Publications

 [ 1984 - 1989 ]    [ 1990 - 1994 ]    [ 1995 - 1999 ]    [ 2000 - 2004 ]    [ 2005 - 2009 ]    [ 2010 - 2014 ] 
[ 2015 - 2020 ]   [ 2021 - 2025 ]

2005 - 2009

• Case, D. A., Cheatham, T. E., Darden, T., Gohlke, H., Luo, R., Merz, K. M., Onufriev, A., Simmerling, C., Wang, B., and Woods, R. J. (2005) The Amber biomolecular simulation programs, Journal of Computational Chemistry 26, 1668-1688. 
• Cui, G. L., Wang, B., and Merz, K. M. (2005) Computational studies of the farnesyltransferase ternary complex - Part I: Substrate binding, Biochemistry 44, 16513-16523. 
• Diaz, N., Suarez, D., Merz, K. M., and Sordo, T. L. (2005) Molecular dynamics simulations of the TEM-1,beta-lactamase complexed with cephalothin, Journal of Medicinal Chemistry 48, 780-791. 
• Dixon, S., Merz, K. M., Lauri, G., and Ianni, J. C. (2005) QMQSAR: Utilization of a semiempirical probe potential in a field-based QSAR method, Journal of Computational Chemistry 26, 23-34. 
• Monard, G., Bernal-Uruchurtu, M. I., van der Vaart, A., Merz, K. M., and Ruiz-Lopez, M. F. (2005) Simulation of liquid water using semiempirical Hamiltonians and the divide and conquer approach, Journal of Physical Chemistry A 109, 3425-3432. 
• Park, H., and Merz, K. M. (2005) Force field design and molecular dynamics simulations of the carbapenema- and cephamycin-resistant dinuclear zinc metallo-beta-lactamase from Bacteroides fragilis and its complex with a biphenyl tetrazole inhibitor, Journal of Medicinal Chemistry 48, 1630-1637. 
• Park, H., Brothers, E. N., and Merz, K. M. (2005) Hybrid QM/MM and DFT investigations of the catalytic mechanism and inhibition of the dinuclear zinc metallo-beta-lactamase CcrA from Bacteroides fragilis, Journal of the American Chemical Society 127, 4232-4241. 
• Raha, K., and Merz, K. M. (2005) 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, Journal of Medicinal Chemistry 48, 4558-4575. 
• Raha, K., van der Vaart, A. J., Riley, K. E., Peters, M. B., Westerhofft, L. M., Kim, H., and Merz, K. M. (2005) Pairwise decomposition of residue interaction energies using semiempirical quantum mechanical methods in studies of protein-ligand interaction, Journal of the American Chemical Society 127, 6583-6594. 
• Riley, K. E., and Merz, K. M. (2005) Effects of fluorine substitution on the edge-to-face interaction of the benzene dimer, Journal of Physical Chemistry B 109, 17752-17756. 
• Riley, K. E., Brothers, E. N., Ayers, K. B., and Merz, K. M. (2005) Accurate atomic and molecular calculations without gradient corrections: Scaled SVWNV density functional, Journal of Chemical Theory and Computation 1, 546-553. 
• Wang, B., and Merz, K. M. (2005) Validation of the binding site structure of the cellular retinol-binding protein (CRBP) by ligand NMR chemical shift perturbations, Journal of the American Chemical Society 127, 5310-5311.
• Yu, N., Yennawar, H. P., and Merz, K. M. (2005) Refinement of protein crystal structures using energy restraints derived from linear-scaling quantum mechanics, Acta Crystallographica Section D-Biological Crystallography 61, 322-332. 
• Estiu, G., and Merz, K. M. (2006) Catalyzed decomposition of urea. Molecular dynamics simulations of the binding of urea to urease, Biochemistry 45, 4429-4443. 
•  Estiu, G., Suarez, D., and Merz, K. M., Jr. (2006) Quantum mechanical and molecular dynamics simulations of ureases and Zn beta-lactamases, Journal of Computational Chemistry 27, 1240-1262. 
• Peters, M. B., and Merz, K. M. (2006) Semiempirical comparative binding energy analysis (SE-COMBINE) of a series of trypsin inhibitors, Journal of Chemical Theory and Computation 2, 383-399. 
• Peters, M. B., Raha, K., and Merz, K. M. (2006) Quantum mechanics in structure-based drug design, Current Opinion in Drug Discovery & Development 9, 370-379.
• Riley, K. E., and Merz, K. M., Jr. (2006) Role of solvation in the energy stabilization inside the hydrophobic core of the protein rubredoxin, Journal of Physical Chemistry B 110, 15650-15653. 
• Wang, B., and Merz, K. M. (2006) A fast QM/MM (Quantum Mechanical/Molecular Mechanical) approach to calculate nuclear magnetic resonance chemical shifts for macromolecules, Journal of Chemical Theory and Computation 2, 209-215. 
• Wang, P.-F., Flynn, A. J., Naor, M. M., Jensen, J. H., Cui, G., Merz, K. M., Jr., Kenyon, G. L., and McLeish, M. J. (2006) Exploring the role of the active site cysteine in human muscle creatine kinase, Biochemistry 45, 11464-11472. 
• Westerhoff, L. M., and Merz, K. M. (2006) Quantum mechanical description of the interactions between DNA and water, Journal of Molecular Graphics & Modelling 24, 440-455. 
• Wollacott, A. M., and Merz, K. M., Jr. (2006) Development of a parametrized force field to reproduce semiempirical geometries, Journal of Chemical Theory and Computation 2, 1070-1077. 
• Yu, N., Hayik, S. A., Wang, B., Liao, N., Reynolds, C. H., and Merz, K. M., Jr. (2006) Assigning the protonation states of the key aspartates in beta-secretase using QM/MM X-ray structure refinement, Journal of Chemical Theory and Computation 2, 1057-1069.
• Yu, N., Li, X., Cui, G., Hayik, S. A., and Merz, K. M., Jr. (2006) Critical assessment of quantum mechanics based energy restraints in protein crystal structure refinement, Protein Science 15, 2773-2784. 
• Zuo, X. B., Cui, G. L., Merz, K. M., Zhang, L. G., Lewis, F. D., and Tiede, D. M. (2006) X-ray diffraction "fingerprinting" of DNA structure in solution for quantitative evaluation of molecular dynamics simulation, Proceedings of the National Academy of Sciences of the United States of America 103, 3534-3539. 
• Ababou, A., van der Vaart, A., Gogonea, V., and Merz, K. M., Jr. (2007) Interaction energy decomposition in protein-protein association: A quantum mechanical study of barnase-barstar complex, Biophysical Chemistry 125, 221-236. 
• Cui, G., and Merz, K. M., Jr. (2007) Computational studies of the farnesyltransferase ternary complex part II: The conformational activation of farnesyldiphosphate, Biochemistry 46, 12375-12381.
• Cui, G., Li, X., and Merz, K. M., Jr. (2007) Understanding the substrate selectivity and the product regioselectivity of Orf2-catalyzed aromatic prenylations, Biochemistry 46, 1303-1311.
• da Silva, E. F., Kuznetsova, T., Kvamme, B., and Merz, K. M., Jr. (2007) Molecular dynamics study of ethanolamine as a pure liquid and in aqueous solution, Journal of Physical Chemistry B 111, 3695-3703.
• Estiu, G., and Merz, K. M., Jr. (2007) Competitive hydrolytic and elimination mechanisms in the urease catalyzed decomposition of urea, Journal of Physical Chemistry B 111, 10263-10274.
• Estiu, G., and Merz, K. M., Jr. (2007) The hydrolysis of amides and the proficiency of amidohydrolases. The burden borne by k(w), Journal of Physical Chemistry B 111, 6507-6519. 
• Holt, B. T. O. t., and Merz, K. M., Jr. (2007) Insights into Cu(I) exchange in HAH1 using quantum mechanical and molecular simulations, Biochemistry 46, 8816-8826. 
• Mitin, A. V., and Merz, K. M., Jr. (2007) An improved 6-31G*basis set for atoms ga through kr, International Journal of Quantum Chemistry 107, 3028-3038.
• Raha, K., Peters, M. B., Wang, B., Yu, N., Wollacott, A. M., Westerhoff, L. M., and Merz, K. M., Jr. (2007) The role of quantum mechanics in structure-based drug design, Drug Discovery Today 12, 725-731. 
• Riley, K. E., and Merz, K. M., Jr. (2007) Assessment of density functional theory methods for the computation of heats of formation and ionization potentials of systems containing third row transition metals, Journal of Physical Chemistry A 111, 6044-6053.
• Riley, K. E., and Merz, K. M., Jr. (2007) Insights into the strength and origin of halogen bonding: The halobenzene-formaldehyde dimer, Journal of Physical Chemistry A 111, 1688-1694.
• Riley, K. E., Cui, G., and Merz, K. M., Jr. (2007) 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, Journal of Physical Chemistry B 111, 5700-5707.
• Riley, K. E., Op't Holt, B. T., and Merz, K. M., Jr. (2007) Critical assessment of the performance of density functional methods for several atomic and molecular properties, Journal of Chemical Theory and Computation 3, 407-433. 
• Wang, B., Westerhoff, L. M., and Merz, K. M., Jr. (2007) A critical assessment of the performance of protein-ligand scoring functions based on NMR chemical shift perturbations, Journal of Medicinal Chemistry 50, 5128-5134. 
• Wollacott, A. M., and Merz, K. M., Jr. (2007) Assessment of semiempirical quantum mechanical methods for the evaluation of protein structures, Journal of Chemical Theory and Computation 3, 1609-1619. 
• Wollacott, A. M., and Merz, K. M., Jr. (2007) Haptic applications for molecular structure manipulation, Journal of Molecular Graphics & Modelling 25, 801-805. 
• Cui, G., and Merz, K. M., Jr. (2008) The intrinsic dynamics and function of nickel-binding regulatory protein: Insights from elastic network analysis (vol 94, pg 3769, 2008), Biophysical Journal 94, 5081-5081. 
• Cui, G., and Merz, K. M., Jr. (2008) The intrinsic dynamics and function of nickel-binding regulatory protein: Insights from elastic network analysis, Biophysical Journal 94, 3769-3778.
• Fusti-Molnar, L., and Merz, K. M., Jr. (2008) An efficient and accurate molecular alignment and docking technique using ab initio quality scoring, Journal of Chemical Physics 129.
• Genoni, A., Merz, K. M., Jr., and Sironi, M. (2008) A Hylleraas functional based perturbative technique to relax the extremely localized molecular orbital wavefunction, Journal of Chemical Physics 129.
• Hayik, S. A., Liao, N., and Merz, K. M., Jr. (2008) A combined QM/MM Poisson-Boltzmann approach, Journal of Chemical Theory and Computation 4, 1200-1207. 
• Williams, D. E., Peters, M. B., Wang, B., and Merz, K. M., Jr. (2008) MNDO parameters for the prediction of F-19 NMR chemical shifts in biologically relevant compounds, Journal of Physical Chemistry A 112, 8829-8838. 
• da Silva, E. F., Svendsen, H. F., and Merz, K. M. (2009) Explicitly Representing the Solvation Shell in Continuum Solvent Calculations, Journal of Physical Chemistry A 113, 6404-6409. 
• He, X., Fusti-Molnar, L., and Merz, K. M., Jr. (2009) Accurate Benchmark Calculations on the Gas-Phase Basicities of Small Molecules, Journal of Physical Chemistry A 113, 10096-10103. 
• He, X., Fusti-Molnar, L., Cui, G., and Merz, K. M., Jr. (2009) Importance of Dispersion and Electron Correlation in ab Initio Protein Folding, Journal of Physical Chemistry B 113, 5290-5300. 
• He, X., Wang, B., and Merz, K. M., Jr. (2009) Protein NMR Chemical Shift Calculations Based on the Automated Fragmentation QM/MM Approach, Journal of Physical Chemistry B 113, 10380-10388. 
• Mitin, A. V., and Merz, K. M., Jr. (2009) An Improved 6-31G* Basis Set for Atoms Ga Through Kr (vol 107, pg 3028, 2007), International Journal of Quantum Chemistry 109, 1158-1158.
• Molnar, L. F., He, X., Wang, B., and Merz, K. M., Jr. (2009) Further analysis and comparative study of intermolecular interactions using dimers from the S22 database, Journal of Chemical Physics 131, O65102.
• Sindhikara, D. J., Roitberg, A. E., and Merz, K. M., Jr. (2009) Apo and Nickel-Bound Forms of the Pyrococcus horikoshii Species of the Metalloregulatory Protein: NikR Characterized by Molecular Dynamics Simulations, Biochemistry 48, 12024-12033. 
• Wang, B., Dossey, A. T., Walse, S. S., Edison, A. S., and Merz, K. M., Jr. (2009) Relative Configuration of Natural Products Using NMR Chemical Shifts, Journal of Natural Products 72, 709-713. 
• Weaver, M. N., and Merz, K. M., Jr. (2009) Assessment of the CCSD and CCSD(T) coupled-cluster methods in calculating heats of formation for Cu complexes, Molecular Physics 107, 1251-1259. 
• Weaver, M. N., Yang, Y., and Merz, K. M., Jr. (2009) Assessment of the CCSD and CCSD(T) Coupled-Cluster Methods in Calculating Heats of Formation for Zn Complexes, Journal of Physical Chemistry A 113, 10081-10088. 
• Williams, D. E., Peters, M. B., Wang, B., Roitberg, A. E., and Merz, K. M., Jr. (2009) AM1 Parameters for the Prediction of (1)H and (13)C NMR Chemical Shifts in Proteins, Journal of Physical Chemistry A 113, 11550-11559.
• X. Li; X. He; B. Wang; K. M. Merz. Jr. (2009) Conformational Variability of Benzamidinium Based Inhibitors Journal of the American Chemical Society, 131, 7742–7754.
  
• Yang, Y., Weaver, M. N., and Merz, K. M., Jr. (2009) 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, Journal of Physical Chemistry A 113, 9843-9851.