Kenneth M. Merz Jr.

80 papers C 1Journal 79

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Automated Force Field Developer and Optimizer Platform: Torsion Reparameterization. J. Chem. Inf. Model. Alejandro Blanco-Gonzalez, William Betancourt, Ryan Snyder, Shi Zhang, Timothy J. Giese, Zeke Piskulich, Andreas W. Götz, Kenneth M. Merz Jr., Darrin M. York, Hasan Metin Aktulga, Madushanka Manathunga
2026	J	`jnl`	Beyond Summary: Reviews That Shape the Field of Computational Molecular Sciences. J. Chem. Inf. Model. Thereza A. Soares, Kenneth M. Merz Jr.
2026	J	`jnl`	QUICK and Robust ESP and RESP Charges for Computational Biochemistry: Open-Source GPU Implementation. J. Chem. Inf. Model. Vikrant Tripathy, Etienne Palos, Kenneth M. Merz Jr., Francesco Paesani, Andreas W. Götz
2025	J	`jnl`	Aliphatic Polyester Recognition and Reactivity at the Active Cleft of a Fungal Cutinase. J. Chem. Inf. Model. Pietro Vidossich, Madushanka Manathunga, Andreas W. Götz, Kenneth M. Merz Jr., Marco de Vivo
2025	J	`jnl`	Benchmarking MedMNIST dataset on real quantum hardware. CoRR Gurinder Singh, Hongni Jin, Kenneth M. Merz Jr.
2025	J	`jnl`	Computational Chemistry in the Global South: A Latin American Perspective. J. Chem. Inf. Model. Sergio Pantano, Luciana Capece, Laura Gagliardi, Kenneth M. Merz Jr., Victor S. Batista, Thereza A. Soares
2025	J	`jnl`	Domain-Aware Quantum Circuit for QML. CoRR Gurinder Singh, Thaddeus Pellegrini, Kenneth M. Merz Jr.
2025	J	`jnl`	PEAS: An Application for Autonomous Precision Conformation Sampling. J. Chem. Inf. Model. Mithony Keng, Kenneth M. Merz Jr.
2025	J	`jnl`	QFGN: A Quantum Approach to High-Fidelity Implicit Neural Representations. CoRR Hongni Jin, Gurinder Singh, Kenneth M. Merz Jr.
2025	J	`jnl`	Recent Developments in Amber Biomolecular Simulations. J. Chem. Inf. Model. David A. Case, David S. Cerutti, Vinícius Wilian D. Cruzeiro, Thomas A. Darden, Robert E. Duke, Mahdieh Ghazimirsaeed, George M. Giambasu, Timothy J. Giese, Andreas W. Götz, Julie A. Harris, Koushik Kasavajhala, Tai-Sung Lee, Zhen Li, Charles Lin, Jian Liu, Yinglong Miao, Romelia Salomón-Ferrer, Jana Shen, Ryan Snyder, Jason M. Swails, Ross C. Walker, Jinan Wang, Xiongwu Wu, Jinzhe Zeng, Thomas E. Cheatham III, Daniel R. Roe, Adrian E. Roitberg, Carlos Simmerling, Darrin M. York, Maria C. Nagan, Kenneth M. Merz Jr.
2025	J	`jnl`	Reflections on the 65 Years of the J. Chem. Inf. Model. Thereza A. Soares, Kenneth M. Merz Jr.
2025	J	`jnl`	State Ensemble Energy Recognition (SEER): A Hybrid Gas-Phase Molecular Charge State Predictor. J. Chem. Inf. Model. Mithony Keng, Kenneth M. Merz Jr.
2024	J	`jnl`	EDITORIAL: Chemical Compound Space Exploration by Multiscale High-Throughput Screening and Machine Learning. J. Chem. Inf. Model. Ganna Gryn'ova, Tristan Bereau, Carolin Müller, Pascal Friederich, Rebecca C. Wade, Ariane Nunes-Alves, Thereza A. Soares, Kenneth M. Merz Jr.
2024	J	`jnl`	Editorial: Cutting-Edge Methodologies in Omics Data Analysis. J. Chem. Inf. Model. Kenneth M. Merz Jr., Guo-Wei Wei, Feng Zhu
2024	J	`jnl`	Editorial: Machine Learning in Bio-cheminformatics. J. Chem. Inf. Model. Kenneth M. Merz Jr., Guo-Wei Wei, Feng Zhu
2024	J	`jnl`	Editorial: Machine Learning in Materials Science. J. Chem. Inf. Model. Kenneth M. Merz Jr., Yee-Siew Choong, Zoe Cournia, Olexandr Isayev, Thereza A. Soares, Guo-Wei Wei, Feng Zhu
2024	J	`jnl`	Eliminating the Deadwood: A Machine Learning Model for CCS Knowledge-Based Conformational Focusing for Lipids. J. Chem. Inf. Model. Mithony Keng, Kenneth M. Merz Jr.
2024	J	`jnl`	Enhancing Coarse-Grained Models through Machine Learning. J. Chem. Inf. Model. Tarak Karmakar, Thereza A. Soares, Kenneth M. Merz Jr.
2024	J	`jnl`	In Memoriam: Dr. George W. A. Milne. J. Chem. Inf. Model. Kenneth M. Merz Jr.
2024	J	`jnl`	Integrating Machine Learning and Quantum Circuits for Proton Affinity Predictions. CoRR Hongni Jin, Kenneth M. Merz Jr.
2024	J	`jnl`	Modeling Zinc Complexes Using Neural Networks. J. Chem. Inf. Model. Hongni Jin, Kenneth M. Merz Jr.
2024	J	`jnl`	Molecular Gas-Phase Conformational Ensembles. J. Chem. Inf. Model. Susanta Das, Kenneth M. Merz Jr.
2023	J	`jnl`	AlphaFold2 in Molecular Discovery. J. Chem. Inf. Model. Ariane Nunes-Alves, Kenneth M. Merz Jr.
2023	J	`jnl`	AmberTools. J. Chem. Inf. Model. David A. Case, Hasan Metin Aktulga, Kellon Belfon, David S. Cerutti, G. Andrés Cisneros, Vinícius Wilian D. Cruzeiro, Negin Forouzesh, Timothy J. Giese, Andreas W. Götz, Holger Gohlke, Saeed Izadi, Koushik Kasavajhala, Mehmet Cagri Kaymak, Edward King, Tom Kurtzman, Tai-Sung Lee, Pengfei Li, Jian Liu, Tyler Luchko, Ray Luo, Madushanka Manathunga, Matías R. Machado, Hai Minh Nguyen, Kurt A. O'Hearn, Alexey V. Onufriev, Feng Pan, Sergio Pantano, Ruxi Qi, Ali Rahnamoun, Ali Risheh, Stephan Schott-Verdugo, Akhil Shajan, Jason M. Swails, Junmei Wang, Haixin Wei, Xiongwu Wu, Yongxian Wu, Shi Zhang, Shiji Zhao, Qiang Zhu, Thomas E. Cheatham, Daniel R. Roe, Adrian E. Roitberg, Carlos Simmerling, Darrin M. York, Maria C. Nagan, Kenneth M. Merz Jr.
2023	J	`jnl`	Editorial: Harnessing the Power of Large Language Model-Based Chatbots for Scientific Discovery. J. Chem. Inf. Model. Kenneth M. Merz Jr., Guo-Wei Wei, Feng Zhu
2023	J	`jnl`	Editorial: Machine Learning in Bio-cheminformatics. J. Chem. Inf. Model. Kenneth M. Merz Jr., Guo-Wei Wei, Feng Zhu
2023	C	`conf`	End-to-End Differentiable Reactive Molecular Dynamics Simulations Using JAX. ISC Mehmet Cagri Kaymak, Samuel S. Schoenholz, Ekin D. Cubuk, Kurt A. O'Hearn, Kenneth M. Merz Jr., Hasan Metin Aktulga
2023	J	`jnl`	Guidelines for Reporting Molecular Dynamics Simulations in JCIM Publications. J. Chem. Inf. Model. Thereza A. Soares, Zoe Cournia, Kevin J. Naidoo, Rommie E. Amaro, Habibah A. Wahab, Kenneth M. Merz Jr.
2023	J	`jnl`	Modeling Reactions from Chemical Theories to Machine Learning. J. Chem. Inf. Model. Kevin J. Naidoo, Kenneth M. Merz Jr., Guo-Wei Wei
2023	J	`jnl`	Quantum Mechanics/Molecular Mechanics Simulations on NVIDIA and AMD Graphics Processing Units. J. Chem. Inf. Model. Madushanka Manathunga, Hasan Metin Aktulga, Andreas W. Götz, Kenneth M. Merz Jr.
2023	J	`jnl`	Rapid and Automated J. Chem. Inf. Model. Susanta Das, Laleh Dinpazhoh, Kiyoto Aramis Tanemura, Kenneth M. Merz Jr.
2022	J	`jnl`	Editorial on Machine Learning. J. Chem. Inf. Model. Guo-Wei Wei, Feng Zhu, Kenneth M. Merz Jr.
2022	J	`jnl`	Effect of an Inhibitor on the ACE2-Receptor-Binding Domain of SARS-CoV-2. J. Chem. Inf. Model. Gaurav Sharma, Lin Frank Song, Kenneth M. Merz Jr.
2022	J	`jnl`	The (Re)-Evolution of Quantitative Structure-Activity Relationship (QSAR) Studies Propelled by the Surge of Machine Learning Methods. J. Chem. Inf. Model. Thereza A. Soares, Ariane Nunes-Alves, Angelica Mazzolari, Fiorella Ruggiu, Guo-Wei Wei, Kenneth M. Merz Jr.
2021	J	`jnl`	AutoGraph: Autonomous Graph-Based Clustering of Small-Molecule Conformations. J. Chem. Inf. Model. Kiyoto Aramis Tanemura, Susanta Das, Kenneth M. Merz Jr.
2021	J	`jnl`	Correction to "Parameterization of Monovalent Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models". J. Chem. Inf. Model. Arkajyoti Sengupta, Zhen Li, Lin Frank Song, Pengfei Li, Kenneth M. Merz Jr.
2021	J	`jnl`	Open-Source Multi-GPU-Accelerated QM/MM Simulations with AMBER and QUICK. J. Chem. Inf. Model. Vinícius Wilian D. Cruzeiro, Madushanka Manathunga, Kenneth M. Merz Jr., Andreas W. Götz
2021	J	`jnl`	Parameterization of Monovalent Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models. J. Chem. Inf. Model. Arkajyoti Sengupta, Zhen Li, Lin Frank Song, Pengfei Li, Kenneth M. Merz Jr.
2020	J	`jnl`	Confronting Racism in Chemistry Journals. J. Chem. Inf. Model. Cynthia J. Burrows, Jiaxing Huang, Shu Wang, Hyun Jae Kim, Gerald J. Meyer, Kirk Schanze, T. Randall Lee, Jodie L. Lutkenhaus, David Kaplan, Christopher Jones, Carolyn R. Bertozzi, Laura Kiessling, Mary Beth Mulcahy, Craig Lindsley, M. G. Finn, Joel D. Blum, Prashant Kamat, Wonyong Choi, Shane Snyder, Courtney Aldrich, Stuart Rowan, Bin Liu, Dennis Liotta, Paul S. Weiss, Deqing Zhang, Krishna N. Ganesh, Harry A. Atwater, J. Justin Gooding, David T. Allen, Christopher A. Voigt, Jonathan V. Sweedler, Alanna Schepartz, Vincent Rotello, Sébastien Lecommandoux, Shana J. Sturla, Sharon Hammes-Schiffer, Jillian Buriak, Jonathan W. Steed, Hongwei Wu, Julie Zimmerman, Bryan Brooks, Phillip Savage, William Tolman, Thomas F. Hofmann, Joan F. Brennecke, Thomas A. Holme, Kenneth M. Merz Jr., Gustavo Scuseria, William Jorgensen, Gunda I. Georg, Shaomeng Wang, Philip Proteau, John R. Yates, Peter Stang, Gilbert C. Walker, Marc Hillmyer, Lynne S. Taylor, Teri W. Odom, Erick Carreira, Kai Rossen, Paul Chirik, Scott J. Miller, Joan-Emma Shea, Anne McCoy, Martin Zanni, Gregory Hartland, Gregory D. Scholes, Joseph A. Loo, James Milne, Sarah B. Tegen, Daniel T. Kulp, Julia Laskin
2020	J	`jnl`	Converging Interests: Chemoinformatics, History, and Bibliometrics. J. Chem. Inf. Model. Wenxi Zhao, Dmitriy Korobskiy, Shreya Chandrasekharan, Kenneth M. Merz Jr., George Chacko
2020	J	`jnl`	Editorial: Method and Data Sharing and Reproducibility of Scientific Results. J. Chem. Inf. Model. Kenneth M. Merz Jr., Rommie E. Amaro, Zoe Cournia, Matthias Rarey, Thereza A. Soares, Alexander Tropsha, Habibah A. Wahab, Renxiao Wang
2020	J	`jnl`	Evolution of Alchemical Free Energy Methods in Drug Discovery. J. Chem. Inf. Model. Lin Frank Song, Kenneth M. Merz Jr.
2020	J	`jnl`	Generative Models for Molecular Design. J. Chem. Inf. Model. Kenneth M. Merz Jr., Gianni De Fabritiis, Guo-Wei Wei
2020	J	`jnl`	Impact of the Journal of Chemical Information and Modeling Special Issue on Women in Computational Chemistry. J. Chem. Inf. Model. Angelica Mazzolari, Ariane Nunes-Alves, Habibah A. Wahab, Rommie E. Amaro, Zoe Cournia, Kenneth M. Merz Jr.
2020	J	`jnl`	JCIM Special Issue on Generative Models for Molecular Design. J. Chem. Inf. Model. Kenneth M. Merz Jr., Gianni De Fabritiis, Guo-Wei Wei
2020	J	`jnl`	MRP.py: A Parametrizer of Post-Translationally Modified Residues. J. Chem. Inf. Model. Patrick G. Sahrmann, Patrick H. Donnan, Kenneth M. Merz Jr., Steven O. Mansoorabadi, Douglas C. Goodwin
2020	J	`jnl`	Update to Our Reader, Reviewer, and Author Communities - April 2020. J. Chem. Inf. Model. Cynthia J. Burrows, Shu Wang, Hyun Jae Kim, Gerald J. Meyer, Kirk Schanze, T. Randall Lee, Jodie L. Lutkenhaus, David Kaplan, Christopher Jones, Carolyn R. Bertozzi, Laura Kiessling, Mary Beth Mulcahy, Craig Lindsley, M. G. Finn, Joel D. Blum, Prashant Kamat, Courtney Aldrich, Stuart Rowan, Bin Liu, Dennis Liotta, Paul S. Weiss, Deqing Zhang, Krishna N. Ganesh, Patrick M. Sexton, Harry A. Atwater, J. Justin Gooding, David T. Allen, Christopher A. Voigt, Jonathan V. Sweedler, Alanna Schepartz, Vincent Rotello, Sébastien Lecommandoux, Shana J. Sturla, Sharon Hammes-Schiffer, Jillian Buriak, Jonathan W. Steed, Hongwei Wu, Julie Zimmerman, Bryan Brooks, Phillip Savage, William Tolman, Thomas F. Hofmann, Joan F. Brennecke, Thomas A. Holme, Kenneth M. Merz Jr., Gustavo Scuseria, William Jorgensen, Gunda I. Georg, Shaomeng Wang, Philip Proteau, John R. Yates, Peter Stang, Gilbert C. Walker, Marc Hillmyer, Lynne S. Taylor, Teri W. Odom, Erick Carreira, Kai Rossen, Paul Chirik, Scott J. Miller, Anne McCoy, Joan-Emma Shea, Martin Zanni, Catherine Murphy, Gregory D. Scholes, Joseph A. Loo
2020	J	`jnl`	Validation of Free Energy Methods in AMBER. J. Chem. Inf. Model. Hsu-Chun Tsai, Yujun Tao, Tai-Sung Lee, Kenneth M. Merz Jr., Darrin M. York
2020	J	`jnl`	What Makes a Paper Be Highly Cited? 60 Years of the Journal of Chemical Information and Modeling. J. Chem. Inf. Model. Ariane Nunes-Alves, Angelica Mazzolari, Kenneth M. Merz Jr.
2019	J	`jnl`	Random Forest Refinement of Pairwise Potentials for Protein-Ligand Decoy Detection. J. Chem. Inf. Model. Jun Pei, Zheng Zheng, Hyunji Kim, Lin Frank Song, Sarah Walworth, Margaux R. Merz, Kenneth M. Merz Jr.
2019	J	`jnl`	Random Forest Refinement of the KECSA2 Knowledge-Based Scoring Function for Protein Decoy Detection. J. Chem. Inf. Model. Jun Pei, Zheng Zheng, Kenneth M. Merz Jr.
2019	J	`jnl`	Using AMBER18 for Relative Free Energy Calculations. J. Chem. Inf. Model. Lin Frank Song, Tai-Sung Lee, Chun Zhu, Darrin M. York, Kenneth M. Merz Jr.
2018	J	`jnl`	Detailed potential of mean force studies on host-guest systems from the SAMPL6 challenge. J. Comput. Aided Mol. Des. Lin Frank Song, Nupur Bansal, Zheng Zheng, Kenneth M. Merz Jr.
2018	J	`jnl`	Investing in the Future. J. Chem. Inf. Model. Kenneth M. Merz Jr.
2017	J	`jnl`	On the fly estimation of host-guest binding free energies using the movable type method: participation in the SAMPL5 blind challenge. J. Comput. Aided Mol. Des. Nupur Bansal, Zheng Zheng, David S. Cerutti, Kenneth M. Merz Jr.
2017	J	`jnl`	The Ecstasy and Agony of Assay Interference Compounds. J. Chem. Inf. Model. Courtney Aldrich, Carolyn R. Bertozzi, Gunda I. Georg, Laura Kiessling, Craig Lindsley, Dennis Liotta, Kenneth M. Merz Jr., Alanna Schepartz, Shaomeng Wang
2016	J	`jnl`	MCPB.py: A Python Based Metal Center Parameter Builder. J. Chem. Inf. Model. Pengfei Li, Kenneth M. Merz Jr.
2015	J	`jnl`	Introducing the Review Manuscript Type. J. Chem. Inf. Model. Kenneth M. Merz Jr.
2015	J	`jnl`	Letter from the Editors. J. Chem. Inf. Model. Kenneth M. Merz Jr., Matthias Rarey, Alexander Tropsha, Habibah A. Wahab
2015	J	`jnl`	Reduction of Urease Activity by Interaction with the Flap Covering the Active Site. J. Chem. Inf. Model. Lee Macomber, Mona S. Minkara, Robert P. Hausinger, Kenneth M. Merz Jr.
2014	J	`jnl`	New Manuscript Type: Application Note. J. Chem. Inf. Model. Kenneth M. Merz Jr.
2013	J	`jnl`	Development of the Knowledge-Based and Empirical Combined Scoring Algorithm (KECSA) To Score Protein-Ligand Interactions. J. Chem. Inf. Model. Zheng Zheng, Kenneth M. Merz Jr.
2012	J	`jnl`	Comment on "a minimal implementation of the AMBER-GAUSSIAN interface for J. Comput. Chem. Benjamin P. Roberts, Gustavo de M. Seabra, Adrian E. Roitberg, Kenneth M. Merz Jr., Erik Deumens, Juan Torras, Samuel B. Trickey
2012	J	`jnl`	Prediction of trypsin/molecular fragment binding affinities by free energy decomposition and empirical scores. J. Comput. Aided Mol. Des. Mark L. Benson, John C. Faver, Melek N. Ucisik, Danial S. Dashti, Zheng Zheng, Kenneth M. Merz Jr.
2012	J	`jnl`	QM/MM refinement and analysis of protein bound retinoic acid. J. Comput. Chem. Xue Li, Zheng Fu, Kenneth M. Merz Jr.
2011	J	`jnl`	Accurate assessment of the strain energy in a protein-bound drug using QM/MM X-ray refinement and converged quantum chemistry. J. Comput. Chem. Zheng Fu, Xue Li, Kenneth M. Merz Jr.
2011	J	`jnl`	Ligand Identification Scoring Algorithm (LISA). J. Chem. Inf. Model. Zheng Zheng, Kenneth M. Merz Jr.
2006	J	`jnl`	Quantum mechanical and molecular dynamics simulations of ureases and Zn beta-lactamases. J. Comput. Chem. Guillermina Estiu, Dimas Suárez, Kenneth M. Merz Jr.
2005	J	`jnl`	QMQSAR: Utilization of a semiempirical probe potential in a field-based QSAR method. J. Comput. Chem. Steven L. Dixon, Kenneth M. Merz Jr., Giorgio Lauri, James C. Ianni
2005	J	`jnl`	The Amber biomolecular simulation programs. J. Comput. Chem. David A. Case, Thomas E. Cheatham III, Tom Darden, Holger Gohlke, Ray Luo, Kenneth M. Merz Jr., Alexey Onufriev, Carlos Simmerling, Bing Wang, Robert J. Woods
2004	J	`jnl`	PM3-compatible zinc parameters optimized for metalloenzyme active sites. J. Comput. Chem. Edward N. Brothers, Dimas Suárez, David W. Deerfield II, Kenneth M. Merz Jr.
2002	J	`jnl`	Can we separate active from inactive conformations? J. Comput. Aided Mol. Des. David J. Diller, Kenneth M. Merz Jr.
2002	J	`jnl`	Computation of the physio-chemical properties and data mining of large molecular collections. J. Comput. Chem. Ailan Cheng, David J. Diller, Steven L. Dixon, William J. Egan, George Lauri, Kenneth M. Merz Jr.
2002	J	`jnl`	Molecular dynamics simulations of the dinuclear zinc--lactamase from Bacteroides fragilis complexed with imipenem. J. Comput. Chem. Dimas Suárez, Natalia Díaz, Kenneth M. Merz Jr.
2000	J	`jnl`	Linear scaling molecular orbital calculations of biological systems using the semiempirical divide and conquer method. J. Comput. Chem. Arjan van der Vaart, Valentin Gogonea, Steven L. Dixon, Kenneth M. Merz Jr.
1995	J	`jnl`	A Highly Portable Parallel Implementation of AMBER4 Using the Message Passing Interface Standart. J. Comput. Chem. James J. Vincent, Kenneth M. Merz Jr.
1995	J	`jnl`	An Examination of a Density Functional/Molecular Mechanical Coupled Potential. J. Comput. Chem. Robert V. Stanton, David S. Hartsough, Kenneth M. Merz Jr.
1994	J	`jnl`	A Force Field for Monosaccharides and (1->4) Linked Polysaccharides. J. Comput. Chem. Timothy M. Glennon, Yajun Zheng, Scott M. Le Grand, Brad A. Shutzberg, Kenneth M. Merz Jr.
1993	J	`jnl`	Rapid approximation to molecular surface area via the use of Boolean logic and look-up tables. J. Comput. Chem. Scott M. Le Grand, Kenneth M. Merz Jr.
1993	J	`jnl`	The application of the genetic algorithm to the minimization of potential energy functions. J. Glob. Optim. Scott M. Le Grand, Kenneth M. Merz Jr.