Published in J Comput Chem on November 15, 2006
Dynamical networks in tRNA:protein complexes. Proc Natl Acad Sci U S A (2009) 2.31
New insights on the mechanism of the K(+-) independent activity of crenarchaeota pyruvate kinases. PLoS One (2015) 1.39
Dynamics of Recognition between tRNA and elongation factor Tu. J Mol Biol (2008) 1.32
Wordom: a user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces. J Comput Chem (2010) 1.31
Exploring residue component contributions to dynamical network models of allostery. J Chem Theory Comput (2012) 1.11
Insights into diterpene cyclization from structure of bifunctional abietadiene synthase from Abies grandis. J Biol Chem (2012) 1.09
Computational modeling of allosteric communication reveals organizing principles of mutation-induced signaling in ABL and EGFR kinases. PLoS Comput Biol (2011) 1.06
Gromita: a fully integrated graphical user interface to gromacs 4. Bioinform Biol Insights (2009) 1.04
NetworkView: 3D display and analysis of protein·RNA interaction networks. Bioinformatics (2012) 0.99
Signaling mechanisms of LOV domains: new insights from molecular dynamics studies. Photochem Photobiol Sci (2013) 0.98
Weighted Implementation of Suboptimal Paths (WISP): An Optimized Algorithm and Tool for Dynamical Network Analysis. J Chem Theory Comput (2014) 0.97
Atomic-level characterization of the activation mechanism of SERCA by calcium. PLoS One (2011) 0.94
Spontaneous Inward Opening of the Dopamine Transporter Is Triggered by PIP2-Regulated Dynamics of the N-Terminus. ACS Chem Neurosci (2015) 0.91
NbIT--a new information theory-based analysis of allosteric mechanisms reveals residues that underlie function in the leucine transporter LeuT. PLoS Comput Biol (2014) 0.91
Exit strategies for charged tRNA from GluRS. J Mol Biol (2010) 0.89
Atomistic insights into regulatory mechanisms of the HER2 tyrosine kinase domain: a molecular dynamics study. Biophys J (2009) 0.89
DNA-recognition process described by MD simulations of the lactose repressor protein on a specific and a non-specific DNA sequence. Nucleic Acids Res (2013) 0.88
A multiscale modeling approach to investigate molecular mechanisms of pseudokinase activation and drug resistance in the HER3/ErbB3 receptor tyrosine kinase signaling network. Mol Biosyst (2011) 0.88
A mechanistic understanding of allosteric immune escape pathways in the HIV-1 envelope glycoprotein. PLoS Comput Biol (2013) 0.88
A functional selectivity mechanism at the serotonin-2A GPCR involves ligand-dependent conformations of intracellular loop 2. J Am Chem Soc (2014) 0.86
Multiple templates-based homology modeling enhances structure quality of AT1 receptor: validation by molecular dynamics and antagonist docking. J Mol Model (2010) 0.86
Functional implications of multistage copper binding to the prion protein. Proc Natl Acad Sci U S A (2009) 0.86
Computational modeling of allosteric regulation in the hsp90 chaperones: a statistical ensemble analysis of protein structure networks and allosteric communications. PLoS Comput Biol (2014) 0.85
Probing molecular mechanisms of the Hsp90 chaperone: biophysical modeling identifies key regulators of functional dynamics. PLoS One (2012) 0.85
Interplay of flavin's redox states and protein dynamics: an insight from QM/MM simulations of dihydronicotinamide riboside quinone oxidoreductase 2. J Phys Chem B (2011) 0.84
Elucidating the role of disulfide bond on amyloid formation and fibril reversibility of somatostatin-14: relevance to its storage and secretion. J Biol Chem (2014) 0.83
Three force fields' views of the 3(10) helix. Biophys J (2011) 0.83
Structural basis of PROTAC cooperative recognition for selective protein degradation. Nat Chem Biol (2017) 0.83
Identification of calcium binding sites on calsequestrin 1 and their implications for polymerization. Mol Biosyst (2013) 0.82
Peptide inhibitors disrupt the serotonin 5-HT2C receptor interaction with phosphatase and tensin homolog to allosterically modulate cellular signaling and behavior. J Neurosci (2013) 0.81
Multiple pathways promote dynamical coupling between catalytic domains in Escherichia coli prolyl-tRNA synthetase. Biochemistry (2013) 0.81
Molecular-dynamics simulations of insertion of chemically modified DNA nanostructures into a water-chloroform interface. Biophys J (2008) 0.81
Modeling and molecular dynamics of the intrinsically disordered e7 proteins from high- and low-risk types of human papillomavirus. J Mol Model (2013) 0.81
Atomic-level mechanisms for phospholamban regulation of the calcium pump. Biophys J (2015) 0.81
Space warping order parameters and symmetry: application to multiscale simulation of macromolecular assemblies. J Phys Chem B (2012) 0.81
Structural and dynamical insights on HLA-DR2 complexes that confer susceptibility to multiple sclerosis in Sardinia: a molecular dynamics simulation study. PLoS One (2013) 0.81
Exploration of the valproic acid binding site on histone deacetylase 8 using docking and molecular dynamic simulations. J Mol Model (2011) 0.80
Effect of oxidatively damaged DNA on the active site preorganization during nucleotide incorporation in a high fidelity polymerase from Bacillus stearothermophilus. Proteins (2008) 0.80
Cooperative DNA Recognition Modulated by an Interplay between Protein-Protein Interactions and DNA-Mediated Allostery. PLoS Comput Biol (2015) 0.79
Role of coupled dynamics in the catalytic activity of prokaryotic-like prolyl-tRNA synthetases. Biochemistry (2012) 0.79
Structure-functional prediction and analysis of cancer mutation effects in protein kinases. Comput Math Methods Med (2014) 0.79
Interdomain salt-bridges in the Ebola virus protein VP40 and their role in domain association and plasma membrane localization. Protein Sci (2016) 0.79
On the modularity of the intrinsic flexibility of the µ opioid receptor: a computational study. PLoS One (2014) 0.78
Order through disorder: hyper-mobile C-terminal residues stabilize the folded state of a helical peptide. a molecular dynamics study. PLoS One (2010) 0.78
A conserved P-loop anchor limits the structural dynamics that mediate nucleotide dissociation in EF-Tu. Sci Rep (2015) 0.78
Allosteric cross-talk in chromatin can mediate drug-drug synergy. Nat Commun (2017) 0.78
Investigating Molecular Mechanisms of Activation and Mutation of the HER2 Receptor Tyrosine Kinase through Computational Modeling and Simulation. Cancer Res J (2011) 0.77
In silico and in vitro studies to elucidate the role of Cu2+ and galanthamine as the limiting step in the amyloid beta (1-42) fibrillation process. Protein Sci (2013) 0.77
Unexpected Allosteric Network Contributes to LRH-1 Co-regulator Selectivity. J Biol Chem (2015) 0.77
Histidine 114 Is Critical for ATP Hydrolysis by the Universally Conserved ATPase YchF. J Biol Chem (2015) 0.77
Cross dimerization of amyloid-β and αsynuclein proteins in aqueous environment: a molecular dynamics simulations study. PLoS One (2014) 0.77
Molecular modeling of ErbB4/HER4 kinase in the context of the HER4 signaling network helps rationalize the effects of clinically identified HER4 somatic mutations on the cell phenotype. Biotechnol J (2013) 0.77
Characterizing a partially ordered miniprotein through folding molecular dynamics simulations: Comparison with the experimental data. Protein Sci (2015) 0.77
Break CDK2/Cyclin E1 interface allosterically with small peptides. PLoS One (2014) 0.77
Long-Range Signaling in MutS and MSH Homologs via Switching of Dynamic Communication Pathways. PLoS Comput Biol (2016) 0.76
Molecular modeling studies demonstrate key mutations that could affect the ligand recognition by influenza AH1N1 neuraminidase. J Mol Model (2015) 0.76
Probing the global and local dynamics of aminoacyl-tRNA synthetases using all-atom and coarse-grained simulations. J Mol Model (2014) 0.76
Contributions of Charged Residues in Structurally Dynamic Capsid Surface Loops to Rous Sarcoma Virus Assembly. J Virol (2016) 0.76
Structure and dynamics analysis on plexin-B1 Rho GTPase binding domain as a monomer and dimer. J Phys Chem B (2014) 0.76
Lightweight object oriented structure analysis: tools for building tools to analyze molecular dynamics simulations. J Comput Chem (2014) 0.76
A disulfide linked model of the complement protein C8gamma complexed with C8alpha indel peptide. J Mol Model (2008) 0.76
Molecular dynamics simulations and structure-based network analysis reveal structural and functional aspects of G-protein coupled receptor dimer interactions. J Comput Aided Mol Des (2016) 0.75
Biophysical studies of cholesterol effects on chromatin. J Lipid Res (2017) 0.75
New open conformation of SMYD3 implicates conformational selection and allostery. AIMS Biophys (2016) 0.75
Conserved residues of the Pro103-Arg115 loop are involved in triggering the allosteric response of the Escherichia coli ADP-glucose pyrophosphorylase. Protein Sci (2015) 0.75
Dynamical footprint of cross-reactivity in a human autoimmune T-cell receptor. Sci Rep (2017) 0.75
Distance-Based Configurational Entropy of Proteins from Molecular Dynamics Simulations. PLoS One (2015) 0.75
Molecular Dynamics Simulation Reveals Correlated Inter-Lobe Motion in Protein Lysine Methyltransferase SMYD2. PLoS One (2015) 0.75
The C-terminal Helix of Pseudomonas aeruginosa Elongation Factor Ts Tunes EF-Tu Dynamics to Modulate Nucleotide Exchange. J Biol Chem (2016) 0.75
Predicted 3D Model of the Rabies Virus Glycoprotein Trimer. Biomed Res Int (2016) 0.75
Multiple steps to activate FAK's kinase domain: adaptation to confined environments? Biophys J (2013) 0.75
Allosteric control of antibody-prion recognition through oxidation of a disulfide bond between the CH and CL chains. Protein Eng Des Sel (2016) 0.75
C(α) torsion angles as a flexible criterion to extract secrets from a molecular dynamics simulation. J Mol Model (2014) 0.75
Homology modeling and molecular dynamics simulations of MUC1-9/H-2K(b) complex suggest novel binding interactions. J Mol Model (2010) 0.75
A theoretical study of the unfolding pathway of reduced human serum albumin. J Mol Model (2015) 0.75
Multiscale design of coarse-grained elastic network-based potentials for the μ opioid receptor. J Mol Model (2016) 0.75
Mechanism of mRNA-STAR domain interaction: Molecular dynamics simulations of Mammalian Quaking STAR protein. Sci Rep (2017) 0.75
Mapping the intrinsically disordered properties of the flexible loop domain of Bcl-2: a molecular dynamics simulation study. J Mol Model (2016) 0.75