PubRank

Michael Feig

Author PubWeight™ 84.66‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem 2004 17.97
2 Improved treatment of the protein backbone in empirical force fields. J Am Chem Soc 2004 5.96
3 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. J Chem Theory Comput 2012 5.57
4 New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations. J Comput Chem 2003 3.81
5 An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins. Biophys J 2003 2.91
6 Solvation and hydration of proteins and nucleic acids: a theoretical view of simulation and experiment. Acc Chem Res 2002 1.69
7 Highly accurate biomolecular electrostatics in continuum dielectric environments. J Comput Chem 2008 1.66
8 A generalized Born formalism for heterogeneous dielectric environments: application to the implicit modeling of biological membranes. J Chem Phys 2005 1.56
9 A distinct type of glycerol-3-phosphate acyltransferase with sn-2 preference and phosphatase activity producing 2-monoacylglycerol. Proc Natl Acad Sci U S A 2010 1.55
10 Dynamic error correction and regulation of downstream bubble opening by human RNA polymerase II. Mol Cell 2005 1.43
11 Evolution and physics in comparative protein structure modeling. Acc Chem Res 2002 1.29
12 Physics-based protein structure refinement through multiple molecular dynamics trajectories and structure averaging. Proteins 2013 1.20
13 The requirement for mechanical coupling between head and S2 domains in smooth muscle myosin ATPase regulation and its implications for dimeric motor function. J Mol Biol 2005 1.17
14 Balancing an accurate representation of the molecular surface in generalized born formalisms with integrator stability in molecular dynamics simulations. J Comput Chem 2006 1.16
15 Implicit solvent simulations of DNA and DNA-protein complexes: agreement with explicit solvent vs experiment. J Phys Chem B 2006 1.16
16 Reduced native state stability in crowded cellular environment due to protein-protein interactions. J Am Chem Soc 2013 1.13
17 Inclusion of many-body effects in the additive CHARMM protein CMAP potential results in enhanced cooperativity of α-helix and β-hairpin formation. Biophys J 2012 1.12
18 NTP-driven translocation and regulation of downstream template opening by multi-subunit RNA polymerases. Biochem Cell Biol 2005 1.11
19 Aberrant activity of the DNA repair enzyme AlkB. J Inorg Biochem 2004 1.10
20 Protein crowding affects hydration structure and dynamics. J Am Chem Soc 2012 1.08
21 Molecular dynamics simulations of large integral membrane proteins with an implicit membrane model. J Phys Chem B 2006 1.07
22 Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase. Biochim Biophys Acta 2010 1.06
23 Conformational sampling of peptides in cellular environments. Biophys J 2007 1.04
24 Conformational sampling of peptides in the presence of protein crowders from AA/CG-multiscale simulations. J Phys Chem B 2012 1.01
25 Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors. J Comput Chem 2008 1.00
26 Deciphering the mismatch recognition cycle in MutS and MSH2-MSH6 using normal-mode analysis. Biophys J 2009 1.00
27 Protein Structure Refinement through Structure Selection and Averaging from Molecular Dynamics Ensembles. J Chem Theory Comput 2012 1.00
28 PRIMO/PRIMONA: a coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy. Proteins 2010 0.99
29 Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions. J Comput Chem 2008 0.96
30 Energetic and structural details of the trigger-loop closing transition in RNA polymerase II. Biophys J 2013 0.95
31 Synthetic curcuminoids modulate the arachidonic acid metabolism of human platelet 12-lipoxygenase and reduce sprout formation of human endothelial cells. Mol Cancer Ther 2006 0.95
32 Purification and characterization of the FeII- and alpha-ketoglutarate-dependent xanthine hydroxylase from Aspergillus nidulans. Biochemistry 2007 0.93
33 A correlation-based method for the enhancement of scoring functions on funnel-shaped energy landscapes. Proteins 2006 0.93
34 Conformational sampling of influenza fusion peptide in membrane bilayers as a function of termini and protonation states. J Phys Chem B 2010 0.93
35 PRIMO: A Transferable Coarse-grained Force Field for Proteins. J Chem Theory Comput 2013 0.91
36 Dynamic Heterogeneous Dielectric Generalized Born (DHDGB): An implicit membrane model with a dynamically varying bilayer thickness. J Chem Theory Comput 2013 0.90
37 The unorthodox SNAP50 zinc finger domain contributes to cooperative promoter recognition by human SNAPC. J Biol Chem 2006 0.90
38 Conformational change in MSH2-MSH6 upon binding DNA coupled to ATPase activity. Biophys J 2009 0.89
39 Effect of membrane thickness on conformational sampling of phospholamban from computer simulations. Biophys J 2010 0.89
40 DNA bending propensity in the presence of base mismatches: implications for DNA repair. J Phys Chem B 2013 0.88
41 Sampling of near-native protein conformations during protein structure refinement using a coarse-grained model, normal modes, and molecular dynamics simulations. Proteins 2008 0.87
42 Evidence that the Bacillus subtilis SpoIIGA protein is a novel type of signal-transducing aspartic protease. J Biol Chem 2008 0.86
43 Base-flipping mechanism in postmismatch recognition by MutS. Biophys J 2011 0.86
44 Role of conformational sampling of Ser16 and Thr17-phosphorylated phospholamban in interactions with SERCA. Biochim Biophys Acta 2012 0.83
45 Scoring confidence index: statistical evaluation of ligand binding mode predictions. J Comput Aided Mol Des 2009 0.83
46 Computational simulation strategies for analysis of multisubunit RNA polymerases. Chem Rev 2013 0.82
47 Structural basis for the enantiospecificities of R- and S-specific phenoxypropionate/alpha-ketoglutarate dioxygenases. Protein Sci 2006 0.80
48 Effect of flanking residues on the conformational sampling of the internal fusion peptide from Ebola virus. Proteins 2011 0.79
49 Molecular mechanism by which palmitate inhibits PKR autophosphorylation. Biochemistry 2011 0.79
50 Density-biased sampling: a robust computational method for studying pore formation in membranes. J Chem Theory Comput 2015 0.78
51 Conformational preferences of DNA in reduced dielectric environments. J Phys Chem B 2014 0.77
52 Substrate specificity of SpoIIGA, a signal-transducing aspartic protease in Bacilli. J Biochem 2011 0.76
53 Molecular dynamics trajectory compression with a coarse-grained model. IEEE/ACM Trans Comput Biol Bioinform 2011 0.76
54 Intrinsic Base-Pair Rearrangement in the Hairpin Ribozyme Directs RNA Conformational Sampling and Tertiary Interface Formation. J Phys Chem B 2016 0.76
55 Interionic hydration structures of NaCl in aqueous solution: a combined study of quantum mechanical cluster calculations and QM/EFP-MD simulations. J Phys Chem B 2012 0.75
56 Interactions of amino acid side-chain analogs within membrane environments. J Phys Chem B 2015 0.75
57 Binding site multiplicity with fatty acid ligands: implications for the regulation of PKR kinase autophosphorylation with palmitate. Proteins 2014 0.75
58 Solvent electronic polarization effects on Na(+)-Na(+) and Cl(-)-Cl(-) pair associations in aqueous solution. J Phys Chem B 2013 0.75
59 Crowding in Cellular Environments at an Atomistic Level from Computer Simulations. J Phys Chem B 2017 0.75
60 Thermodynamics of Macromolecular Association in Heterogeneous Crowding Environments: Theoretical and Simulation Studies with a Simplified Model. J Phys Chem B 2016 0.75