Published in J Am Chem Soc on March 30, 2005
Metallo-β-lactamase structure and function. Ann N Y Acad Sci (2012) 1.36
Mechanistic studies on the mononuclear ZnII-containing metallo-beta-lactamase ImiS from Aeromonas sobria. Biochemistry (2006) 1.17
Evolving carbapenemases: can medicinal chemists advance one step ahead of the coming storm? J Med Chem (2010) 1.09
NDM-1, the ultimate promiscuous enzyme: substrate recognition and catalytic mechanism. FASEB J (2013) 1.02
Metal content of metallo-beta-lactamase L1 is determined by the bioavailability of metal ions. Biochemistry (2008) 0.99
Catalytic role of the metal ion in the metallo-beta-lactamase GOB. J Biol Chem (2009) 0.95
Common mechanistic features among metallo-beta-lactamases: a computational study of Aeromonas hydrophila CphA enzyme. J Biol Chem (2009) 0.94
Flexibility of Catalytic Zinc Coordination in Thermolysin and HDAC8: A Born-Oppenheimer ab initio QM/MM Molecular Dynamics Study. J Chem Theory Comput (2009) 0.94
Overcoming differences: The catalytic mechanism of metallo-β-lactamases. FEBS Lett (2015) 0.92
Role of zinc content on the catalytic efficiency of B1 metallo beta-lactamases. J Am Chem Soc (2007) 0.91
QM/MM studies of monozinc β-lactamase CphA suggest that the crystal structure of an enzyme-intermediate complex represents a minor pathway. J Am Chem Soc (2010) 0.89
Spectroscopic and mechanistic studies of heterodimetallic forms of metallo-β-lactamase NDM-1. J Am Chem Soc (2014) 0.89
Molecular basis of NDM-1, a new antibiotic resistance determinant. PLoS One (2011) 0.88
Structural basis for carbapenem-hydrolyzing mechanisms of carbapenemases conferring antibiotic resistance. Int J Mol Sci (2015) 0.86
Zinc and antibiotic resistance: metallo-beta-lactamases and their synthetic analogues. J Biol Inorg Chem (2008) 0.85
A conserved lysine in beta-lactam synthetase assists ring cyclization: Implications for clavam and carbapenem biosynthesis. Chembiochem (2009) 0.84
Probing the effect of the non-active-site mutation Y229W in New Delhi metallo-β-lactamase-1 by site-directed mutagenesis, kinetic studies, and molecular dynamics simulations. PLoS One (2013) 0.83
Biochemical characteristics of New Delhi metallo-β-lactamase-1 show unexpected difference to other MBLs. PLoS One (2013) 0.83
Covalent inhibitors of fatty acid amide hydrolase: a rationale for the activity of piperidine and piperazine aryl ureas. J Med Chem (2011) 0.82
Biapenem inactivation by B2 metallo β-lactamases: energy landscape of the post-hydrolysis reactions. PLoS One (2012) 0.81
A quantum mechanics/molecular mechanics study on the hydrolysis mechanism of New Delhi metallo-β-lactamase-1. J Comput Aided Mol Des (2013) 0.81
Cephalosporins inhibit human metallo β-lactamase fold DNA repair nucleases SNM1A and SNM1B/apollo. Chem Commun (Camb) (2016) 0.79
Biapenem inactivation by B2 metallo β-lactamases: energy landscape of the hydrolysis reaction. PLoS One (2013) 0.78
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
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
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
Quantum mechanical and molecular dynamics simulations of ureases and Zn beta-lactamases. J Comput Chem (2006) 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
Computational studies of the farnesyltransferase ternary complex part I: substrate binding. Biochemistry (2005) 0.93
Simulations of allosteric motions in the zinc sensor CzrA. J Am Chem Soc (2011) 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
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
Enzymatic catalysis of urea decomposition: elimination or hydrolysis? J Am Chem Soc (2004) 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
The hydrolysis of amides and the proficiency of amidohydrolases. The burden borne by kw. J Phys Chem B (2007) 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
Apparent anti-Woodward-Hoffmann addition to a nickel bis(dithiolene) complex: the reaction mechanism involves reduced, dimetallic intermediates. Inorg Chem (2013) 0.87
Ureases: quantum chemical calculations on cluster models. J Am Chem Soc (2003) 0.87
Computational studies of the farnesyltransferase ternary complex part II: the conformational activation of farnesyldiphosphate. Biochemistry (2007) 0.87
PM3-compatible zinc parameters optimized for metalloenzyme active sites. J Comput Chem (2004) 0.87
Wide-open flaps are key to urease activity. J Am Chem Soc (2012) 0.86
Catalyzed decomposition of urea. Molecular dynamics simulations of the binding of urea to urease. Biochemistry (2006) 0.86
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
Finding a needle in the haystack: computational modeling of Mg2+ binding in the active site of protein farnesyltransferase. Biochemistry (2010) 0.85
QM/MM refinement and analysis of protein bound retinoic acid. J Comput Chem (2011) 0.85
Divide-and-Conquer Hartree-Fock Calculations on Proteins. J Chem Theory Comput (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
Relative configuration of natural products using NMR chemical shifts. J Nat Prod (2009) 0.85
Conformational Analysis of Free and Bound Retinoic Acid. J Chem Theory Comput (2012) 0.85
Importance of dispersion and electron correlation in ab initio protein folding. J Phys Chem B (2009) 0.84
Role of solvation in the energy stabilization inside the hydrophobic core of the protein rubredoxin. J Phys Chem B (2006) 0.84
Fast semiempirical calculations for nuclear magnetic resonance chemical shifts: a divide-and-conquer approach. J Chem Phys (2004) 0.84
Computational study of the resistance shown by the subtype B/HIV-1 protease to currently known inhibitors. Biochemistry (2010) 0.83
The mechanism of alkene addition to a nickel bis(dithiolene) complex: the role of the reduced metal complex. J Am Chem Soc (2012) 0.83
Molecular dynamics simulations of the TEM-1 beta-lactamase complexed with cephalothin. J Med Chem (2005) 0.83
Assessment of Semiempirical Quantum Mechanical Methods for the Evaluation of Protein Structures. J Chem Theory Comput (2007) 0.82
A critical assessment of the performance of protein-ligand scoring functions based on NMR chemical shift perturbations. J Med Chem (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
Computational studies on ethylene addition to nickel bis(dithiolene). J Phys Chem A (2011) 0.81
Molecular dynamics study of ethanolamine as a pure liquid and in aqueous solution. J Phys Chem B (2007) 0.81
Novel acyclic diaminocarbene ligands with increased steric demand and their application in gold catalysis. Org Lett (2010) 0.80
Structure and dynamics of the N-terminal domain of the Cu(I) binding protein CusB. Biochemistry (2013) 0.80
Haptic applications for molecular structure manipulation. J Mol Graph Model (2006) 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
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
Model for the fast estimation of basis set superposition error in biomolecular systems. J Chem Phys (2011) 0.80
The intrinsic dynamics and function of nickel-binding regulatory protein: insights from elastic network analysis. Biophys J (2008) 0.79
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
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
Explicitly representing the solvation shell in continuum solvent calculations. J Phys Chem A (2009) 0.78
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
On calculating a polymer's enthalpy of formation with quantum chemical methods. J Phys Chem B (2007) 0.78
Statistics-based model for basis set superposition error correction in large biomolecules. Phys Chem Chem Phys (2012) 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
MNDO parameters for the prediction of 19F NMR chemical shifts in biologically relevant compounds. J Phys Chem A (2008) 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
Computational exploration of alternative catalysts for olefin purification: cobalt and copper analogues inspired by nickel bis(dithiolene) electrocatalysis. Inorg Chem (2014) 0.76
A unified set of experimental organometallic data used to evaluate modern theoretical methods. Dalton Trans (2016) 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
Comment on "A minimal implementation of the AMBER-GAUSSIAN interface for ab initio QM/MM-MD simulation". J Comput Chem (2012) 0.76