PubRank

Kenneth M Merz

Author PubWeight™ 115.67‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 The Amber biomolecular simulation programs. J Comput Chem 2005 28.84
2 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
3 Critical Assessment of the Performance of Density Functional Methods for Several Atomic and Molecular Properties. J Chem Theory Comput 2007 1.42
4 Structural Survey of Zinc Containing Proteins and the Development of the Zinc AMBER Force Field (ZAFF). J Chem Theory Comput 2010 1.37
5 Formal Estimation of Errors in Computed Absolute Interaction Energies of Protein-ligand Complexes. J Chem Theory Comput 2011 1.32
6 Insights into the strength and origin of halogen bonding: the halobenzene-formaldehyde dimer. J Phys Chem A 2007 1.28
7 Pose scoring by NMR. J Am Chem Soc 2004 1.27
8 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
9 Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent. J Chem Theory Comput 2013 1.16
10 Assessment of the "6-31+G** + LANL2DZ" mixed basis set coupled with density functional theory methods and the effective core potential: prediction of heats of formation and ionization potentials for first-row-transition-metal complexes. J Phys Chem A 2009 1.16
11 A quantum mechanics-based scoring function: study of zinc ion-mediated ligand binding. J Am Chem Soc 2004 1.15
12 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
13 The energy computation paradox and ab initio protein folding. PLoS One 2011 1.10
14 The role of quantum mechanics in structure-based drug design. Drug Discov Today 2007 1.09
15 Prediction of aqueous solubility of a diverse set of compounds using quantitative structure-property relationships. J Med Chem 2003 1.08
16 Can we separate active from inactive conformations? J Comput Aided Mol Des 2002 1.06
17 Refinement of protein crystal structures using energy restraints derived from linear-scaling quantum mechanics. Acta Crystallogr D Biol Crystallogr 2005 1.06
18 Further analysis and comparative study of intermolecular interactions using dimers from the S22 database. J Chem Phys 2009 1.01
19 Understanding the substrate selectivity and the product regioselectivity of Orf2-catalyzed aromatic prenylations. Biochemistry 2007 0.99
20 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
21 Solution structure of Mycobacterium tuberculosis NmtR in the apo state: insights into Ni(II)-mediated allostery. Biochemistry 2012 0.97
22 Pairwise additivity of energy components in protein-ligand binding: the HIV II protease-Indinavir case. J Chem Phys 2011 0.97
23 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
24 Quantum mechanical and molecular dynamics simulations of ureases and Zn beta-lactamases. J Comput Chem 2006 0.96
25 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
26 Protein NMR chemical shift calculations based on the automated fragmentation QM/MM approach. J Phys Chem B 2009 0.95
27 The Effects of Computational Modeling Errors on the Estimation of Statistical Mechanical Variables. J Chem Theory Comput 2012 0.95
28 The hydrolysis of urea and the proficiency of urease. J Am Chem Soc 2004 0.94
29 Interaction energy decomposition in protein-protein association: a quantum mechanical study of barnase-barstar complex. Biophys Chem 2006 0.93
30 Simulations of allosteric motions in the zinc sensor CzrA. J Am Chem Soc 2011 0.93
31 Computational studies of the farnesyltransferase ternary complex part I: substrate binding. Biochemistry 2005 0.93
32 Critical assessment of quantum mechanics based energy restraints in protein crystal structure refinement. Protein Sci 2006 0.92
33 Quantum mechanics in structure-based drug design. Curr Opin Drug Discov Devel 2006 0.91
34 Molecular recognition and drug-lead identification: what can molecular simulations tell us? Curr Med Chem 2010 0.91
35 Catalytic mechanism of aromatic prenylation by NphB. Biochemistry 2012 0.91
36 Insights into the structure and dynamics of the dinuclear zinc beta-lactamase site from Bacteroides fragilis. Biochemistry 2002 0.91
37 Insight into the cation-π interaction at the metal binding site of the copper metallochaperone CusF. J Am Chem Soc 2011 0.90
38 Enzymatic catalysis of urea decomposition: elimination or hydrolysis? J Am Chem Soc 2004 0.90
39 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
40 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
41 Molecular dynamics simulations of the dinuclear zinc-beta-lactamase from Bacteroides fragilis complexed with imipenem. J Comput Chem 2002 0.89
42 QM/MM X-ray refinement of zinc metalloenzymes. J Inorg Biochem 2010 0.89
43 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
44 The hydrolysis of amides and the proficiency of amidohydrolases. The burden borne by kw. J Phys Chem B 2007 0.88
45 Computation of the physio-chemical properties and data mining of large molecular collections. J Comput Chem 2002 0.88
46 QMQSAR: utilization of a semiempirical probe potential in a field-based QSAR method. J Comput Chem 2005 0.88
47 PM3-compatible zinc parameters optimized for metalloenzyme active sites. J Comput Chem 2004 0.87
48 Computational studies of the farnesyltransferase ternary complex part II: the conformational activation of farnesyldiphosphate. Biochemistry 2007 0.87
49 Ureases: quantum chemical calculations on cluster models. J Am Chem Soc 2003 0.87
50 Insights into the mechanistic dichotomy of the protein farnesyltransferase peptide substrates CVIM and CVLS. J Am Chem Soc 2012 0.86
51 Competitive hydrolytic and elimination mechanisms in the urease catalyzed decomposition of urea. J Phys Chem B 2007 0.86
52 Catalyzed decomposition of urea. Molecular dynamics simulations of the binding of urea to urease. Biochemistry 2006 0.86
53 Wide-open flaps are key to urease activity. J Am Chem Soc 2012 0.86
54 Apo and nickel-bound forms of the Pyrococcus horikoshii species of the metalloregulatory protein: NikR characterized by molecular dynamics simulations. Biochemistry 2009 0.85
55 QM/MM refinement and analysis of protein bound retinoic acid. J Comput Chem 2011 0.85
56 Conformational Analysis of Free and Bound Retinoic Acid. J Chem Theory Comput 2012 0.85
57 Finding a needle in the haystack: computational modeling of Mg2+ binding in the active site of protein farnesyltransferase. Biochemistry 2010 0.85
58 Divide-and-Conquer Hartree-Fock Calculations on Proteins. J Chem Theory Comput 2010 0.85
59 Relative configuration of natural products using NMR chemical shifts. J Nat Prod 2009 0.85
60 Fast semiempirical calculations for nuclear magnetic resonance chemical shifts: a divide-and-conquer approach. J Chem Phys 2004 0.84
61 Role of solvation in the energy stabilization inside the hydrophobic core of the protein rubredoxin. J Phys Chem B 2006 0.84
62 Importance of dispersion and electron correlation in ab initio protein folding. J Phys Chem B 2009 0.84
63 Computational study of the resistance shown by the subtype B/HIV-1 protease to currently known inhibitors. Biochemistry 2010 0.83
64 Molecular dynamics simulations of the TEM-1 beta-lactamase complexed with cephalothin. J Med Chem 2005 0.83
65 A critical assessment of the performance of protein-ligand scoring functions based on NMR chemical shift perturbations. J Med Chem 2007 0.82
66 Assessment of Semiempirical Quantum Mechanical Methods for the Evaluation of Protein Structures. J Chem Theory Comput 2007 0.82
67 Prediction of trypsin/molecular fragment binding affinities by free energy decomposition and empirical scores. J Comput Aided Mol Des 2012 0.81
68 A Mixed QM/MM Scoring Function to Predict Protein-Ligand Binding Affinity. J Chem Theory Comput 2010 0.81
69 Energetics of zinc-mediated interactions in the allosteric pathways of metal sensor proteins. J Am Chem Soc 2012 0.81
70 Molecular dynamics study of ethanolamine as a pure liquid and in aqueous solution. J Phys Chem B 2007 0.81
71 Structure and dynamics of the N-terminal domain of the Cu(I) binding protein CusB. Biochemistry 2013 0.80
72 Haptic applications for molecular structure manipulation. J Mol Graph Model 2006 0.80
73 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
74 Conformational analysis and parallel QM/MM X-ray refinement of protein bound anti-Alzheimer drug donepezil. J Chem Theory Comput 2013 0.80
75 Novel acyclic diaminocarbene ligands with increased steric demand and their application in gold catalysis. Org Lett 2010 0.80
76 Pairwise decomposition of residue interaction energies using semiempirical quantum mechanical methods in studies of protein-ligand interaction. J Am Chem Soc 2005 0.80
77 Model for the fast estimation of basis set superposition error in biomolecular systems. J Chem Phys 2011 0.80
78 Ligand Identification Scoring Algorithm (LISA). J Chem Inf Model 2011 0.79
79 The intrinsic dynamics and function of nickel-binding regulatory protein: insights from elastic network analysis. Biophys J 2008 0.79
80 Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods. J Biomol NMR 2013 0.79
81 AM1 parameters for the prediction of 1H and 13C NMR chemical shifts in proteins. J Phys Chem A 2009 0.79
82 The Utility of the HSAB Principle via the Fukui Function in Biological Systems. J Chem Theory Comput 2010 0.79
83 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
84 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
85 Explicitly representing the solvation shell in continuum solvent calculations. J Phys Chem A 2009 0.78
86 Statistics-based model for basis set superposition error correction in large biomolecules. Phys Chem Chem Phys 2012 0.77
87 Exploring the role of the active site cysteine in human muscle creatine kinase. Biochemistry 2006 0.77
88 Computer-aided Drug Design: Using Numbers to your Advantage. ACS Med Chem Lett 2013 0.77
89 Force field design and molecular dynamics simulations of the carbapenem- and cephamycin-resistant dinuclear zinc metallo-beta-lactamase from Bacteroides fragilis and its complex with a biphenyl tetrazole inhibitor. J Med Chem 2005 0.77
90 Development of the knowledge-based and empirical combined scoring algorithm (KECSA) to score protein-ligand interactions. J Chem Inf Model 2013 0.77
91 MNDO parameters for the prediction of 19F NMR chemical shifts in biologically relevant compounds. J Phys Chem A 2008 0.77
92 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
93 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
94 KECSA-Movable Type Implicit Solvation Model (KMTISM). J Chem Theory Comput 2015 0.76
95 Insights into Cu(I) exchange in HAH1 using quantum mechanical and molecular simulations. Biochemistry 2007 0.76
96 Quantum mechanical description of the interactions between DNA and water. J Mol Graph Model 2005 0.76
97 Role of substrate dynamics in protein prenylation reactions. Acc Chem Res 2014 0.76
98 Comment on "A minimal implementation of the AMBER-GAUSSIAN interface for ab initio QM/MM-MD simulation". J Comput Chem 2012 0.76
99 An efficient and accurate molecular alignment and docking technique using ab initio quality scoring. J Chem Phys 2008 0.75
100 Assessment of the CCSD and CCSD(T) Coupled-Cluster Methods in Calculating Heats of Formation for Cu Complexes. Mol Phys 2009 0.75
101 Accurate benchmark calculations on the gas-phase basicities of small molecules. J Phys Chem A 2009 0.75
102 Reduction of urease activity by interaction with the flap covering the active site. J Chem Inf Model 2015 0.75
103 Effects of fluorine substitution on the edge-to-face interaction of the benzene dimer. J Phys Chem B 2005 0.75
104 Introducing the Review Manuscript Type. J Chem Inf Model 2015 0.75
105 Evolution of Alchemical Free Energy Methods in Drug Discovery. J Chem Inf Model 2020 0.75
106 Receptor-Ligand Binding Free Energies from a Consecutive Histograms Monte Carlo Sampling Method. J Chem Theory Comput 2020 0.75
107 A Hylleraas functional based perturbative technique to relax the extremely localized molecular orbital wavefunction. J Chem Phys 2008 0.75
108 Letter from the editors. J Chem Inf Model 2015 0.75
109 Importance of loop dynamics in the neocarzinostatin chromophore binding and release mechanisms. Phys Chem Chem Phys 2010 0.75