Published in Biophys J on March 23, 2007
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
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
Predicting bioactive conformations and binding modes of macrocycles. J Comput Aided Mol Des (2016) 0.77
Molecular cloning of a functional thrombin receptor reveals a novel proteolytic mechanism of receptor activation. Cell (1991) 11.51
The coagulation cascade: initiation, maintenance, and regulation. Biochemistry (1991) 6.29
Free energy via molecular simulation: applications to chemical and biomolecular systems. Annu Rev Biophys Biophys Chem (1989) 5.23
The refined 1.9 A crystal structure of human alpha-thrombin: interaction with D-Phe-Pro-Arg chloromethylketone and significance of the Tyr-Pro-Pro-Trp insertion segment. EMBO J (1989) 4.49
Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. J Mol Biol (2003) 3.89
Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf. J Comput Chem (2004) 3.12
Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA. J Am Chem Soc (2001) 2.55
Beyond the benzene dimer: an investigation of the additivity of pi-pi interactions. J Phys Chem A (2005) 1.45
Continuum solvent studies of the stability of RNA hairpin loops and helices. J Biomol Struct Dyn (1998) 1.43
Evaluating the molecular mechanics poisson-boltzmann surface area free energy method using a congeneric series of ligands to p38 MAP kinase. J Med Chem (2005) 1.37
Thrombin-induced chemotaxis and aggregation of neutrophils. J Cell Physiol (1986) 1.28
Binding affinities for sulfonamide inhibitors with human thrombin using Monte Carlo simulations with a linear response method. J Med Chem (1997) 1.16
Thrombin structure and function: why thrombin is the primary target for antithrombotics. Blood Coagul Fibrinolysis (1991) 1.15
In-depth study of tripeptide-based alpha-ketoheterocycles as inhibitors of thrombin. Effective utilization of the S1' subsite and its implications to structure-based drug design. J Med Chem (2005) 1.12
Design and synthesis of a series of potent and orally bioavailable noncovalent thrombin inhibitors that utilize nonbasic groups in the P1 position. J Med Chem (1998) 1.08
A new quantum method for electrostatic solvation energy of protein. J Chem Phys (2006) 0.92
Discovery and evaluation of potent P1 aryl heterocycle-based thrombin inhibitors. J Med Chem (2004) 0.91
Thrombotic complications of antithrombotic therapy: a paradox with implications for clinical practice. Ann Intern Med (1997) 0.87
Quantum mechanical map for protein-ligand binding with application to beta-trypsin/benzamidine complex. J Chem Phys (2004) 0.86
Statistical molecular design, parallel synthesis, and biological evaluation of a library of thrombin inhibitors. J Med Chem (2001) 0.86
Quantum computational analysis for drug resistance of HIV-1 reverse transcriptase to nevirapine through point mutations. Proteins (2005) 0.85
Design and synthesis of potent and selective macrocyclic thrombin inhibitors. Bioorg Med Chem Lett (2003) 0.84
Correlation of binding affinities with non-bonded interaction energies of thrombin-inhibitor complexes. Acta Crystallogr D Biol Crystallogr (1995) 0.83
Estimation of binding affinities for selective thrombin inhibitors via Monte Carlo simulations. J Med Chem (2001) 0.82
Fractionation of peptide with disulfide bond for quantum mechanical calculation of interaction energy with molecules. J Chem Phys (2004) 0.81
Synthesis and SAR of thrombin inhibitors incorporating a novel 4-amino-morpholinone sscaffold: analysis of X-ray crystal structure of enzyme inhibitor complex. J Med Chem (2003) 0.80
Synthesis of novel thrombin inhibitors. Use of ring-closing metathesis reactions for synthesis of P2 cyclopentene- and cyclohexenedicarboxylic acid derivatives. J Med Chem (2003) 0.80
Quantum study of mutational effect in binding of efavirenz to HIV-1 RT. Proteins (2005) 0.80
Design of highly potent noncovalent thrombin inhibitors that utilize a novel lipophilic binding pocket in the thrombin active site. J Med Chem (1997) 0.80
Functionality map analysis of the active site cleft of human thrombin. J Comput Aided Mol Des (1996) 0.79
Global dynamics and transition state theories: Comparative study of reaction rate constants for gas-phase chemical reactions. J Comput Chem (2009) 1.16
Electrostatic polarization makes a substantial contribution to the free energy of avidin-biotin binding. J Am Chem Soc (2010) 1.10
Developing polarized protein-specific charges for protein dynamics: MD free energy calculation of pKa shifts for Asp26/Asp20 in thioredoxin. Biophys J (2008) 1.07
Selectivity of neutral/weakly basic P1 group inhibitors of thrombin and trypsin by a molecular dynamics study. Chemistry (2008) 0.93
Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation. Phys Chem Chem Phys (2012) 0.92
A new quantum method for electrostatic solvation energy of protein. J Chem Phys (2006) 0.92
Folding of a helix at room temperature is critically aided by electrostatic polarization of intraprotein hydrogen bonds. J Am Chem Soc (2010) 0.90
An efficient approach for ab initio energy calculation of biopolymers. J Chem Phys (2005) 0.86
Quantum mechanical map for protein-ligand binding with application to beta-trypsin/benzamidine complex. J Chem Phys (2004) 0.86
Fully quantum mechanical energy optimization for protein-ligand structure. J Comput Chem (2004) 0.86
Quantum computational analysis for drug resistance of HIV-1 reverse transcriptase to nevirapine through point mutations. Proteins (2005) 0.85
Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4. J Comput Aided Mol Des (2014) 0.85
Simulation of NMR data reveals that proteins' local structures are stabilized by electronic polarization. J Am Chem Soc (2009) 0.85
A numerically stable restrained electrostatic potential charge fitting method. J Comput Chem (2012) 0.84
Electronic polarization is important in stabilizing the native structures of proteins. J Phys Chem B (2009) 0.84
A new method for direct calculation of total energy of protein. J Chem Phys (2005) 0.84
Polarization of intraprotein hydrogen bond is critical to thermal stability of short helix. J Phys Chem B (2011) 0.83
Efficient bond function basis set for pi-pi interaction energies. J Comput Chem (2008) 0.82
Insights on Na(+) binding and conformational dynamics in multidrug and toxic compound extrusion transporter NorM. Proteins (2013) 0.82
Intra-protein hydrogen bonding is dynamically stabilized by electronic polarization. J Chem Phys (2009) 0.82
Some practical approaches to treating electrostatic polarization of proteins. Acc Chem Res (2014) 0.82
Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies. J Phys Chem A (2014) 0.82
New method for direct linear-scaling calculation of electron density of proteins. J Phys Chem A (2005) 0.81
Discovery and characterization of novel, potent, and selective cytochrome P450 2J2 inhibitors. Drug Metab Dispos (2012) 0.81
Nonadiabatic effects in the H+D2 reaction. J Chem Phys (2006) 0.81
Folding dynamics of a small protein at room temperature via simulated coherent two-dimensional infrared spectroscopy. Phys Chem Chem Phys (2010) 0.81
Molecular dynamic simulation of the Kv1.2 voltage-gated potassium channel in open and closed state conformations. J Phys Chem B (2008) 0.80
Class I phospho-inositide-3-kinases (PI3Ks) isoform-specific inhibition study by the combination of docking and molecular dynamics simulation. J Chem Inf Model (2010) 0.80
The F130L mutation in streptavidin reduces its binding affinity to biotin through electronic polarization effect. J Comput Chem (2013) 0.80
Energy and electron transfer in beta-alkynyl-linked porphyrin-[60]fullerene dyads. J Phys Chem B (2006) 0.80
Understanding the molecular mechanism of enzyme dynamics of ribonuclease A through protonation/deprotonation of HIS48. J Am Chem Soc (2011) 0.80
Acidic pH retards the fibrillization of human Islet Amyloid Polypeptide due to electrostatic repulsion of histidines. J Chem Phys (2013) 0.80
Quantum mechanical studies of residue-specific hydrophobic interactions in p53-MDM2 binding. J Phys Chem B (2008) 0.80
Electrostatic polarization is critical for the strong binding in streptavidin-biotin system. J Comput Chem (2012) 0.79
Quantum study of HIV-1 protease-bridge water interaction. J Chem Phys (2007) 0.79
Effect of strong electric field on the conformational integrity of insulin. J Phys Chem A (2014) 0.79
Improving the scoring of protein-ligand binding affinity by including the effects of structural water and electronic polarization. J Chem Inf Model (2013) 0.79
NMR scalar coupling constant reveals that intraprotein hydrogen bonds are dynamically stabilized by electronic polarization. J Phys Chem B (2009) 0.79
Selective binding of antiinfluenza drugs and their analogues to 'open' and 'closed' conformations of H5N1 neuraminidase. J Phys Chem B (2010) 0.79
Solvent effect on the folding dynamics and structure of E6-associated protein characterized from ab initio protein folding simulations. J Chem Phys (2012) 0.79
Dynamical stability and assembly cooperativity of β-sheet amyloid oligomers--effect of polarization. J Phys Chem B (2012) 0.78
Protein's electronic polarization contributes significantly to its catalytic function. J Chem Phys (2011) 0.78
A coupled two-dimensional main chain torsional potential for protein dynamics: generation and implementation. J Mol Model (2013) 0.78
Folding of a helix is critically stabilized by polarization of backbone hydrogen bonds: study in explicit water. J Phys Chem B (2012) 0.78
Effect of interprotein polarization on protein-protein binding energy. J Comput Chem (2012) 0.78
Structure and dynamics of a dizinc metalloprotein: effect of charge transfer and polarization. J Phys Chem B (2011) 0.78
Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method. Adv Exp Med Biol (2015) 0.78
Ab initio QM/MM free energy simulations of peptide bond formation in the ribosome support an eight-membered ring reaction mechanism. J Am Chem Soc (2012) 0.78
The critical effect of polarization on the dynamical structure of guanine quadruplex DNA. Phys Chem Chem Phys (2013) 0.78
Assessing the accuracy of the general AMBER force field for 2,2,2-trifluoroethanol as solvent. J Mol Model (2013) 0.77
Fragment quantum mechanical calculation of proteins and its applications. Acc Chem Res (2014) 0.77
An implementation of hydrophobic force in implicit solvent molecular dynamics simulation for packed proteins. J Mol Model (2013) 0.77
Accessing the applicability of polarized protein-specific charge in linear interaction energy analysis. J Comput Chem (2014) 0.77
Theoretical method for full ab initio calculation of DNA/RNA-ligand interaction energy. J Chem Phys (2004) 0.77
Molecular dynamics simulation and computational two-dimensional infrared spectroscopic study of model amyloid β-peptide oligomers. J Phys Chem A (2013) 0.77
Communication: The electrostatic polarization is essential to differentiate the helical propensity in polyalanine mutants. J Chem Phys (2011) 0.77
Predicting mutation-induced Stark shifts in the active site of a protein with a polarized force field. J Phys Chem A (2013) 0.77
Purification of untagged HIV-1 reverse transcriptase by affinity chromatography. Protein Expr Purif (2010) 0.77
Patterns of brain activity distinguishing free and forced actions: contribution from sensory cortices. Front Integr Neurosci (2012) 0.77
Electronic polarization stabilizes tertiary structure prediction of HP-36. J Mol Model (2014) 0.77
Quantifying the stabilizing energy of the intraprotein hydrogen bond due to local mutation. J Phys Chem B (2011) 0.77
Molecular dynamics simulation study on the molecular structures of the amylin fibril models. J Phys Chem B (2012) 0.77
Electrostatically embedded generalized molecular fractionation with conjugate caps method for full quantum mechanical calculation of protein energy. J Phys Chem A (2013) 0.77
Beyond QM/MM: fragment quantum mechanical methods. Acc Chem Res (2014) 0.76
Combined effect of confinement and affinity of crowded environment on conformation switching of adenylate kinase. J Mol Model (2014) 0.76
An improved fragment-based quantum mechanical method for calculation of electrostatic solvation energy of proteins. J Chem Phys (2013) 0.76
Dynamical binding of hydrogen-bond surrogate derived Bak helices to antiapoptotic protein Bcl-xL. J Phys Chem B (2009) 0.76
Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations. Phys Chem Chem Phys (2014) 0.76
Replica exchange molecular dynamics simulation of structure variation from α/4β-fold to 3α-fold protein. J Mol Model (2011) 0.76
Communications: Electron polarization critically stabilizes the Mg2+ complex in the catalytic core domain of HIV-1 integrase. J Chem Phys (2010) 0.76
The generalized molecular fractionation with conjugate caps/molecular mechanics method for direct calculation of protein energy. J Chem Phys (2006) 0.76
pH-dependent conformational ensemble and polymorphism of amyloid-β core fragment. J Phys Chem B (2013) 0.76
Novel theoretically designed HIV-1 non-nucleoside reverse transcriptase inhibitors derived from nevirapine. J Mol Model (2014) 0.75
Development of an effective polarizable bond method for biomolecular simulation. J Phys Chem B (2013) 0.75
Effect of self-assembly of fullerene nano-particles on lipid membrane. PLoS One (2013) 0.75
Exploring the molecular mechanism of stabilization of the adhesion domains of human CD2 by N-glycosylation. J Phys Chem B (2012) 0.75
Molecular dynamics study of DNA binding by INT-DBD under a polarized force field. J Comput Chem (2013) 0.75
Quantum scattering calculation of the O(1D)+HBr reaction. J Chem Phys (2004) 0.75