Published in J Phys Chem B on May 18, 2007
Discovery of omecamtiv mecarbil the first, selective, small molecule activator of cardiac Myosin. ACS Med Chem Lett (2010) 0.93
Reaction pathways and free energy profiles for spontaneous hydrolysis of urea and tetramethylurea: unexpected substituent effects. Org Biomol Chem (2013) 0.80
Reaction Pathway and Free Energy Barrier for Urea Elimination in Aqueous Solution. Chem Phys Lett (2015) 0.75
The Amber biomolecular simulation programs. J Comput Chem (2005) 28.84
Large-scale validation of a quantum mechanics based scoring function: predicting the binding affinity and the binding mode of a diverse set of protein-ligand complexes. J Med Chem (2005) 1.42
Critical Assessment of the Performance of Density Functional Methods for Several Atomic and Molecular Properties. J Chem Theory Comput (2007) 1.42
Structural Survey of Zinc Containing Proteins and the Development of the Zinc AMBER Force Field (ZAFF). J Chem Theory Comput (2010) 1.37
Formal Estimation of Errors in Computed Absolute Interaction Energies of Protein-ligand Complexes. J Chem Theory Comput (2011) 1.32
Insights into the strength and origin of halogen bonding: the halobenzene-formaldehyde dimer. J Phys Chem A (2007) 1.28
Pose scoring by NMR. J Am Chem Soc (2004) 1.27
X-ray diffraction "fingerprinting" of DNA structure in solution for quantitative evaluation of molecular dynamics simulation. Proc Natl Acad Sci U S A (2006) 1.21
Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent. J Chem Theory Comput (2013) 1.16
A quantum mechanics-based scoring function: study of zinc ion-mediated ligand binding. J Am Chem Soc (2004) 1.15
Hybrid QM/MM and DFT investigations of the catalytic mechanism and inhibition of the dinuclear zinc metallo-beta-lactamase CcrA from Bacteroides fragilis. J Am Chem Soc (2005) 1.12
The energy computation paradox and ab initio protein folding. PLoS One (2011) 1.10
The role of quantum mechanics in structure-based drug design. Drug Discov Today (2007) 1.09
Prediction of aqueous solubility of a diverse set of compounds using quantitative structure-property relationships. J Med Chem (2003) 1.08
Can we separate active from inactive conformations? J Comput Aided Mol Des (2002) 1.06
Refinement of protein crystal structures using energy restraints derived from linear-scaling quantum mechanics. Acta Crystallogr D Biol Crystallogr (2005) 1.06
Further analysis and comparative study of intermolecular interactions using dimers from the S22 database. J Chem Phys (2009) 1.01
Understanding the substrate selectivity and the product regioselectivity of Orf2-catalyzed aromatic prenylations. Biochemistry (2007) 0.99
Assigning the protonation states of the key aspartates in β-Secretase using QM/MM X-ray structure refinement. J Chem Theory Comput (2006) 0.98
Solution structure of Mycobacterium tuberculosis NmtR in the apo state: insights into Ni(II)-mediated allostery. Biochemistry (2012) 0.97
Pairwise additivity of energy components in protein-ligand binding: the HIV II protease-Indinavir case. J Chem Phys (2011) 0.97
Assessment of the CCSD and CCSD(T) coupled-cluster methods in calculating heats of formation for Zn complexes. J Phys Chem A (2009) 0.97
Quantum mechanical and molecular dynamics simulations of ureases and Zn beta-lactamases. J Comput Chem (2006) 0.96
Assessment of density functional theory methods for the computation of heats of formation and ionization potentials of systems containing third row transition metals. J Phys Chem A (2007) 0.96
Protein NMR chemical shift calculations based on the automated fragmentation QM/MM approach. J Phys Chem B (2009) 0.95
The Effects of Computational Modeling Errors on the Estimation of Statistical Mechanical Variables. J Chem Theory Comput (2012) 0.95
The hydrolysis of urea and the proficiency of urease. J Am Chem Soc (2004) 0.94
Interaction energy decomposition in protein-protein association: a quantum mechanical study of barnase-barstar complex. Biophys Chem (2006) 0.93
Simulations of allosteric motions in the zinc sensor CzrA. J Am Chem Soc (2011) 0.93
Computational studies of the farnesyltransferase ternary complex part I: substrate binding. Biochemistry (2005) 0.93
Critical assessment of quantum mechanics based energy restraints in protein crystal structure refinement. Protein Sci (2006) 0.92
Quantum mechanics in structure-based drug design. Curr Opin Drug Discov Devel (2006) 0.91
Molecular recognition and drug-lead identification: what can molecular simulations tell us? Curr Med Chem (2010) 0.91
Catalytic mechanism of aromatic prenylation by NphB. Biochemistry (2012) 0.91
Insights into the structure and dynamics of the dinuclear zinc beta-lactamase site from Bacteroides fragilis. Biochemistry (2002) 0.91
Enzymatic catalysis of urea decomposition: elimination or hydrolysis? J Am Chem Soc (2004) 0.90
Insight into the cation-π interaction at the metal binding site of the copper metallochaperone CusF. J Am Chem Soc (2011) 0.90
Accurate assessment of the strain energy in a protein-bound drug using QM/MM X-ray refinement and converged quantum chemistry. J Comput Chem (2011) 0.90
An Efficient Method to Evaluate Intermolecular Interaction Energies in Large Systems Using Overlapping Multicenter ONIOM and the Fragment Molecular Orbital Method. J Phys Chem Lett (2012) 0.89
QM/MM X-ray refinement of zinc metalloenzymes. J Inorg Biochem (2010) 0.89
Molecular dynamics simulations of the dinuclear zinc-beta-lactamase from Bacteroides fragilis complexed with imipenem. J Comput Chem (2002) 0.89
Molecular dynamics and quantum chemical studies on the catalytic mechanism of Delta5-3-ketosteroid isomerase: the catalytic diad versus the cooperative hydrogen bond mechanism. J Am Chem Soc (2003) 0.88
QMQSAR: utilization of a semiempirical probe potential in a field-based QSAR method. J Comput Chem (2005) 0.88
Computation of the physio-chemical properties and data mining of large molecular collections. J Comput Chem (2002) 0.88
PM3-compatible zinc parameters optimized for metalloenzyme active sites. J Comput Chem (2004) 0.87
Computational studies of the farnesyltransferase ternary complex part II: the conformational activation of farnesyldiphosphate. Biochemistry (2007) 0.87
Ureases: quantum chemical calculations on cluster models. J Am Chem Soc (2003) 0.87
Insights into the mechanistic dichotomy of the protein farnesyltransferase peptide substrates CVIM and CVLS. J Am Chem Soc (2012) 0.86
Competitive hydrolytic and elimination mechanisms in the urease catalyzed decomposition of urea. J Phys Chem B (2007) 0.86
Catalyzed decomposition of urea. Molecular dynamics simulations of the binding of urea to urease. Biochemistry (2006) 0.86
Wide-open flaps are key to urease activity. J Am Chem Soc (2012) 0.86
QM/MM refinement and analysis of protein bound retinoic acid. J Comput Chem (2011) 0.85
Finding a needle in the haystack: computational modeling of Mg2+ binding in the active site of protein farnesyltransferase. Biochemistry (2010) 0.85
Apo and nickel-bound forms of the Pyrococcus horikoshii species of the metalloregulatory protein: NikR characterized by molecular dynamics simulations. Biochemistry (2009) 0.85
Divide-and-Conquer Hartree-Fock Calculations on Proteins. J Chem Theory Comput (2010) 0.85
Conformational Analysis of Free and Bound Retinoic Acid. J Chem Theory Comput (2012) 0.85
Relative configuration of natural products using NMR chemical shifts. J Nat Prod (2009) 0.85
Fast semiempirical calculations for nuclear magnetic resonance chemical shifts: a divide-and-conquer approach. J Chem Phys (2004) 0.84
Role of solvation in the energy stabilization inside the hydrophobic core of the protein rubredoxin. J Phys Chem B (2006) 0.84
Importance of dispersion and electron correlation in ab initio protein folding. J Phys Chem B (2009) 0.84
Computational study of the resistance shown by the subtype B/HIV-1 protease to currently known inhibitors. Biochemistry (2010) 0.83
Molecular dynamics simulations of the TEM-1 beta-lactamase complexed with cephalothin. J Med Chem (2005) 0.83
A critical assessment of the performance of protein-ligand scoring functions based on NMR chemical shift perturbations. J Med Chem (2007) 0.82
Assessment of Semiempirical Quantum Mechanical Methods for the Evaluation of Protein Structures. J Chem Theory Comput (2007) 0.82
Energetics of zinc-mediated interactions in the allosteric pathways of metal sensor proteins. J Am Chem Soc (2012) 0.81
A Mixed QM/MM Scoring Function to Predict Protein-Ligand Binding Affinity. J Chem Theory Comput (2010) 0.81
Prediction of trypsin/molecular fragment binding affinities by free energy decomposition and empirical scores. J Comput Aided Mol Des (2012) 0.81
Molecular dynamics study of ethanolamine as a pure liquid and in aqueous solution. J Phys Chem B (2007) 0.81
Structure and dynamics of the N-terminal domain of the Cu(I) binding protein CusB. Biochemistry (2013) 0.80
Novel acyclic diaminocarbene ligands with increased steric demand and their application in gold catalysis. Org Lett (2010) 0.80
Haptic applications for molecular structure manipulation. J Mol Graph Model (2006) 0.80
Mechanistic insights into Mg2+-independent prenylation by CloQ from classical molecular mechanics and hybrid quantum mechanics/molecular mechanics molecular dynamics simulations. Biochemistry (2014) 0.80
Pairwise decomposition of residue interaction energies using semiempirical quantum mechanical methods in studies of protein-ligand interaction. J Am Chem Soc (2005) 0.80
Conformational analysis and parallel QM/MM X-ray refinement of protein bound anti-Alzheimer drug donepezil. J Chem Theory Comput (2013) 0.80
Model for the fast estimation of basis set superposition error in biomolecular systems. J Chem Phys (2011) 0.80
AM1 parameters for the prediction of 1H and 13C NMR chemical shifts in proteins. J Phys Chem A (2009) 0.79
Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods. J Biomol NMR (2013) 0.79
The intrinsic dynamics and function of nickel-binding regulatory protein: insights from elastic network analysis. Biophys J (2008) 0.79
Ligand Identification Scoring Algorithm (LISA). J Chem Inf Model (2011) 0.79
The Utility of the HSAB Principle via the Fukui Function in Biological Systems. J Chem Theory Comput (2010) 0.79
An ab initio investigation of the interactions involving the aromatic group of the set of fluorinated N-(4-sulfamylbenzoyl)benzylamine inhibitors and human carbonic anhydrase II. J Phys Chem B (2007) 0.79
Parameterization of highly charged metal ions using the 12-6-4 LJ-type nonbonded model in explicit water. J Phys Chem B (2014) 0.78
Explicitly representing the solvation shell in continuum solvent calculations. J Phys Chem A (2009) 0.78
Statistics-based model for basis set superposition error correction in large biomolecules. Phys Chem Chem Phys (2012) 0.77
Development of the knowledge-based and empirical combined scoring algorithm (KECSA) to score protein-ligand interactions. J Chem Inf Model (2013) 0.77
MNDO parameters for the prediction of 19F NMR chemical shifts in biologically relevant compounds. J Phys Chem A (2008) 0.77
Exploring the role of the active site cysteine in human muscle creatine kinase. Biochemistry (2006) 0.77
Computer-aided Drug Design: Using Numbers to your Advantage. ACS Med Chem Lett (2013) 0.77
Insights into Cu(I) exchange in HAH1 using quantum mechanical and molecular simulations. Biochemistry (2007) 0.76
Comment on "A minimal implementation of the AMBER-GAUSSIAN interface for ab initio QM/MM-MD simulation". J Comput Chem (2012) 0.76
Quantum mechanical description of the interactions between DNA and water. J Mol Graph Model (2005) 0.76
Origin of product selectivity in a prenyl transfer reaction from the same intermediate: exploration of multiple FtmPT1-catalyzed prenyl transfer pathways. Biochemistry (2014) 0.76
KECSA-Movable Type Implicit Solvation Model (KMTISM). J Chem Theory Comput (2015) 0.76
Role of substrate dynamics in protein prenylation reactions. Acc Chem Res (2014) 0.76
Validation of the binding site structure of the cellular retinol-binding protein (CRBP) by ligand NMR chemical shift perturbations. J Am Chem Soc (2005) 0.76
An efficient and accurate molecular alignment and docking technique using ab initio quality scoring. J Chem Phys (2008) 0.75
Accurate benchmark calculations on the gas-phase basicities of small molecules. J Phys Chem A (2009) 0.75
Assessment of the CCSD and CCSD(T) Coupled-Cluster Methods in Calculating Heats of Formation for Cu Complexes. Mol Phys (2009) 0.75