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

• Chakravorty, D. K., Merz, K. M. (2015) Role of Substrate Dynamics in protein Prenylation Reactions Accounts of Chemical Research 48, 439-448
• Li, P., Song, F., Merz, K. M. (2015) Parameterization of Highly Charged Metal Ions Using the 12-6-4 LJ-type Nonbonded Model in Explicit Water  Journal of Physical Chemistry B 119, 883–895
• Li, P., Song, F., Merz, K. M. (2015) Systematic Parameterization of Monovalent Ions Employing the Nonbonded Model Journal of Chemical Theory and Computation in press
• Zheng, Z., Wang, T., Li, P., Merz, K. M. (2015) KECSA-Movable Type Implicit Solvation Model (KMTISM) Journal of Chemical Theory and Computation 11, 667–682

• Macomber, L.,  Minkara, M. S., Hausinger, R.P., Merz, K. M. (2015) Inhibition of Urease by Modification of a Cysteinyl Residue in the Flap Covering the Active Site Journal of Chemical Information and Modeling 55, 354–361
• Miao, Y., Merz, K. M. (2015) Acceleration of High Angular Momentum Electron Repulsion Integrals and Integral Derivatives on Graphics Processing Units Journal of Chemical Theory and Computation 11, 1449–1462.
• ​J. B. P. da Silva, J. B. P., Hallwass, F., da Silva, A. G.,  Moreira, D. R.,  Ramos, M. N.,  Espindola, J. W. P., de Oliveira, A. D. T.,  Brondani, D. J.,  Leite, A. C. L.,  Merz, K. M. (2015) Intermolecular interaction of thiosemicarbazone derivatives to solvents and a potential Aedes aegypti target  Journal of Molecular Structure, 1093, 219–227. 
• Pan, L.-L, Zheng, Z., Wang, T., Merz, K. M. (2105) A Free Energy Based Conformational Search Algorithm Using the “Movable Type” Sampling Method  Journal of Chemical Theory and Computation, 11, 5853–5864. 
• Ucisik, M. N.,  Merz, K. M. (2015) N‑Terminal Domain of the Cu(I)Binding Protein CusB In Encyclopedia of Inorganic and Bioinorganic Chemistry, John Wiley & Sons, Ltd., West Sussex, United Kingdom. 
• Minkara, M. S., Weaver, M. N., Gorske, J.,  Bowers, C. R., Merz, K. M. (2015) Implementation of Protocols To Enable Doctoral Training in Physical and Computational Chemistry of a Blind Graduate Student Journal of Chemical Education, 92, 1280–1283. 
• J. B. P. da Silva; D. M. do A.F. Navarro; A. G. da Silva; G. K. N. Santos; K. A. Dutra; D. R. Moreira; M. N. Ramos; J. W. P. Espíndola; A. D. T. de Oliveira; D. J. Brondani; A. C. L. Leite; M. Z. Hernandes; V. R.A. Pereira; L. F. da Rocha; M. C. A. B. de Castro; B. C. de Oliveira; Q. Land, 3, K. M. Merz Jr.(2015) Thiosemicarbazones as Aedes aegypti larvicidal European Journal of Medicinal Chemistry100, 162–175.
• Ucisik, M. N., Chakravorty, D. K., Merz, K. M. (2015) Models for the Metal Transfer Complex of the N-Terminal Region of CusB and CusF  Biochemistry, 54, 4226–4235.
• Minkara, M. S., Weaver, M. N.,  Merz, K. M. (2015) Effect of 10.5 M Aqueous Urea on Helicobacter pylori Urease: A Molecular Dynamics Study Biochemistry, 54, 4121–4130. 
• Chakravorty, D. K.,  Li, P., Tran, T. T., Bayse, C. A., Merz, K. M. (2016) Metal Ion Capture Mechanism of a Copper Metallochaperone Biochemistry, 55, 501–509.
• Bansal, N., Zheng, Z., Merz, K. M. (2106) Incorporation of side chain flexibility into protein binding pockets using MTflex, Bioorganic and Medicinal Chemistry 24, 4978–4987.
• Bansal, N., Zheng, Z., Cerutti, D.S., Merz, K. M. (2017) On the fly estimation of host–guest binding free energies using the movable type method: participation in the SAMPL5 blind challenge, Journal of Computer Aided Molecular Design,  31, 47-60.
• ​Li, P., Merz, K. M. (2017) Metal Ion Modeling Using Classical Mechanics Chemical Reviews, 117. 1564–1686. 
• Yu, Z., Li, P., and Merz, K. M., Jr. (2017) Using Ligand-Induced Protein Chemical Shift Perturbations To Determine Protein-Ligand Structures, Biochemistry, 56, 2349-2362. ​
• Burns, L.A., Faver, J. C., Zheng, Z., Marshall, M. S., Smith, D. G. A., Vanommeslaeghe, K., MacKerell, A. D., Merz, K. M. Jr., Sherrill, C. D. (2017) The BioFragment Database (BFDb): An Open-Data Platform for ComputationalChemistry Analysis of Noncovalent Interactions, J. Chem. Phys., 147, 161727.
• Aldrich, C., Bertozzi, C., Georg, G. I., Kiessling, L., Lindsley, C., Liotta, D., Merz, K. M. Jr.; Schepartz, A., Wang, S. (2017) The Ecstasy and Agony of Assay Interference Compounds, ACS Cent. Sci., 3, 143–147. 
• Pan, L.-L., Song, L. F., Miao, Y., Yang, Y., Merz, K. M. Jr (2017) Mechanism of Formation of the Nonstandard Product in the Prenyltransferase Reaction of the G115T Mutant of FtmPT1: A Case of Reaction Dynamics Calling the Shots?, Biochemistry, 56, 2995–3007. 
• Yu, Z., Li, P., Merz, K. M. Jr. (2017) Extended Zinc AMBER Force Field (EZAFF), J. Chem. Theory Comput., 14, 242–254.
• Genoni, A., Bucinsky, L., Claiser, C., Contreras-Garcia, J., Dittrich, B., Dominiak, P. M.,  Espinosa, E., Gatti, C., Giannozzi, P., Gillet, J.-M., Jayatilaka, D., Macchi, P., Madsen, A. Ø.,  Massa, L. J.,  Matta, C. F., Merz, K. M. Jr.,  Nakashima, P. N. H., Ott, H.,  Ryde, U., Schwarz, K.,  Sierka, M., Grabowsky, S. (2018) Quantum Crystallography: Current Developments and Future Perspectives, Chem. - A Eur. J., 24, 10881-10905.
• Bansal, N., Zheng, Z., Song, L. F., Pei, J., Merz, K. M. Jr (2018) The Role of the Active Site Flap in Streptavidin/Biotin Complex Formation, J. Am. Chem. Soc., 140, 5434–5446.
• Zhong, H. A., Santos, E. M., Vasileiou, C.,  Zheng, Z., Geiger, J. H., Borhan, B., Merz, K. M. Jr. (2018) Free-Energy-Based Protein Design: Re-Engineering Cellular Retinoic Acid Binding Protein II Assisted by the Moveable-Type Approach J. Am. Chem. Soc., 140, 3483–3486. 
•  “Generation of Pairwise Potentials Using Multidimensional Data Mining” Z. Zheng; J. Pei; N. Bansal; H. Liu; L. F. Song; K. M. Merz Jr. J. Chem. Theory Comput., 2018, 14, 5045-5067. (https://doi.org/10.1021/acs.jctc.8b00516)
• “Detailed Potential of Mean Force Studies on Host–Guest Systems from the SAMPL6 Challenge”L.F. Song, N. Bansal, Z. Zheng; K. M. Merz Jr. Journal of Computer-aided Molecular Design, 2018,32, 1013-1026. (https://doi.org/10.1007/s10822-018-0153-7) 
• “Simulating the Chelate Effect” A. Sengupta; A. Seitz; K. M. Merz, Jr. J. Am. Chem. Soc., 2018, 140, 15166-15169. (https://doi.org/10.1021/jacs.8b09371)
• “Trapping intermediates in metal transfer reactions of the CusCBAF export pump of Escherichia coli” K.N. Chacón; J. Perkins; Z. Mathe; K Alwan; E.N. Ho; M.N. Ucisik; K. M. Merz, Jr.; N. J. BlackburnCommunications biology, 2018,1, 192. (https://doi.org/10.1038/s42003-018-0181-9)
• “Validation of AMBER/GAFF for Relative Free Energy Calculations” L. Song; T.S. Lee; C. Zhu; D.M. York; K. M. Merz, Jr. ChemRxiv, 2019.Being reviewed by J. Chem Inf. Model. (https://bit.ly/2Vprrba)
• “Random Forest Refinement of the KECSA2 Knowledge-based Scoring Function for Protein Decoy Detection” J. Pei; Z. Zheng; K. M. Merz, Jr. J. Chem Inf. Model.2019, ASAP. https://doi.org/10.1021/acs.jcim.8b00734)