Rapid approximation to molecular surface area via the use of Boolean logic and look-up tables. - Scott M. Le Grand; Kenneth M. Merz Jr. (J. Comput. Chem., 1993)

The application of the genetic algorithm to the minimization of potential energy functions. - Scott M. Le Grand; Kenneth M. Merz Jr. (J. Glob. Optim., 1993)

A Force Field for Monosaccharides and (1->4) Linked Polysaccharides. - Timothy M. Glennon; Yajun Zheng; Scott M. Le Grand; Brad A. Shutzberg; Kenneth M. Merz Jr. (J. Comput. Chem., 1994)

An Examination of a Density Functional/Molecular Mechanical Coupled Potential. - Robert V. Stanton; David S. Hartsough; Kenneth M. Merz Jr. (J. Comput. Chem., 1995)

A Highly Portable Parallel Implementation of AMBER4 Using the Message Passing Interface Standart. - James J. Vincent; Kenneth M. Merz Jr. (J. Comput. Chem., 1995)

Linear scaling molecular orbital calculations of biological systems using the semiempirical divide and conquer method. - Arjan van der Vaart; Valentin Gogonea; Steven L. Dixon; Kenneth M. Merz Jr. (J. Comput. Chem., 2000)

Can we separate active from inactive conformations? - David J. Diller; Kenneth M. Merz Jr. (J. Comput. Aided Mol. Des., 2002)

Computation of the physio-chemical properties and data mining of large molecular collections. - Ailan Cheng; David J. Diller; Steven L. Dixon; William J. Egan; George Lauri; Kenneth M. Merz Jr. (J. Comput. Chem., 2002)

Molecular dynamics simulations of the dinuclear zinc–lactamase from Bacteroides fragilis complexed with imipenem. - Dimas Suárez; Natalia Díaz; Kenneth M. Merz Jr. (J. Comput. Chem., 2002)

PM3-compatible zinc parameters optimized for metalloenzyme active sites. - Edward N. Brothers; Dimas Suárez; David W. Deerfield II; Kenneth M. Merz Jr. (J. Comput. Chem., 2004)

The Amber biomolecular simulation programs. - David A. Case; Thomas E. Cheatham III; Tom Darden; Holger Gohlke; Ray Luo 001; Kenneth M. Merz Jr.; Alexey Onufriev; Carlos Simmerling; Bing Wang; Robert J. Woods (J. Comput. Chem., 2005)

QMQSAR: Utilization of a semiempirical probe potential in a field-based QSAR method. - Steven L. Dixon; Kenneth M. Merz Jr.; Giorgio Lauri; James C. Ianni (J. Comput. Chem., 2005)

Quantum mechanical and molecular dynamics simulations of ureases and Zn beta-lactamases. - Guillermina Estiu; Dimas Suárez; Kenneth M. Merz Jr. (J. Comput. Chem., 2006)

Accurate assessment of the strain energy in a protein-bound drug using QM/MM X-ray refinement and converged quantum chemistry. - Zheng Fu; Xue Li; Kenneth M. Merz Jr. (J. Comput. Chem., 2011)

Ligand Identification Scoring Algorithm (LISA). - Zheng Zheng 002; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2011)

Prediction of trypsin/molecular fragment binding affinities by free energy decomposition and empirical scores. - Mark L. Benson; John C. Faver; Melek N. Ucisik; Danial S. Dashti; Zheng Zheng 002; Kenneth M. Merz Jr. (J. Comput. Aided Mol. Des., 2012)

QM/MM refinement and analysis of protein bound retinoic acid. - Xue Li; Zheng Fu; Kenneth M. Merz Jr. (J. Comput. Chem., 2012)

Comment on "a minimal implementation of the AMBER-GAUSSIAN interface for Ab Initio QM/MM-MD simulation". - Benjamin P. Roberts; Gustavo de M. Seabra; Adrian E. Roitberg; Kenneth M. Merz Jr.; Erik Deumens; Juan Torras; Samuel B. Trickey (J. Comput. Chem., 2012)

Development of the Knowledge-Based and Empirical Combined Scoring Algorithm (KECSA) To Score Protein-Ligand Interactions. - Zheng Zheng 002; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2013)

New Manuscript Type: Application Note. - Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2014)

Reduction of Urease Activity by Interaction with the Flap Covering the Active Site. - Lee Macomber; Mona S. Minkara; Robert P. Hausinger; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2015)

Introducing the Review Manuscript Type. - Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2015)

Letter from the Editors. - Kenneth M. Merz Jr.; Matthias Rarey; Alexander Tropsha; Habibah A. Wahab (J. Chem. Inf. Model., 2015)

MCPB.py: A Python Based Metal Center Parameter Builder. - Pengfei Li 003; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2016)

On the fly estimation of host-guest binding free energies using the movable type method: participation in the SAMPL5 blind challenge. - Nupur Bansal; Zheng Zheng 002; David S. Cerutti; Kenneth M. Merz Jr. (J. Comput. Aided Mol. Des., 2017)

The Ecstasy and Agony of Assay Interference Compounds. - Courtney Aldrich; Carolyn R. Bertozzi; Gunda I. Georg; Laura Kiessling; Craig Lindsley; Dennis Liotta; Kenneth M. Merz Jr.; Alanna Schepartz; Shaomeng Wang (J. Chem. Inf. Model., 2017)

Detailed potential of mean force studies on host-guest systems from the SAMPL6 challenge. - Lin Frank Song; Nupur Bansal; Zheng Zheng 002; Kenneth M. Merz Jr. (J. Comput. Aided Mol. Des., 2018)

Investing in the Future. - Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2018)

Random Forest Refinement of Pairwise Potentials for Protein-Ligand Decoy Detection. - Jun Pei; Zheng Zheng 002; Hyunji Kim; Lin Frank Song; Sarah Walworth; Margaux R. Merz; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2019)

Random Forest Refinement of the KECSA2 Knowledge-Based Scoring Function for Protein Decoy Detection. - Jun Pei; Zheng Zheng 002; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2019)

Using AMBER18 for Relative Free Energy Calculations. - Lin Frank Song; Tai-Sung Lee; Chun Zhu; Darrin M. York; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2019)

Confronting Racism in Chemistry Journals. - Cynthia J. Burrows; Jiaxing Huang 002; 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; et al. (J. Chem. Inf. Model., 2020)

Update to Our Reader, Reviewer, and Author Communities - April 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 R. Bertozzi; Laura Kiessling; Mary Beth Mulcahy; et al. (J. Chem. Inf. Model., 2020)

Impact of the Journal of Chemical Information and Modeling Special Issue on Women in Computational Chemistry. - Angelica Mazzolari; Ariane Nunes-Alves; Habibah A. Wahab; Rommie E. Amaro; Zoe Cournia; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2020)

Editorial: Method and Data Sharing and Reproducibility of Scientific Results. - Kenneth M. Merz Jr.; Rommie E. Amaro; Zoe Cournia; Matthias Rarey; Thereza A. Soares; Alexander Tropsha; Habibah A. Wahab; Renxiao Wang (J. Chem. Inf. Model., 2020)

JCIM Special Issue on Generative Models for Molecular Design. - Kenneth M. Merz Jr.; Gianni De Fabritiis; Guo-Wei Wei 001 (J. Chem. Inf. Model., 2020)

Generative Models for Molecular Design. - Kenneth M. Merz Jr.; Gianni De Fabritiis; Guo-Wei Wei 001 (J. Chem. Inf. Model., 2020)

What Makes a Paper Be Highly Cited? 60 Years of the Journal of Chemical Information and Modeling. - Ariane Nunes-Alves; Angelica Mazzolari; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2020)

MRP.py: A Parametrizer of Post-Translationally Modified Residues. - Patrick G. Sahrmann; Patrick H. Donnan; Kenneth M. Merz Jr.; Steven O. Mansoorabadi; Douglas C. Goodwin (J. Chem. Inf. Model., 2020)

Evolution of Alchemical Free Energy Methods in Drug Discovery. - Lin Frank Song; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2020)

Validation of Free Energy Methods in AMBER. - Hsu-Chun Tsai; Yujun Tao; Tai-Sung Lee; Kenneth M. Merz Jr.; Darrin M. York (J. Chem. Inf. Model., 2020)

Converging Interests: Chemoinformatics, History, and Bibliometrics. - Wenxi Zhao; Dmitriy Korobskiy; Shreya Chandrasekharan; Kenneth M. Merz Jr.; George Chacko (J. Chem. Inf. Model., 2020)

Open-Source Multi-GPU-Accelerated QM/MM Simulations with AMBER and QUICK. - Vinícius Wilian D. Cruzeiro; Madushanka Manathunga; Kenneth M. Merz Jr.; Andreas W. Götz (J. Chem. Inf. Model., 2021)

Correction to "Parameterization of Monovalent Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models". - Arkajyoti Sengupta; Zhen Li 038; Lin Frank Song; Pengfei Li 003; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2021)

Parameterization of Monovalent Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models. - Arkajyoti Sengupta; Zhen Li 038; Lin Frank Song; Pengfei Li 003; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2021)

AutoGraph: Autonomous Graph-Based Clustering of Small-Molecule Conformations. - Kiyoto Aramis Tanemura; Susanta Das; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2021)

Effect of an Inhibitor on the ACE2-Receptor-Binding Domain of SARS-CoV-2. - Gaurav Sharma; Lin Frank Song; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2022)

The (Re)-Evolution of Quantitative Structure-Activity Relationship (QSAR) Studies Propelled by the Surge of Machine Learning Methods. - Thereza A. Soares; Ariane Nunes-Alves; Angelica Mazzolari; Fiorella Ruggiu; Guo-Wei Wei 001; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2022)

Editorial on Machine Learning. - Guo-Wei Wei 001; Feng Zhu 004; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2022)

End-to-End Differentiable Reactive Molecular Dynamics Simulations Using JAX. - Mehmet Cagri Kaymak; Samuel S. Schoenholz; Ekin D. Cubuk; Kurt A. O'Hearn; Kenneth M. Merz Jr.; Hasan Metin Aktulga (ISC, 2023)

Editorial: Machine Learning in Bio-cheminformatics. - Kenneth M. Merz Jr.; Guo-Wei Wei 001; Feng Zhu 004 (J. Chem. Inf. Model., 2023)

Quantum Mechanics/Molecular Mechanics Simulations on NVIDIA and AMD Graphics Processing Units. - Madushanka Manathunga; Hasan Metin Aktulga; Andreas W. Götz; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2023)

Guidelines for Reporting Molecular Dynamics Simulations in JCIM Publications. - Thereza A. Soares; Zoe Cournia; Kevin J. Naidoo; Rommie E. Amaro; Habibah A. Wahab; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2023)

Rapid and Automated Ab Initio Metabolite Collisional Cross Section Prediction from SMILES Input. - Susanta Das; Laleh Dinpazhoh; Kiyoto Aramis Tanemura; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2023)

Editorial: Harnessing the Power of Large Language Model-Based Chatbots for Scientific Discovery. - Kenneth M. Merz Jr.; Guo-Wei Wei 001; Feng Zhu 004 (J. Chem. Inf. Model., 2023)

AmberTools. - 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; et al. (J. Chem. Inf. Model., 2023)

AlphaFold2 in Molecular Discovery. - Ariane Nunes-Alves; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2023)

Modeling Reactions from Chemical Theories to Machine Learning. - Kevin J. Naidoo; Kenneth M. Merz Jr.; Guo-Wei Wei 001 (J. Chem. Inf. Model., 2023)

Integrating Machine Learning and Quantum Circuits for Proton Affinity Predictions. - Hongni Jin; Kenneth M. Merz Jr. (CoRR, 2024)

Molecular Gas-Phase Conformational Ensembles. - Susanta Das; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2024)

EDITORIAL: Chemical Compound Space Exploration by Multiscale High-Throughput Screening and Machine Learning. - Ganna Gryn'ova; Tristan Bereau; Carolin Müller; Pascal Friederich; Rebecca C. Wade; Ariane Nunes-Alves; Thereza A. Soares; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2024)

Modeling Zinc Complexes Using Neural Networks. - Hongni Jin; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2024)

Enhancing Coarse-Grained Models through Machine Learning. - Tarak Karmakar; Thereza A. Soares; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2024)

Eliminating the Deadwood: A Machine Learning Model for CCS Knowledge-Based Conformational Focusing for Lipids. - Mithony Keng; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2024)

Editorial: Machine Learning in Materials Science. - Kenneth M. Merz Jr.; Yee-Siew Choong; Zoe Cournia; Olexandr Isayev; Thereza A. Soares; Guo-Wei Wei 001; Feng Zhu 004 (J. Chem. Inf. Model., 2024)

Editorial: Cutting-Edge Methodologies in Omics Data Analysis. - Kenneth M. Merz Jr.; Guo-Wei Wei 001; Feng Zhu 004 (J. Chem. Inf. Model., 2024)

In Memoriam: Dr. George W. A. Milne. - Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2024)

Recent Developments in Amber Biomolecular Simulations. - 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; et al. (J. Chem. Inf. Model., 2025)

State Ensemble Energy Recognition (SEER): A Hybrid Gas-Phase Molecular Charge State Predictor. - Mithony Keng; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2025)

Computational Chemistry in the Global South: A Latin American Perspective. - Sergio Pantano; Luciana Capece; Laura Gagliardi; Kenneth M. Merz Jr.; Victor S. Batista; Thereza A. Soares (J. Chem. Inf. Model., 2025)

Aliphatic Polyester Recognition and Reactivity at the Active Cleft of a Fungal Cutinase. - Pietro Vidossich; Madushanka Manathunga; Andreas W. Götz; Kenneth M. Merz Jr.; Marco de Vivo (J. Chem. Inf. Model., 2025)

Benchmarking MedMNIST dataset on real quantum hardware. - Gurinder Singh 006; Hongni Jin; Kenneth M. Merz Jr. (CoRR, 2025)

QFGN: A Quantum Approach to High-Fidelity Implicit Neural Representations. - Hongni Jin; Gurinder Singh 006; Kenneth M. Merz Jr. (CoRR, 2025)