Published in J Am Chem Soc on June 06, 2001
Functional, biophysical, and structural bases for antibacterial activity of tigecycline. Antimicrob Agents Chemother (2006) 1.60
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Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential. J Comput Chem (2009) 1.46
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Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition. Q Rev Biophys (2011) 1.12
Diarylaniline derivatives as a distinct class of HIV-1 non-nucleoside reverse transcriptase inhibitors. J Med Chem (2010) 1.06
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Design, synthesis, biochemical studies, cellular characterization, and structure-based computational studies of small molecules targeting the urokinase receptor. Bioorg Med Chem (2012) 1.01
Cellular interaction through LewisX cluster: theoretical studies. J Mol Model (2008) 0.99
Simulation of the interaction between ScyTx and small conductance calcium-activated potassium channel by docking and MM-PBSA. Biophys J (2004) 0.98
Insights into subunit interactions in the heterotetrameric structure of potato ADP-glucose pyrophosphorylase. Biophys J (2008) 0.97
Scoring and lessons learned with the CSAR benchmark using an improved iterative knowledge-based scoring function. J Chem Inf Model (2011) 0.96
Blockade of neuronal α7-nAChR by α-conotoxin ImI explained by computational scanning and energy calculations. PLoS Comput Biol (2011) 0.96
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Structural insight into the role of thrombospondin-1 binding to calreticulin in calreticulin-induced focal adhesion disassembly. Biochemistry (2010) 0.95
Differential effects of genistein on prostate cancer cells depend on mutational status of the androgen receptor. PLoS One (2013) 0.94
Alanine zipper-like coiled-coil domains are necessary for homotypic dimerization of plant GAGA-factors in the nucleus and nucleolus. PLoS One (2011) 0.93
Molecular modeling to provide insight into the substrate binding and catalytic mechanism of human biliverdin-IXα reductase. J Phys Chem B (2012) 0.93
Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors. J Comput Aided Mol Des (2003) 0.90
Simulating structural and thermodynamic properties of carcinogen-damaged DNA. Biophys J (2003) 0.89
Interaction of I50V mutant and I50L/A71V double mutant HIV-protease with inhibitor TMC114 (darunavir): molecular dynamics simulation and binding free energy studies. J Phys Chem B (2012) 0.89
An improved method to predict the entropy term with the MM/PBSA approach. J Comput Aided Mol Des (2008) 0.88
Validating CHARMM parameters and exploring charge distribution rules in structure-based drug design. J Chem Theory Comput (2009) 0.88
In-silico screening using flexible ligand binding pockets: a molecular dynamics-based approach. J Comput Aided Mol Des (2005) 0.88
Computational studies of difference in binding modes of peptide and non-peptide inhibitors to MDM2/MDMX based on molecular dynamics simulations. Int J Mol Sci (2012) 0.88
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Molecular determinants of epidermal growth factor binding: a molecular dynamics study. PLoS One (2013) 0.88
Energetic basis for drug resistance of HIV-1 protease mutants against amprenavir. J Comput Aided Mol Des (2012) 0.88
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Contributions of stacking, preorganization, and hydrogen bonding to the thermodynamic stability of duplexes between RNA and 2'-O-methyl RNA with locked nucleic acids. Biochemistry (2009) 0.88
Fragment-based drug discovery using a multidomain, parallel MD-MM/PBSA screening protocol. J Chem Inf Model (2013) 0.87
Understanding microscopic binding of human microsomal prostaglandin E synthase-1 (mPGES-1) trimer with substrate PGH2 and cofactor GSH: insights from computational alanine scanning and site-directed mutagenesis. J Phys Chem B (2010) 0.87
PHOENIX: a scoring function for affinity prediction derived using high-resolution crystal structures and calorimetry measurements. J Chem Inf Model (2011) 0.87
Unveiling the gating mechanism of ECF transporter RibU. Sci Rep (2013) 0.87
Identification of high affinity fatty acid binding sites on human serum albumin by MM-PBSA method. Biophys J (2007) 0.87
Insights into the functional role of protonation states in the HIV-1 protease-BEA369 complex: molecular dynamics simulations and free energy calculations. J Mol Model (2009) 0.86
Revealing origin of decrease in potency of darunavir and amprenavir against HIV-2 relative to HIV-1 protease by molecular dynamics simulations. Sci Rep (2014) 0.86
Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches. J R Soc Interface (2011) 0.86
Molecular dynamics and free energy analysis of neuraminidase-ligand interactions. Protein Sci (2004) 0.86
Molecular recognition in a diverse set of protein-ligand interactions studied with molecular dynamics simulations and end-point free energy calculations. J Chem Inf Model (2013) 0.85
The molecular mechanism studies of chirality effect of PHA-739358 on Aurora kinase A by molecular dynamics simulation and free energy calculations. J Comput Aided Mol Des (2011) 0.85
An induced pocket for the binding of potent fusion inhibitor CL-385319 with H5N1 influenza virus hemagglutinin. PLoS One (2012) 0.84
Software and resources for computational medicinal chemistry. Future Med Chem (2011) 0.84
Functional asymmetry in the lysyl-tRNA synthetase explored by molecular dynamics, free energy calculations and experiment. BMC Struct Biol (2003) 0.84
Understanding the molecular mechanism of the broad and potent neutralization of HIV-1 by antibody VRC01 from the perspective of molecular dynamics simulation and binding free energy calculations. J Mol Model (2012) 0.83
Stereochemistry and position-dependent effects of carcinogens on TATA/TBP binding. Biophys J (2005) 0.83
A fluid salt-bridging cluster and the stabilization of p53. J Mol Biol (2007) 0.83
Mechanism of the difference in the binding affinity of E. coli tRNAGln to glutaminyl-tRNA synthetase caused by noninterface nucleotides in variable loop. Biophys J (2006) 0.83
Unique example of amyloid aggregates stabilized by main chain H-bond instead of the steric zipper: molecular dynamics study of the amyloidogenic segment of amylin wild-type and mutants. J Mol Model (2011) 0.83
Enantiomeric discrimination of chiral organic salts by chiral aza-15-crown-5 ether with C 1 symmetry: experimental and theoretical approaches. J Mol Model (2015) 0.82
A computational study of the open and closed forms of the N-lobe human serum transferrin apoprotein. Biophys J (2003) 0.82
Small molecule inhibitors of SHP2 tyrosine phosphatase discovered by virtual screening. Bioorg Med Chem Lett (2011) 0.82
Diamidine compounds for selective inhibition of protein arginine methyltransferase 1. J Med Chem (2014) 0.82
Insights into drug resistance of mutations D30N and I50V to HIV-1 protease inhibitor TMC-114: free energy calculation and molecular dynamic simulation. J Mol Model (2009) 0.82
Examining the Assumptions Underlying Continuum-Solvent Models. J Chem Theory Comput (2015) 0.81
Computational simulation of the docking of Prochlorothrix hollandica plastocyanin to potosystem I: modeling the electron transfer complex. Biophys J (2002) 0.81
In silico discovery of potential VEGFR-2 inhibitors from natural derivatives for anti-angiogenesis therapy. Int J Mol Sci (2014) 0.81
Energy landscape and dynamics of the beta-hairpin G peptide and its isomers: Topology and sequences. Protein Sci (2003) 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
Develop and test a solvent accessible surface area-based model in conformational entropy calculations. J Chem Inf Model (2012) 0.81
Computational analysis of the cathepsin B inhibitors activities through LR-MMPBSA binding affinity calculation based on docked complex. J Comput Chem (2009) 0.81
A computational and experimental approach to investigate bepridil binding with cardiac troponin. J Phys Chem B (2011) 0.81
Insights into Protein-Ligand Interactions: Mechanisms, Models, and Methods. Int J Mol Sci (2016) 0.81
Interaction of wild type, G68R and L125M isoforms of the arylamine-N-acetyltransferase from Mycobacterium tuberculosis with isoniazid: a computational study on a new possible mechanism of resistance. J Mol Model (2012) 0.80
Investigation on the mechanism for the binding and drug resistance of wild type and mutations of G86 residue in HIV-1 protease complexed with Darunavir by molecular dynamic simulation and free energy calculation. J Mol Model (2014) 0.80
Glycopeptide analogues of PSGL-1 inhibit P-selectin in vitro and in vivo. Nat Commun (2015) 0.80
Problems of robustness in Poisson-Boltzmann binding free energies. J Chem Theory Comput (2015) 0.80
Lumican Peptides: Rational Design Targeting ALK5/TGFBRI. Sci Rep (2017) 0.80
Thermodynamics and molecular dynamics simulations of calcium binding to the regulatory site of human cardiac troponin C: evidence for communication with the structural calcium binding sites. J Biol Inorg Chem (2012) 0.80
Computer-assisted combinatorial design of bicyclic thymidine analogs as inhibitors of Mycobacterium tuberculosis thymidine monophosphate kinase. J Comput Aided Mol Des (2010) 0.79
Flexible 5-guanidino-4-nitroimidazole DNA lesions: structures and thermodynamics. Biochemistry (2006) 0.79
Probing immobilization mechanism of alpha-chymotrypsin onto carbon nanotube in organic media by molecular dynamics simulation. Sci Rep (2015) 0.79
Binding modes of three inhibitors 8CA, F8A and I4A to A-FABP studied based on molecular dynamics simulation. PLoS One (2014) 0.79
Structure prediction and validation of the ERK8 kinase domain. PLoS One (2013) 0.79
Antitumor and modeling studies of a penetratin-peptide that targets E2F-1 in small cell lung cancer. Cancer Biol Ther (2013) 0.79
A transcriptional-switch model for Slr1738-controlled gene expression in the cyanobacterium Synechocystis. BMC Struct Biol (2012) 0.79
Receptor-ligand molecular docking. Biophys Rev (2013) 0.78
Implicit solvent methods for free energy estimation. Eur J Med Chem (2014) 0.78
Studies of chirality effect of 4-(phenylamino)-pyrrolo[2,1-f][1,2,4]triazine on p38alpha by molecular dynamics simulations and free energy calculations. J Comput Aided Mol Des (2009) 0.78
Revealing the favorable dissociation pathway of type II kinase inhibitors via enhanced sampling simulations and two-end-state calculations. Sci Rep (2015) 0.78
Recent Developments in Molecular Simulation Approaches to Study Spherical Virus Capsids. Mol Simul (2014) 0.78
Molecular dynamics studies of the 3D structure and planar ligand binding of a quadruplex dimer. J Mol Model (2010) 0.78
Implicit ligand theory: rigorous binding free energies and thermodynamic expectations from molecular docking. J Chem Phys (2012) 0.78
A computational study on thiourea analogs as potent MK-2 inhibitors. Int J Mol Sci (2012) 0.77
Probing Origin of Binding Difference of inhibitors to MDM2 and MDMX by Polarizable Molecular Dynamics Simulation and QM/MM-GBSA Calculation. Sci Rep (2015) 0.77
Molecular modeling to investigate the binding of Congo red toward GNNQQNY protofibril and in silico virtual screening for the identification of new aggregation inhibitors. J Mol Model (2012) 0.77
Insights into the structural function of the complex of HIV-1 protease with TMC-126: molecular dynamics simulations and free-energy calculations. J Mol Model (2011) 0.77
Identification of HIV inhibitors guided by free energy perturbation calculations. Curr Pharm Des (2012) 0.77
In silico identification of structure requirement for novel thiazole and oxazole derivatives as potent fructose 1,6-bisphosphatase inhibitors. Int J Mol Sci (2011) 0.77
Virtual ligand screening combined with NMR to identify Dvl PDZ domain inhibitors targeting the Wnt signaling. Methods Mol Biol (2012) 0.77
Quantum and molecular dynamics study for binding of macrocyclic inhibitors to human alpha-thrombin. Biophys J (2007) 0.77
Steered molecular dynamics approach for promising drugs for influenza A virus targeting M2 channel proteins. Eur Biophys J (2015) 0.77
Molecular docking of (5E)-3-(2-aminoethyl)-5-(2- thienylmethylene)-1, 3-thiazolidine-2, 4-dione on HIV-1 reverse transcriptase: novel drug acting on enzyme. Bioinformation (2012) 0.77
Binding of BIS like and other ligands with the GSK-3β kinase: a combined docking and MM-PBSA study. J Mol Model (2011) 0.77
Studying the mechanism that enables paullones to selectively inhibit glycogen synthase kinase 3 rather than cyclin-dependent kinase 5 by molecular dynamics simulations and free-energy calculations. J Mol Model (2010) 0.76
Comparison of radii sets, entropy, QM methods, and sampling on MM-PBSA, MM-GBSA, and QM/MM-GBSA ligand binding energies of F. tularensis enoyl-ACP reductase (FabI). J Comput Chem (2015) 0.76
Structural basis for decreased affinity of Emodin binding to Val66-mutated human CK2 alpha as determined by molecular dynamics. J Mol Model (2009) 0.76
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