Publications

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

2010 - 2014

• Faver, J., and Merz, K. M., Jr. (2010) Utility of the Hard/Soft Acid-Base Principle via the Fukui Function in Biological Systems, Journal of Chemical Theory and Computation 6, 548-559. 
• Genoni, A., Morra, G., Merz, K. M., Jr., and Colombo, G. (2010) Computational Study of the Resistance Shown by the Subtype B/HIV-1 Protease to Currently Known Inhibitors, Biochemistry 49, 4283-4295.
• Hayik, S. A., Dunbrack, R., Jr., and Merz, K. M., Jr. (2010) Mixed Quantum Mechanics/Molecular Mechanics Scoring Function To Predict Protein-Ligand Binding Affinity, Journal of Chemical Theory and Computation 6, 3079-3091. 
• He, X., and Merz, K. M., Jr. (2010) Divide and Conquer Hartree-Fock Calculations on Proteins, Journal of Chemical Theory and Computation 6, 405-411.     
• Li, X., Hayik, S. A., and Merz, K. M., Jr. (2010) QM/MM X-ray refinement of zinc metalloenzymes, Journal of Inorganic Biochemistry 104, 512-522.
• Merz, K. M., Jr. (2010) Limits of Free Energy Computation for Protein-Ligand Interactions, Journal of Chemical Theory and Computation 6, 1769-1776. 
• Morra, G., Genoni, A., Neves, M. A. C., Merz, K. M., Jr., and Colombo, G. (2010) Molecular Recognition and Drug-Lead Identification: What Can Molecular Simulations Tell Us?, Current Medicinal Chemistry 17, 25-41.
• Peters, M. B., Yang, Y., Wang, B., Fuesti-Molnar, L., Weaver, M. N., and Merz, K. M., Jr. (2010) Structural Survey of Zinc-Containing Proteins and Development of the Zinc AMBER Force Field (ZAFF), Journal of Chemical Theory and Computation 6, 2935-2947. 
• Seo, H., Roberts, B. P., Abboud, K. A., Merz, K. M., Jr., and Hong, S. (2010) Novel Acyclic Diaminocarbene Ligands with Increased Steric Demand and Their Application in Gold Catalysis, Organic Letters 12, 4860-4863. 
• Wang, B., and Merz, K. M., Jr. (2010) Importance of loop dynamics in the neocarzinostatin chromophore binding and release mechanisms, Physical Chemistry Chemical Physics 12, 3443-3449.
• Yang, Y., Chakravorty, D. K., and Merz, K. M., Jr. (2010) Finding a Needle in the Haystack: Computational Modeling of Mg(2+) Binding in the Active Site of Protein Farnesyltransferase, Biochemistry 49, 9658-9666. 
• Faver, J. C., Benson, M. L., He, X., Roberts, B. P., Wang, B., Marshall, M. S., Kennedy, M. R., Sherrill, C. D., and Merz, K. M., Jr. (2011) Formal Estimation of Errors in Computed Absolute Interaction Energies of Protein-Ligand Complexes, Journal of Chemical Theory and Computation 7, 790-797. 
• Faver, J. C., Benson, M. L., He, X., Roberts, B. P., Wang, B., Marshall, M. S., Sherrill, C. D., and Merz, K. M., Jr. (2011) The Energy Computation Paradox and ab initio Protein Folding, Plos One 6, e18868.
• Faver, J. C., Zheng, Z., and Merz, K. M., Jr. (2011) Model for the fast estimation of basis set superposition error in biomolecular systems, Journal of Chemical Physics 135.
• Fu, Z., Li, X., and Merz, K. M., Jr. (2011) Accurate Assessment of the Strain Energy in a Protein-Bound Drug Using QM/MM X-ray Refinement and Converged Quantum Chemistry, Journal of Computational Chemistry 32, 2587-2597. 
• Mitin, A. V., Kubicki, J. D., and Merz, K. M., Jr. (2011) Electronic Structure, Chemical Bonding, and Oxidation Numbers of First-row Transition Metals in MePIm(2) Complexes and Their Cations, International Journal of Quantum Chemistry 111, 3630-3642. 
• Ucisik, M. N., Dashti, D. S., Faver, J. C., and Merz, K. M., Jr. (2011) Pairwise additivity of energy components in protein-ligand binding: The HIV II protease-Indinavir case, Journal of Chemical Physics 135, 085101. 
• Zheng, Z., and Merz, K. M., Jr. (2011) Ligand Identification Scoring Algorithm (LISA), Journal of Chemical Information and Modeling 51, 1296-1306. 
• Li, X., Fu, Z. and Merz, K. M. Jr. (2012) QM/MM Refinement and Analysis of Protein Bound Retinoic Acid, Journal of Computational Chemistry 33, 301-310.
• Chakravorty, D. K., Wang, B., Ucisik, M. N., and Merz, K. M. (2011) Insight Into the Cation-π Interaction at the Metal Binding Site of CusF Journal of the American Chemical Society 133, 19330–19333.  
  
• Chakravorty, D. K., Wang, B., Lee, C. W., Giedroc, D. P., and Merz, K. M. (2011) Simulations of Allosteric Motions in the Zinc Sensor CzrA Journal of the American Chemical Society 134, 3367-3376.
• Yang, Y., Wang, B., Ucisik, M. N., Cui, G., Fierke, C. A., and Merz, K. M. (2012) Insights into the Mechanistic Dichotomy of the Protein Farnesyltransferase Peptide Substrates CVIM and CVLS Journal of the American Chemical Society 134, 820-823.
• Fu, A., Li, X., Merz, K. M. (2012) Conformational Analysis of Free and Bound Retinoic Acid  Journal of Chemical Theory and Computation 8, 1436–1448.  
  
• Faver, J., Zheng, Z, Merz, K. M.  (2012) Statistics-based Model for Basis Set Superposition Error Correction in Large Biomolecules Physical Chemistry Chemical Physics 14, 7795-7799. 
  
• Lee, C.-W., Chakravorty, D. K., Chang, F.- M., Reyes-Caballero, H., Ye, Y., Merz, K. M., Giedroc, D. P. (2012) Solution Structure of Mycobacterium tuberculosis NmtR in the Apo-state: Insights into Ni(II)-mediated Allostery  Biochemistry 51, 2619-2629.
• Yang, Y., Miao, Y., Wang, B., Cui, G., Merz, K. M. (2012)  Catalytic Mechanism of Aromatic Prenylation by NphB Biochemistry 51, 2606-2618.
• Benson M.L., Faver J.C., Ucisik M.N., Dashti D.S., Zheng Z., Merz K.M. (2012) Prediction of trypsin/molecular fragment binding affinities by free energy decomposition and empirical scores Journal of Computer Aided Molecular Design 26, 647-659.
  
• Faver, J. C., Yang,W., Merz, K. M. (2012) The Effects of Computational Modeling Errors on the Estimation of Statistical Mechanical Variables Journal of Chemical Theory and Computation 8, 3769–3776.
• Roberts, B. P., Miller, B. R., Roitberg, A. E. Merz, K.M. (2012) Wide-open flaps are key to urease activity Journal of the American Chemical Society, 134, 9934-9937.
• Chakravorty, D. K., Parker, T. M.,  Guerra, A. J.,  Sherrill, C. D.,  Giedroc, D. P., Merz K. M. (2013)  Energetics of Zinc-Mediated Interactions in the Allosteric Pathways of Metal Sensor Proteins Journal of the American Chemical Society, 135, 30-33.
• Miao, Y., Merz, K. M. (2013) Acceleration of Electron Repulsion Integral Evaluation on Graphics Processing Units via Use of Recurrence Relations Journal of Chemical Theory and Computation 9, 965–976.
• Fu, Z., Li X., Miao, Y., Merz, K. M. (2013) Conformational Analysis and Parallel QM/MM X-ray Refinement of Protein Bound Anti-Alzheimer Drug Donepezil Journal of Chemical Theory and Computation 9, 1686-1693. 
• Chakravorty, D. K., Wang, B., Lee, C. W., Guerro, A. J., Giedroc, D. P., Merz, K. M. (2013) Solution NMR Refinement of a Metal Ion Bound Protein Using Metal Ion Inclusive Restrained Molecular Dynamics Methods  56, 125-137. Associated PDB 2M30.
• Zheng, Z., Merz, K. M. (2013) Development of the Knowledge-Based and Empirical Combined Scoring Algorithm (KECSA) To Score Protein–Ligand Interactions Journal of Chemical Information and Modeling 53, 1073–1083.   
• Li. P, Roberts, B. P., Chakravorty, D. K., Merz, K. M. (2013) Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent  Journal of Chemical Theory and Computation 9, 2733–2748.  
• Wang, B., He, X., Merz, K. M. (2013) A Quantum Mechanical Study of Vicinal J Spin-Spin Coupling Constants for the Protein Backbone  Journal of Chemical Theory and Computation 9, 4653–4659. 
• Faver, J. C., Ucisik, M. N., W. Yang, W, Merz, K. M. (2013) Computer-aided Drug Design: Using Numbers to your Advantage  Medicinal Chemistry Letters 4, 812–814.
• Ucisik, M. N., Chakravorty, D. K., Merz, K. M. (2013) Structure and Dynamics of the N-Terminal Domain of the Cu(I) Binding Protein CusB , Jr. Biochemistry 52, 6911–6923.
• M. N. Weaver, M.,  Merz, K. M., Dongxia Ma. K., ; Hyun, J.,  Gagliardi, L. (2013) Calculation of Heats of Formation for Zn Complexes: Comparison of Density Functional Theory, Second Order Perturbation Theory, Coupled-Cluster and Complete Active Space Methods  Journal of Chemical Theory and Computation 9, 5277–5285.
• Z. Zheng, Z., Ucisik, M. N., Merz , K. M. (2013) The Movable Type Method Applied to Protein-Ligand Binding Journal of Chemical Theory and Computation 9, 5526–5538. 
  
• Li, P., Merz, K. M. (2014) Taking into Account the Ion-induced Dipole Interaction in the Nonbonded Model of Ions Journal of Chemical Theory and Computation 10, 289–297.
  
• Ucisik, M. N.,  Zheng, Z.,  Faver, J. C.,  Merz, K. M. (2014) Bringing Clarity to the Prediction of Protein-ligand Binding Free Energies via “blurring Journal of Chemical Theory and Computation 10, 1314–1325.    
  
• Borbulevych, O. Y.,  Plumley, J. A.,  Martin, R. I.,  Merz, K. M.,  Westerhoff L. M. (2014) Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package Acta Crystallographica Section D; Biological Crystallography D70, 1233-1247.    
  
• Minkara, M. S., Ucisik, M. N.,  Weaver, M. N., Merz, K. M. (2014) Molecular Dynamics Study of Helicobacter pylori Urease Journal of Chemical Theory and Computation 10, 1852–1862.
• Merz, K. M., Aguiar, E. C.,  da Silva, J. B. P. (2014) Adenine Formation without HCN Journal of Physical Chemistry A 118, 3637–3644.
• Faver, J. C.,  Merz, K. M. (2014) Fragment-based error estimation in biomolecular modeling Drug Discovery Today 19, 45–50. 
• Merz, K. M. (2014) Using Quantum Mechanical Approaches to Study Biological Systems Accounts of Chemical Research 47, 2804-2811. 

• Sherrill, C. D., Merz, K. M. (2014) Quantum Mechanical Methods for Quantifying and Analyzing Non-Covalent Interactions and for Force-Field Development in Many-Body Effects and Electrostatics in Biomolecules Q. Cui, M. Meuwly. P. Ren, Eds   
• Chakravorty, D. K., Merz, K. M. (2014) Studying Allosteric Regulation in Metal Sensor Proteins Using Computational Methods Advances in Protein Chemistry and Structural Biology 96, 181-218

• Base, C. A., Merz, K. M. (2014) Mechanistic Insights into Mg2+-independent Prenylation by CloQ from Classical MM and Hybrid QM/MM Molecular Dynamics Simulations Biochemistry 53, 5034–5041 
  
• Pan, L.-L., Yang, Y., Merz, K. M. (2014) Origin of Product Selectivity in Prenyl Transfer from an Identical Intermediate: Exploration of Multiple FtmPT1 Catalyzed Prenyl Transfer Pathways Biochemistry 53, 6126–6138