Kenneth M. Merz Jr.

Publication Activity (10 Years)

Years Active: 1993-2024
Publications (10 Years): 42

Top Topics

Molecular Dynamics Simulations

Materials Science

Machine Learning

Top Venues

J. Chem. Inf. Model.

J. Comput. Aided Mol. Des.

Publications

Kenneth M. Merz Jr.
In Memoriam: Dr. George W. A. Milne. J. Chem. Inf. Model. 64 (1) (2024)
Kenneth M. Merz Jr., Yee-Siew Choong, Zoe Cournia, Olexandr Isayev, Thereza A. Soares, Guo-Wei Wei, Feng Zhu
Editorial: Machine Learning in Materials Science. J. Chem. Inf. Model. 64 (10) (2024)
Hongni Jin, Kenneth M. Merz Jr.
Modeling Zinc Complexes Using Neural Networks. J. Chem. Inf. Model. 64 (8) (2024)
Tarak Karmakar, Thereza A. Soares, Kenneth M. Merz Jr.
Enhancing Coarse-Grained Models through Machine Learning. J. Chem. Inf. Model. 64 (8) (2024)
Kenneth M. Merz Jr., Guo-Wei Wei, Feng Zhu
Editorial: Machine Learning in Bio-cheminformatics. J. Chem. Inf. Model. 64 (7) (2024)
Susanta Das, Kenneth M. Merz Jr.
Molecular Gas-Phase Conformational Ensembles. J. Chem. Inf. Model. 64 (3) (2024)
Kenneth M. Merz Jr., Guo-Wei Wei, Feng Zhu
Editorial: Cutting-Edge Methodologies in Omics Data Analysis. J. Chem. Inf. Model. 64 (13) (2024)
Ariane Nunes-Alves, Kenneth M. Merz Jr.
AlphaFold2 in Molecular Discovery. J. Chem. Inf. Model. 63 (19) (2023)
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.
AmberTools. J. Chem. Inf. Model. 63 (20) (2023)
Kevin J. Naidoo, Kenneth M. Merz Jr., Guo-Wei Wei
Modeling Reactions from Chemical Theories to Machine Learning. J. Chem. Inf. Model. 63 (23) (2023)
Susanta Das, Laleh Dinpazhoh, Kiyoto Aramis Tanemura, Kenneth M. Merz Jr.
Metabolite Collisional Cross Section Prediction from SMILES Input. J. Chem. Inf. Model. 63 (16) (2023)
Kenneth M. Merz Jr., Guo-Wei Wei, Feng Zhu
Editorial: Machine Learning in Bio-cheminformatics. J. Chem. Inf. Model. 63 (1) (2023)
Kenneth M. Merz Jr., Guo-Wei Wei, Feng Zhu
Editorial: Harnessing the Power of Large Language Model-Based Chatbots for Scientific Discovery. J. Chem. Inf. Model. 63 (17) (2023)
Thereza A. Soares, Zoe Cournia, Kevin J. Naidoo, Rommie E. Amaro, Habibah A. Wahab, Kenneth M. Merz Jr.
Guidelines for Reporting Molecular Dynamics Simulations in JCIM Publications. J. Chem. Inf. Model. 63 (11) (2023)
Madushanka Manathunga, Hasan Metin Aktulga, Andreas W. Götz, Kenneth M. Merz Jr.
Quantum Mechanics/Molecular Mechanics Simulations on NVIDIA and AMD Graphics Processing Units. J. Chem. Inf. Model. 63 (3) (2023)
Mehmet Cagri Kaymak, Samuel S. Schoenholz, Ekin D. Cubuk, Kurt A. O'Hearn, Kenneth M. Merz Jr., Hasan Metin Aktulga
End-to-End Differentiable Reactive Molecular Dynamics Simulations Using JAX. ISC (2023)
Guo-Wei Wei, Feng Zhu, Kenneth M. Merz Jr.
Editorial on Machine Learning. J. Chem. Inf. Model. 62 (17) (2022)
Thereza A. Soares, Ariane Nunes-Alves, Angelica Mazzolari, Fiorella Ruggiu, Guo-Wei Wei, Kenneth M. Merz Jr.
The (Re)-Evolution of Quantitative Structure-Activity Relationship (QSAR) Studies Propelled by the Surge of Machine Learning Methods. J. Chem. Inf. Model. 62 (22) (2022)
Gaurav Sharma, Lin Frank Song, Kenneth M. Merz Jr.
Effect of an Inhibitor on the ACE2-Receptor-Binding Domain of SARS-CoV-2. J. Chem. Inf. Model. 62 (24) (2022)
Kiyoto Aramis Tanemura, Susanta Das, Kenneth M. Merz Jr.
AutoGraph: Autonomous Graph-Based Clustering of Small-Molecule Conformations. J. Chem. Inf. Model. 61 (4) (2021)
Arkajyoti Sengupta, Zhen Li, Lin Frank Song, Pengfei Li, Kenneth M. Merz Jr.
Correction to "Parameterization of Monovalent Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models". J. Chem. Inf. Model. 61 (7) (2021)
Vinícius Wilian D. Cruzeiro, Madushanka Manathunga, Kenneth M. Merz Jr., Andreas W. Götz
Open-Source Multi-GPU-Accelerated QM/MM Simulations with AMBER and QUICK. J. Chem. Inf. Model. 61 (5) (2021)
Arkajyoti Sengupta, Zhen Li, Lin Frank Song, Pengfei Li, Kenneth M. Merz Jr.
Parameterization of Monovalent Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models. J. Chem. Inf. Model. 61 (2) (2021)
Lin Frank Song, Kenneth M. Merz Jr.
Evolution of Alchemical Free Energy Methods in Drug Discovery. J. Chem. Inf. Model. 60 (11) (2020)
Cynthia J. Burrows, Shu Wang, Hyun Jae Kim, Gerald J. Meyer, Kirk Schanze, T. Randall Lee, Jodie L. Lutkenhaus, David Kaplan, Christopher Jones, Carolyn 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 Scholes, Joseph A. Loo
Update to Our Reader, Reviewer, and Author Communities - April 2020. J. Chem. Inf. Model. 60 (6) (2020)
Hsu-Chun Tsai, Yujun Tao, Tai-Sung Lee, Kenneth M. Merz Jr., Darrin M. York
Validation of Free Energy Methods in AMBER. J. Chem. Inf. Model. 60 (11) (2020)
Kenneth M. Merz Jr., Rommie E. Amaro, Zoe Cournia, Matthias Rarey, Thereza A. Soares, Alexander Tropsha, Habibah A. Wahab, Renxiao Wang
Editorial: Method and Data Sharing and Reproducibility of Scientific Results. J. Chem. Inf. Model. 60 (12) (2020)
Kenneth M. Merz Jr., Gianni De Fabritiis, Guo-Wei Wei
Generative Models for Molecular Design. J. Chem. Inf. Model. 60 (12) (2020)
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 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 Scholes, Joseph A. Loo, James Milne, Sarah B. Tegen, Daniel T. Kulp, Julia Laskin
Confronting Racism in Chemistry Journals. J. Chem. Inf. Model. 60 (7) (2020)
Angelica Mazzolari, Ariane Nunes-Alves, Habibah A. Wahab, Rommie E. Amaro, Zoe Cournia, Kenneth M. Merz Jr.
Impact of the Journal of Chemical Information and Modeling Special Issue on Women in Computational Chemistry. J. Chem. Inf. Model. 60 (7) (2020)
Ariane Nunes-Alves, Angelica Mazzolari, Kenneth M. Merz Jr.
What Makes a Paper Be Highly Cited? 60 Years of the Journal of Chemical Information and Modeling. J. Chem. Inf. Model. 60 (12) (2020)
Wenxi Zhao, Dmitriy Korobskiy, Shreya Chandrasekharan, Kenneth M. Merz Jr., George Chacko
Converging Interests: Chemoinformatics, History, and Bibliometrics. J. Chem. Inf. Model. 60 (12) (2020)
Kenneth M. Merz Jr., Gianni De Fabritiis, Guo-Wei Wei
JCIM Special Issue on Generative Models for Molecular Design. J. Chem. Inf. Model. 60 (3) (2020)
Patrick G. Sahrmann, Patrick H. Donnan, Kenneth M. Merz Jr., Steven O. Mansoorabadi, Douglas C. Goodwin
MRP.py: A Parametrizer of Post-Translationally Modified Residues. J. Chem. Inf. Model. 60 (10) (2020)
Jun Pei, Zheng Zheng, Kenneth M. Merz Jr.
Random Forest Refinement of the KECSA2 Knowledge-Based Scoring Function for Protein Decoy Detection. J. Chem. Inf. Model. 59 (5) (2019)
Lin Frank Song, Tai-Sung Lee, Chun Zhu, Darrin M. York, Kenneth M. Merz Jr.
Using AMBER18 for Relative Free Energy Calculations. J. Chem. Inf. Model. 59 (7) (2019)
Jun Pei, Zheng Zheng, Hyunji Kim, Lin Frank Song, Sarah Walworth, Margaux R. Merz, Kenneth M. Merz Jr.
Random Forest Refinement of Pairwise Potentials for Protein-Ligand Decoy Detection. J. Chem. Inf. Model. 59 (7) (2019)
Kenneth M. Merz Jr.
Investing in the Future. J. Chem. Inf. Model. 58 (6) (2018)
Lin Frank Song, Nupur Bansal, Zheng Zheng, Kenneth M. Merz Jr.
Detailed potential of mean force studies on host-guest systems from the SAMPL6 challenge. J. Comput. Aided Mol. Des. 32 (10) (2018)
Courtney Aldrich, Carolyn Bertozzi, Gunda I. Georg, Laura Kiessling, Craig Lindsley, Dennis Liotta, Kenneth M. Merz Jr., Alanna Schepartz, Shaomeng Wang
The Ecstasy and Agony of Assay Interference Compounds. J. Chem. Inf. Model. 57 (3) (2017)
Nupur Bansal, Zheng Zheng, David S. Cerutti, Kenneth M. Merz Jr.
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. 31 (1) (2017)
Pengfei Li, Kenneth M. Merz Jr.
MCPB.py: A Python Based Metal Center Parameter Builder. J. Chem. Inf. Model. 56 (4) (2016)
Kenneth M. Merz Jr., Matthias Rarey, Alexander Tropsha, Habibah A. Wahab
Letter from the Editors. J. Chem. Inf. Model. 55 (4) (2015)
Lee Macomber, Mona S. Minkara, Robert P. Hausinger, Kenneth M. Merz Jr.
Reduction of Urease Activity by Interaction with the Flap Covering the Active Site. J. Chem. Inf. Model. 55 (2) (2015)
Kenneth M. Merz Jr.
Introducing the Review Manuscript Type. J. Chem. Inf. Model. 55 (7) (2015)
Kenneth M. Merz Jr.
New Manuscript Type: Application Note. J. Chem. Inf. Model. 54 (11) (2014)
Zheng Zheng, Kenneth M. Merz Jr.
Development of the Knowledge-Based and Empirical Combined Scoring Algorithm (KECSA) To Score Protein-Ligand Interactions. J. Chem. Inf. Model. 53 (5) (2013)
Xue Li, Zheng Fu, Kenneth M. Merz Jr.
QM/MM refinement and analysis of protein bound retinoic acid. J. Comput. Chem. 33 (3) (2012)
Benjamin P. Roberts, Gustavo de M. Seabra, Adrian E. Roitberg, Kenneth M. Merz Jr., Erik Deumens, Juan Torras, Samuel B. Trickey
QM/MM-MD simulation". J. Comput. Chem. 33 (19) (2012)
Mark L. Benson, John C. Faver, Melek N. Ucisik, Danial S. Dashti, Zheng Zheng, Kenneth M. Merz Jr.
Prediction of trypsin/molecular fragment binding affinities by free energy decomposition and empirical scores. J. Comput. Aided Mol. Des. 26 (5) (2012)
Zheng Fu, Xue Li, Kenneth M. Merz Jr.
Accurate assessment of the strain energy in a protein-bound drug using QM/MM X-ray refinement and converged quantum chemistry. J. Comput. Chem. 32 (12) (2011)
Zheng Zheng, Kenneth M. Merz Jr.
Ligand Identification Scoring Algorithm (LISA). J. Chem. Inf. Model. 51 (6) (2011)
Guillermina Estiu, Dimas Suárez, Kenneth M. Merz Jr.
Quantum mechanical and molecular dynamics simulations of ureases and Zn beta-lactamases. J. Comput. Chem. 27 (12) (2006)
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
The Amber biomolecular simulation programs. J. Comput. Chem. 26 (16) (2005)
Steven L. Dixon, Kenneth M. Merz Jr., Giorgio Lauri, James C. Ianni
QMQSAR: Utilization of a semiempirical probe potential in a field-based QSAR method. J. Comput. Chem. 26 (1) (2005)
Edward N. Brothers, Dimas Suárez, David W. Deerfield II, Kenneth M. Merz Jr.
PM3-compatible zinc parameters optimized for metalloenzyme active sites. J. Comput. Chem. 25 (14) (2004)
Ailan Cheng, David J. Diller, Steven L. Dixon, William J. Egan, George Lauri, Kenneth M. Merz Jr.
Computation of the physio-chemical properties and data mining of large molecular collections. J. Comput. Chem. 23 (1) (2002)
Dimas Suárez, Natalia Díaz, Kenneth M. Merz Jr.
Molecular dynamics simulations of the dinuclear zinc--lactamase from Bacteroides fragilis complexed with imipenem. J. Comput. Chem. 23 (16) (2002)
David J. Diller, Kenneth M. Merz Jr.
Can we separate active from inactive conformations? J. Comput. Aided Mol. Des. 16 (2) (2002)
Arjan van der Vaart, Valentin Gogonea, Steven L. Dixon, Kenneth M. Merz Jr.
Linear scaling molecular orbital calculations of biological systems using the semiempirical divide and conquer method. J. Comput. Chem. 21 (16) (2000)
James J. Vincent, Kenneth M. Merz Jr.
A Highly Portable Parallel Implementation of AMBER4 Using the Message Passing Interface Standart. J. Comput. Chem. 16 (11) (1995)
Robert V. Stanton, David S. Hartsough, Kenneth M. Merz Jr.
An Examination of a Density Functional/Molecular Mechanical Coupled Potential. J. Comput. Chem. 16 (1) (1995)
Timothy M. Glennon, Yajun Zheng, Scott M. Le Grand, Brad A. Shutzberg, Kenneth M. Merz Jr.
A Force Field for Monosaccharides and (1->4) Linked Polysaccharides. J. Comput. Chem. 15 (9) (1994)
Scott M. Le Grand, Kenneth M. Merz Jr.
The application of the genetic algorithm to the minimization of potential energy functions. J. Glob. Optim. 3 (1) (1993)
Scott M. Le Grand, Kenneth M. Merz Jr.
Rapid approximation to molecular surface area via the use of Boolean logic and look-up tables. J. Comput. Chem. 14 (3) (1993)