Recent Publications
Nawrocki G, Im W, Sugita Y, Feig M. “Clustering and dynamics of crowded proteins near membranes and their influence on membrane bending.” Proc Natl Acad Sci U S A. (2019) Nov 18. doi: 10.1073/pnas.1910771116
Heo L, Feig M. “High-Accuracy Protein Structures by Combining Machine-Learning with Physics-Based Refinement.” Proteins. (2019) Nov 6. doi: 10.1002/prot.25847
JasiÅ„ski M, Miszkiewicz J, Feig M, Trylska J. “Thermal Stability of Peptide Nucleic Acid Complexes.” J Phys Chem B. (2019) Oct 3;123(39):8168-8177. doi: 10.1021/acs.jpcb.9b05168
Ostrowska N, Feig M, Trylska J. “Modeling Crowded Environment in Molecular Simulations.” Front Mol Biosci. (2019) Sep 11;6:86. doi: 10.3389/fmolb.2019.00086
Feig M, Sugita Y. “Whole-Cell Models and Simulations in Molecular Detail.” Annu Rev Cell Dev Biol. (2019) Jul 12. doi: 10.1146/annurev-cellbio-100617-062542
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. (2019) Apr 4;. doi: 10.7554/eLife.45345
Yu I, Feig M, Sugita Y. “High-Performance Data Analysis on the Big Trajectory Data of Cellular Scale All-atom Molecular Dynamics Simulations.” J Phys Conf Ser. (2018) Jan. doi: 10.1088/1742-6596/1036/1/012009
Feig M, Nawrocki G, Yu I, Wang PH, Sugita Y. “Challenges and opportunities in connecting simulations with experiments via molecular dynamics of cellular environments.” J Phys Conf Ser. (2018) Jan. doi: 10.1088/1742-6596/1036/1/012010
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.” Phys Chem Chem Phys. (2019) Jan 2;21(2):876-883. doi: 10.1039/c8cp06142d
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.” J Chem Inf Model. (2018) Dec 12. doi: 10.1021/acs.jcim.8b00648
Heo L, Feig M. “Experimental accuracy in protein structure refinement via molecular dynamics simulations.” Proc Natl Acad Sci U S A. (2018) Dec 10. doi: 10.1073/pnas.1811364115
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 Biophys. (2018) Dec 7;11:8. doi: 10.1186/s13628-018-0048-y
Woodard J, Srivastava KR, Rahamim G, Grupi A, Hogan S, Witalka DJ, Nawrocki G, Haas E, Feig M, Lapidus LJ. “Intramolecular Diffusion in α-Synuclein: It Depends on How You Measure It.” Biophys J. (2018) Aug 27. doi: 10.1016/j.bpj.2018.08.023
JasiÅ„ski M, Feig M, Trylska J. “Improved Force Fields for Peptide Nucleic Acids with Optimized Backbone Torsion Parameters.” J Chem Theory Comput. (2018) May 23. doi: 10.1021/acs.jctc.8b00291
Dutagaci B, Heo L, Feig M. “Structure Refinement of Membrane Proteins via Molecular Dynamics Simulations.” Proteins. (2018) Apr 20. doi: 10.1002/prot.25508
Yildirim A, Feig M. “High-resolution 3D models of Caulobacter crescentus chromosome reveal genome structural variability and organization.” Nucleic Acids Res. (2018) Feb 26. doi: 10.1093/nar/gky141
Nawrocki G, Wang PH, Yu I, Sugita Y, Feig M. “Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation.” J Phys Chem B. (2017) Nov 30. doi: 10.1021/acs.jpcb.7b08785
Halder S, Parrell D, Whitten D, Feig M, Kroos L. “Interaction of intramembrane metalloprotease SpoIVFB with substrate Pro-σK.” Proc Natl Acad Sci U S A. (2017) Nov 27. doi: 10.1073/pnas.1711467114
Dutagaci B, Feig M. “Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane Model.” J Chem Inf Model. (2017) Nov 20. doi: 10.1021/acs.jcim.7b00510
Heo L, Feig M. “PREFMD: a web server for protein structure refinement via molecular dynamics simulations.” Bioinformatics. (2017) Nov 8;. doi: 10.1093/bioinformatics/btx726
Kar P, Feig M. “Hybrid All-Atom/Coarse-Grained Simulations of Proteins by Direct Coupling of CHARMM and PRIMO Force Fields.” J Chem Theory Comput. (2017) Oct 9. doi: 10.1021/acs.jctc.7b00840
Heo L, Feig M. “What makes it difficult to refine protein models further via molecular dynamics simulations?” Proteins. (2017) Oct 4. doi: 10.1002/prot.25393
Feig M, Yu I, Wang PH, Nawrocki G, Sugita Y. “Crowding in Cellular Environments at an Atomistic Level from Computer Simulations.” J Phys Chem B. (2017) Jun 30. doi: 10.1021/acs.jpcb.7b03570
Dutagaci B, Wittayanarakul K, Mori T, Feig M. “Discrimination of Native-like States of Membrane Proteins with Implicit Membrane-based Scoring Functions.” J Chem Theory Comput. (2017) May 11. doi: 10.1021/acs.jctc.7b00254
Wang B, Sexton RE, Feig M. “Kinetics of nucleotide entry into RNA polymerase active site provides mechanism for efficiency and fidelity.” Biochim Biophys Acta. (2017) Feb 24. pii: S1874-9399(16)30280-2. doi: 10.1016/j.bbagrm.2017.02.008
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.” J Comput Chem. (2017) Feb 4. doi: 10.1002/jcc.24691
Huang J, Rauscher S, Nawrocki G, Ran T, Feig M, de Groot BL, Grubmüller H, MacKerell AD Jr. “CHARMM36m: an improved force field for folded and intrinsically disordered proteins.” Nat Methods. (2016) Nov 7. doi: 10.1038/nmeth.4067
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. (2016) Nov 1;. doi: 10.7554/eLife.19274
Ando T, Yu I, Feig M, Sugita Y. “Thermodynamics of Macromolecular Association in Heterogeneous Crowding Environments: Theoretical and Simulation Studies with a Simplified Model.” J Phys Chem B. (2016) Oct 31;. doi: 10.1021/acs.jpcb.6b06243
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 Comput Biol. (2016) Oct 21;12(10):e1005159. doi: 10.1371/journal.pcbi.1005159
Ochieng PO, White NA, Feig M, Hoogstraten CG. “Intrinsic Base-Pair Rearrangement in the Hairpin Ribozyme Directs RNA Conformational Sampling and Tertiary Interface Formation.” J Phys Chem B. (2016) Oct 5. doi:10.1021/acs.jpcb.6b05606
Feig M. “Local Protein Structure Refinement via Molecular Dynamics Simulations with locPREFMD.” J Chem Inf Model. (2016) Jul 5. doi:10.1021/acs.jcim.6b00222
Mori T, Miyashita N, Im W, Feig M, Sugita Y. “Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms.” Biochim Biophys Acta. (2016) Jan 5. doi:10.1016/j.bbamem.2015.12.032
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 Interdiscip Rev Comput Mol Sci. (2015) Jul;5(4):310-323. doi:10.1002/wcms.1220
Chodavarapu S, Jones AD, Feig M, Kaguni JM. “DnaC traps DnaB as an open ring and remodels the domain that binds primase.” Nucleic Acids Res. (2016) Jan 8;44(1):210-20. doi:10.1093/nar/gkv961
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. (2015) Oct 20;54(41):6392-401. doi:10.1021/acs.biochem.5b00942
Feig M, Mirjalili V. “Protein structure refinement via molecular-dynamics simulations: What works and what does not?” Proteins. (2015) Aug 3. doi:10.1002/prot.24871
Lehti-Shiu MD, Uygun S, Moghe GD, Panchy N, Fang L, Hufnagel DE, Jasicki HL, Feig M, Shiu SH. “Molecular Evidence for Functional Divergence and Decay of a Transcription Factor Derived from Whole-Genome Duplication in Arabidopsis thaliana.” Plant Physiol. (2015) Aug;168(4):1717-34. doi:10.1104/pp.15.00689
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.” J Biomol Struct Dyn. (2015);33 Suppl 1:6-7. doi:10.1080/07391102.2015.1032625
Sengupta S, Lingnurkar R, Carey TS, Pomaville M, Kar P, Feig M, Wilson CA, Knott JG, Arnosti DN, Henry RW. “The Evolutionarily Conserved C-terminal Domains in the Mammalian Retinoblastoma Tumor Suppressor Family Serve as Dual Regulators of Protein Stability and Transcriptional Potency.” J Biol Chem. (2015) Jun 5;290(23):14462-75. doi:10.1074/jbc.M114.599993
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.” J Mol Graph Model. (2015) May;58:1-9. doi:10.1016/j.jmgm.2015.02.004
Mirjalili V, Feig M. “Interactions of amino acid side-chain analogs within membrane environments.” J Phys Chem B. (2015) Feb 19;119(7):2877-85. doi:10.1021/jp511712u
Mirjalili V, Feig M. “Density-Biased Sampling: A Robust Computational Method for Studying Pore Formation in Membranes.” J Chem Theory Comput. (2015) Jan 13;11(1):343-350. doi:10.1021/ct5009153
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 Res. (2015) Jan;43(2):1133-46. doi:10.1093/nar/gku1370
Kar P, Feig M. “Recent advances in transferable coarse-grained modeling of proteins.” Adv Protein Chem Struct Biol. (2014);96:143-80. doi:10.1016/bs.apcsb.2014.06.005
Yildirim A, Sharma M, Varner BM, Fang L, Feig M. “Conformational preferences of DNA in reduced dielectric environments.” J Phys Chem B. (2014) Sep 18;118(37):10874-81. doi:10.1021/jp505727w
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.” J Chem Theory Comput. (2014) Aug 12;10(8):3459-3472. doi:10.1021/ct500443v
Sharma M, Predeus AV, Kovacs N, Feig M. “Differential mismatch recognition specificities of eukaryotic MutS homologs, MutSα and MutSβ.” Biophys J. (2014) Jun 3;106(11):2483-92. doi:10.1016/j.bpj.2014.04.026
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. (2014) Oct;82(10):2429-42. doi:10.1002/prot.24607
Taylor KA, Feig M, Brooks CL 3rd, Fagnant PM, Lowey S, Trybus KM. “Role of the essential light chain in the activation of smooth muscle myosin by regulatory light chain phosphorylation.” J Struct Biol. (2014) Mar;185(3):375-82. doi:10.1016/j.jsb.2013.12.008
Feig M, Sugita Y. “Reaching new levels of realism in modeling biological macromolecules in cellular environments.” J Mol Graph Model. (2013) Sep;45:144-56. doi:10.1016/j.jmgm.2013.08.017
Kar P, Gopal SM, Cheng YM, Predeus A, Feig M. “PRIMO: A Transferable Coarse-grained Force Field for Proteins.” J Chem Theory Comput. (2013) Aug 13;9(8):3769-3788. doi:10.1021/ct400230y