Publications 2015-2020 - Merz Research Group

Merz Research Group

Publications

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

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.
C hakravorty, 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. J. Chem Inf. Model 2019 59 3128-3135. (https://doi.org/10.1021/acs.jcim.9b00105)
“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, 59, 1919-1929. https://doi.org/10.1021/acs.jcim.8b00734)
“Random Forest Refinement of Pairwise Potentials for Protein-ligand Decoy Detection” J. Pei; Z. Zheng; H. Kim; L. Song; S. Walworth; M. Merz; K. M. Merz, Jr. J. Chem Inf. Model 2019, 59, 3305-3315.https://doi.org/10.1021/acs.jcim.9b00356 (ChemXriv: https://bit.ly/2H3ZNJ4)
“Thermodynamics of Transition Metal Ion Binding to Proteins” L. Song; A. Sengupta; K. M Merz Jr J. Am. Chem. Soc. 2020, 142, 6365-6374 (https://doi.org/10.1021/jacs.0c01329)
“Validation of Free Energy Methods in AMBER” H.-C. Tsai, T.; Yujun; T.-S. Lee; K. M. Merz, Jr.; D. York J. Chem Inf. Model, 2020, 60, 5296-5300. (https://doi.org/10.1021/acs.jcim.0c00285)
“Metabolite Structure Assignment Using in silico NMR Techniques” S. Das; A. Edison; K. M. Merz, Jr. Anal. Chem., 2020, 92, 10412-10419. https://doi.org/10.1021/acs.analchem.0c00768
“Parallel Implementation of Density Functional Theory Methods in the Quantum Interaction Computational Kernel Program” M. Manathunga; Y. Miao; D. Mu; A. Goetz; K. M. Merz Jr. J. Chem. Theory Comput., 2020, 16, 4315-4326.https://doi.org/10.1021/acs.jctc.0c00290 (ChemXriv: https://doi.org/10.26434/chemrxiv.12018963.v1)
“Refinement of Pairwise Potentials via Logistic Regression to Score Protein-Protein Interactions” K. A. Tanemura; J. Pei; K. M. Merz, Jr. Proteins: Struct. Func. Bioinform. 2020, 88, 1559-1568. https://doi.org/10.1002/prot.25973
“OSiRIS: A Distributed Storage and Networking Project Up-date” S. McKee; B. Meekhof; E. Kissel; A. Keen; K. M. Merz, Jr.; M. Thompson Proceedings of CHEP2019 2020, 245, 04012. https://doi.org/10.1051/epjconf/202024504012
"Receptor-Ligand Binding Free Energies from a Consecutive Histograms Monte Carlo Sampling Method" H. Liu, Hao; J. Deng; Z.; Y.-W. Lin; K. M. Merz, Jr.; Z., Zheng J. Chem. Theory Comput., 2020, 16, 6645-6655. https://doi.org/10.1021/acs.jctc.0c00457
"MRP.py: A Parameterizer of Post-Translationally Modified Residues" P. Sahrmann; P. Donnan; K. M. Merz, Jr.; S. Mansoorabadi; D. Goodwin J. Chem. Theory Comput., 2020, 60, 4424-4428. https://doi.org/10.1021/acs.jcim.0c00472
“Pair Potentials as Machine Learning Features” J. Pei; L. F. Song; K. M. Merz, Jr. J. Chem. Theory Comput. 2020, 16, 5385-5400. https://doi.org/10.1021/acs.jctc.9b01246
“Systematic Parameterization of Divalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models” J. Pei; L. F. Song; K. M. Merz, Jr. J. Chem. Theory Comput. 2020, 16, 4429-4442. ttps://doi.org/10.1021/acs.jctc.0c00194
“AMBER 20” David A Case, Kellon Belfon, Ido Ben-Shalom, Scott R Brozell, David Cerutti, Thomas Cheatham, Vinícius Wilian D Cruzeiro, Tom Darden, Robert E Duke, George Giambasu, Mike Gilson, Holger Gohlke, Andreas Götz, Robert Harris, Saeed Izadi, Koushik Kasavajhala, Andriy Kovalenko, Robert Krasny, Tom Kurtzman, Taisung Lee, Scott LeGrand, Pengfei Li, Charles Lin, Jian Liu, Tyler Luchko, Ray Luo, Viet Man, Kenneth M Merz, Yinglong Miao, Gérald Monard, Hai Nguyen, Alexey Onufriev, Feng Pan, Sergio Pantano, Ruxi Qi, Daniel R Roe, Adrian Roitberg, Celeste Sagui, Stephan Schott-Verdugo, Jana Shen, Carlos Simmerling, Jamie Smith, Jason Swails, Ross Walker, Jinan Wang, Leighton Wilson, Romain M Wolf, Xiongwu Wu, Yeyue Xiong, Yi Xue, Darrin York, Peter A Kollman 2020 (http://ambermd.org)
“Evolution of Alchemical Free Energy Methods in Drug Discovery” L. F. Song; K. M. Merz, Jr J. Chem Inf. Model, 2020, 60, 5308-5318. https://doi.org/10.1021/acs.jcim.0c00547
“Converging Interests: Chemoinformatics, History, and Bibliometrics” W. Zhao; D. Korobskiy; S. Chandrasekharan; K. M. Merz, Jr; G. Chacko J. Chem Inf. Model, 2020, 60, 5870-5872. https://doi.org/10.1021/acs.jcim.0c01098
“ReaxFF/AMBER—A Framework for Hybrid Reactive/Nonreactive Force Field Molecular Dynamics Simulations” A. Rahnamoun, M. C. Kaymak, M. Manathunga, A.W. Götz, A.C.T. Van Duin, K. M. Merz, Jr.; H. M. Aktulga J. Chem. Theory Comput. 2020, 16, 7645-7654. https://doi.org/10.1021/acs.jctc.0c00874