks CL. Improved treatment of the protein backbone in empirical force fields. Journal of the American Chemical Society. 126: 698-9. PMID 14733527 DOI: 10.1021/Ja036959E |
0.612 |
|
| 2004 |
Feig M, Onufriev A, Lee MS, Im W, Case DA, Brooks CL. Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. Journal of Computational Chemistry. 25: 265-84. PMID 14648625 DOI: 10.1002/Jcc.10378 |
0.65 |
|
| 2003 |
Im W, Feig M, Brooks CL. An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins. Biophysical Journal. 85: 2900-18. PMID 14581194 DOI: 10.1016/S0006-3495(03)74712-2 |
0.64 |
|
| 2003 |
Lee MS, Feig M, Salsbury FR, Brooks CL. New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations. Journal of Computational Chemistry. 24: 1348-56. PMID 12827676 DOI: 10.1002/Jcc.10272 |
0.741 |
|
| 2003 |
Feig M, MacKerell AD, Brooks CL. Force field influence on the observation of π-helical protein structures in molecular dynamics simulations Journal of Physical Chemistry B. 107: 2831-2836. DOI: 10.1021/Jp027293Y |
0.636 |
|
| 2003 |
Lee MS, Feig M, Salsbury FR, Brooks CL. Erratum: New Analytic Approximation to the Standard Molecular Volume Definition and Its Application to Generalized Born Calculations (Journal of Computational Chemistry (2003) 24:11 (1348-1356)) Journal of Computational Chemistry. 24. DOI: 10.1002/Jcc.10367 |
0.715 |
|
| 2002 |
Feig M, Brooks CL. Evaluating CASP4 predictions with physical energy functions. Proteins. 49: 232-45. PMID 12211003 DOI: 10.1002/Prot.10217 |
0.603 |
|
| 2002 |
Fiser A, Feig M, Brooks CL, Sali A. Evolution and physics in comparative protein structure modeling. Accounts of Chemical Research. 35: 413-21. PMID 12069626 DOI: 10.1021/Ar010061H |
0.624 |
|
| 2002 |
Makarov V, Pettitt BM, Feig M. Solvation and hydration of proteins and nucleic acids: a theoretical view of simulation and experiment. Accounts of Chemical Research. 35: 376-84. PMID 12069622 DOI: 10.1021/Ar0100273 |
0.58 |
|
| 2001 |
Feig M, Zacharias M, Pettitt BM. Conformations of an adenine bulge in a DNA octamer and its influence on DNA structure from molecular dynamics simulations. Biophysical Journal. 81: 352-70. PMID 11423420 DOI: 10.1016/S0006-3495(01)75705-0 |
0.616 |
|
| 2000 |
Feig M, Rotkiewicz P, Kolinski A, Skolnick J, Brooks CL. Accurate reconstruction of all-atom protein representations from side-chain-based low-resolution models. Proteins. 41: 86-97. PMID 10944396 DOI: 10.1002/1097-0134(20001001)41:1<86::Aid-Prot110>3.0.Co;2-Y |
0.607 |
|
| 1999 |
Feig M, Pettitt BM. Sodium and chlorine ions as part of the DNA solvation shell. Biophysical Journal. 77: 1769-81. PMID 10512802 DOI: 10.1016/S0006-3495(99)77023-2 |
0.551 |
|
| 1999 |
Feig M, Pettitt BM. Modeling high-resolution hydration patterns in correlation with DNA sequence and conformation. Journal of Molecular Biology. 286: 1075-95. PMID 10047483 DOI: 10.1006/Jmbi.1998.2486 |
0.591 |
|
| 1999 |
Feig M, Abdullah M, Johnsson L, Pettitt BM. Large scale distributed data repository: Design of a molecular dynamics trajectory database Future Generation Computer Systems. 16: 101-110. DOI: 10.1016/S0167-739X(99)00039-4 |
0.517 |
|
| 1998 |
Feig M, Pettitt BM. A molecular simulation picture of DNA hydration around A- and B-DNA. Biopolymers. 48: 199-209. PMID 10699840 DOI: 10.1002/(Sici)1097-0282(1998)48:4<199::Aid-Bip2>3.0.Co;2-5 |
0.594 |
|
| 1998 |
Feig M, Pettitt BM. Crystallographic water sites from a theoretical perspective. Structure (London, England : 1993). 6: 1351-4. PMID 9817850 DOI: 10.1016/S0969-2126(98)00135-X |
0.515 |
|
| 1998 |
Makarov VA, Feig M, Andrews BK, Pettitt BM. Diffusion of solvent around biomolecular solutes: a molecular dynamics simulation study. Biophysical Journal. 75: 150-8. PMID 9649375 DOI: 10.1016/S0006-3495(98)77502-2 |
0.519 |
|
| 1998 |
Feig M, Pettitt BM. Structural equilibrium of DNA represented with different force fields. Biophysical Journal. 75: 134-49. PMID 9649374 DOI: 10.1016/S0006-3495(98)77501-0 |
0.578 |
|
| 1997 |
Feig M, Pettitt BM. Experiment vs force fields: DNA conformation from molecular dynamics simulations Journal of Physical Chemistry B. 101: X-7363. DOI: 10.1021/Jp971180A |
0.586 |
|
| Show low-probability matches. |
