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ORCIDKenneth M. Merz Jr.
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2020 – today
- 2024
[j66]Kenneth M. Merz Jr.
:
In Memoriam: Dr. George W. A. Milne. J. Chem. Inf. Model. 64(1): 1-2 (2024)- [j65]Susanta Das, Kenneth M. Merz Jr.:
Molecular Gas-Phase Conformational Ensembles. J. Chem. Inf. Model. 64(3): 749-760 (2024) - [j64]Kenneth M. Merz Jr., Guo-Wei Wei, Feng Zhu:
Editorial: Machine Learning in Bio-cheminformatics. J. Chem. Inf. Model. 64(7): 2125-2128 (2024) - [j63]Tarak Karmakar, Thereza A. Soares, Kenneth M. Merz Jr.:
Enhancing Coarse-Grained Models through Machine Learning. J. Chem. Inf. Model. 64(8): 2931-2932 (2024) - [j62]Hongni Jin, Kenneth M. Merz Jr.:
Modeling Zinc Complexes Using Neural Networks. J. Chem. Inf. Model. 64(8): 3140-3148 (2024) - [j61]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): 3959-3960 (2024) - [j60]Kenneth M. Merz Jr., Guo-Wei Wei, Feng Zhu:
Editorial: Cutting-Edge Methodologies in Omics Data Analysis. J. Chem. Inf. Model. 64(13): 4939-4940 (2024) - [j59]Ganna Gryn'ova, Tristan Bereau, Carolin Müller, Pascal Friederich, Rebecca C. Wade, Ariane Nunes-Alves, Thereza A. Soares, Kenneth M. Merz Jr.:
EDITORIAL: Chemical Compound Space Exploration by Multiscale High-Throughput Screening and Machine Learning. J. Chem. Inf. Model. 64(15): 5737-5738 (2024) - [j58]Mithony Keng, Kenneth M. Merz Jr.:
Eliminating the Deadwood: A Machine Learning Model for CCS Knowledge-Based Conformational Focusing for Lipids. J. Chem. Inf. Model. 64(20): 7864-7872 (2024) - [i1]Hongni Jin, Kenneth M. Merz Jr.:
Integrating Machine Learning and Quantum Circuits for Proton Affinity Predictions. CoRR abs/2411.17856 (2024) - 2023
- [j57]Kenneth M. Merz Jr., Guo-Wei Wei, Feng Zhu:
Editorial: Machine Learning in Bio-cheminformatics. J. Chem. Inf. Model. 63(1): 1 (2023) - [j56]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): 711-717 (2023) - [j55]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): 3227-3229 (2023) - [j54]Susanta Das, Laleh Dinpazhoh, Kiyoto Aramis Tanemura, Kenneth M. Merz Jr.:
Rapid and Automated Ab Initio Metabolite Collisional Cross Section Prediction from SMILES Input. J. Chem. Inf. Model. 63(16): 4995-5000 (2023) - [j53]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): 5395 (2023) - [j52]Ariane Nunes-Alves, Kenneth M. Merz Jr.:
AlphaFold2 in Molecular Discovery. J. Chem. Inf. Model. 63(19): 5947-5949 (2023) - [j51]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): 6183-6191 (2023) - [j50]Kevin J. Naidoo, Kenneth M. Merz Jr., Guo-Wei Wei:
Modeling Reactions from Chemical Theories to Machine Learning. J. Chem. Inf. Model. 63(23): 7273 (2023) - [c1]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: 202-219 - 2022
- [j49]Guo-Wei Wei, Feng Zhu, Kenneth M. Merz Jr.:
Editorial on Machine Learning. J. Chem. Inf. Model. 62(17): 3941 (2022) - [j48]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): 5317-5320 (2022) - [j47]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): 6574-6585 (2022) - 2021
- [j46]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): 869-880 (2021) - [j45]Kiyoto Aramis Tanemura, Susanta Das, Kenneth M. Merz Jr.:
AutoGraph: Autonomous Graph-Based Clustering of Small-Molecule Conformations. J. Chem. Inf. Model. 61(4): 1647-1656 (2021) - [j44]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): 2109-2115 (2021) - [j43]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): 3734-3735 (2021) - 2020
- [j42]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): 1072 (2020) - [j41]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 Scholes, Joseph A. Loo:
Update to Our Reader, Reviewer, and Author Communities - April 2020. J. Chem. Inf. Model. 60(6): 2651-2652 (2020) - [j40]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 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): 3325-3327 (2020) - [j39]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): 3328-3330 (2020) - [j38]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): 4424-4428 (2020) - [j37]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): 5296-5300 (2020) - [j36]Lin Frank Song, Kenneth M. Merz Jr.:
Evolution of Alchemical Free Energy Methods in Drug Discovery. J. Chem. Inf. Model. 60(11): 5308-5318 (2020) - [j35]Kenneth M. Merz Jr., Gianni De Fabritiis, Guo-Wei Wei:
Generative Models for Molecular Design. J. Chem. Inf. Model. 60(12): 5635-5636 (2020) - [j34]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): 5866-5867 (2020) - [j33]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): 5868-5869 (2020) - [j32]Wenxi Zhao, Dmitriy Korobskiy, Shreya Chandrasekharan, Kenneth M. Merz Jr., George Chacko:
Converging Interests: Chemoinformatics, History, and Bibliometrics. J. Chem. Inf. Model. 60(12): 5870-5872 (2020)
2010 – 2019
- 2019
- [j31]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): 1919-1929 (2019) - [j30]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): 3128-3135 (2019) - [j29]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): 3305-3315 (2019) - 2018
- [j28]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): 1013-1026 (2018) - [j27]Kenneth M. Merz Jr.:
Investing in the Future. J. Chem. Inf. Model. 58(6): 1153 (2018) - 2017
- [j26]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): 47-60 (2017) - [j25]Courtney Aldrich, Carolyn R. 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): 387-390 (2017) - 2016
- [j24]Pengfei Li, Kenneth M. Merz Jr.:
MCPB.py: A Python Based Metal Center Parameter Builder. J. Chem. Inf. Model. 56(4): 599-604 (2016) - 2015
- [j23]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): 354-361 (2015) - [j22]Kenneth M. Merz Jr., Matthias Rarey, Alexander Tropsha, Habibah A. Wahab:
Letter from the Editors. J. Chem. Inf. Model. 55(4): 719-720 (2015) - [j21]Kenneth M. Merz Jr.:
Introducing the Review Manuscript Type. J. Chem. Inf. Model. 55(7): 1291 (2015) - 2014
- [j20]Kenneth M. Merz Jr.:
New Manuscript Type: Application Note. J. Chem. Inf. Model. 54(11): 3045 (2014) - 2013
- [j19]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): 1073-1083 (2013) - 2012
- [j18]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): 647-659 (2012) - [j17]Xue Li, Zheng Fu, Kenneth M. Merz Jr.:
QM/MM refinement and analysis of protein bound retinoic acid. J. Comput. Chem. 33(3): 301-310 (2012) - [j16]Benjamin P. Roberts, Gustavo de M. Seabra, Adrian E. Roitberg, Kenneth M. Merz Jr., Erik Deumens, Juan Torras, Samuel B. Trickey:
Comment on "a minimal implementation of the AMBER-GAUSSIAN interface for Ab Initio QM/MM-MD simulation". J. Comput. Chem. 33(19): 1643-1644 (2012) - 2011
- [j15]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): 2587-2597 (2011) - [j14]Zheng Zheng, Kenneth M. Merz Jr.:
Ligand Identification Scoring Algorithm (LISA). J. Chem. Inf. Model. 51(6): 1296-1306 (2011)
2000 – 2009
- 2006
- [j13]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): 1240-1262 (2006) - 2005
- [j12]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): 23-34 (2005) - [j11]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): 1668-1688 (2005) - 2004
- [j10]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): 1677-1692 (2004) - 2002
- [j9]David J. Diller, Kenneth M. Merz Jr.:
Can we separate active from inactive conformations? J. Comput. Aided Mol. Des. 16(2): 105-112 (2002) - [j8]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): 172-183 (2002) - [j7]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): 1587-1600 (2002) - 2000
- [j6]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): 1494-1504 (2000)
1990 – 1999
- 1995
- [j5]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): 113-128 (1995) - [j4]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): 1420-1427 (1995) - 1994
- [j3]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): 1019-1040 (1994) - 1993
- [j2]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): 349-352 (1993) - [j1]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): 49-66 (1993)
Coauthor Index
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