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Hwang W, Austin SL, Blondel A, Boittier ED, Boresch S, Buck M, Buckner J, Caflisch A, Chang HT, Cheng X, Choi YK, Chu JW, Crowley MF, Cui Q, Damjanovic A, Deng Y, Devereux M, Ding X, Feig MF, Gao J, Glowacki DR, Gonzales JE, Hamaneh MB, Harder ED, Hayes RL, Huang J, Huang Y, Hudson PS, Im W, Islam SM, Jiang W, Jones MR, Käser S, Kearns FL, Kern NR, Klauda JB, Lazaridis T, Lee J, Lemkul JA, Liu X, Luo Y, MacKerell AD, Major DT, Meuwly M, Nam K, Nilsson L, Ovchinnikov V, Paci E, Park S, Pastor RW, Pittman AR, Post CB, Prasad S, Pu J, Qi Y, Rathinavelan T, Roe DR, Roux B, Rowley CN, Shen J, Simmonett AC, Sodt AJ, Töpfer K, Upadhyay M, van der Vaart A, Vazquez-Salazar LI, Venable RM, Warrensford LC, Woodcock HL, Wu Y, Brooks CL, Brooks BR, Karplus M. CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed. J Phys Chem B 2024; 128:9976-10042. [PMID: 39303207 PMCID: PMC11492285 DOI: 10.1021/acs.jpcb.4c04100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 08/15/2024] [Accepted: 08/22/2024] [Indexed: 09/22/2024]
Abstract
Since its inception nearly a half century ago, CHARMM has been playing a central role in computational biochemistry and biophysics. Commensurate with the developments in experimental research and advances in computer hardware, the range of methods and applicability of CHARMM have also grown. This review summarizes major developments that occurred after 2009 when the last review of CHARMM was published. They include the following: new faster simulation engines, accessible user interfaces for convenient workflows, and a vast array of simulation and analysis methods that encompass quantum mechanical, atomistic, and coarse-grained levels, as well as extensive coverage of force fields. In addition to providing the current snapshot of the CHARMM development, this review may serve as a starting point for exploring relevant theories and computational methods for tackling contemporary and emerging problems in biomolecular systems. CHARMM is freely available for academic and nonprofit research at https://academiccharmm.org/program.
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Affiliation(s)
- Wonmuk Hwang
- Department
of Biomedical Engineering, Texas A&M
University, College
Station, Texas 77843, United States
- Department
of Materials Science and Engineering, Texas
A&M University, College Station, Texas 77843, United States
- Department
of Physics and Astronomy, Texas A&M
University, College Station, Texas 77843, United States
- Center for
AI and Natural Sciences, Korea Institute
for Advanced Study, Seoul 02455, Republic
of Korea
| | - Steven L. Austin
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Arnaud Blondel
- Institut
Pasteur, Université Paris Cité, CNRS UMR3825, Structural
Bioinformatics Unit, 28 rue du Dr. Roux F-75015 Paris, France
| | - Eric D. Boittier
- Department
of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Stefan Boresch
- Faculty of
Chemistry, Department of Computational Biological Chemistry, University of Vienna, Wahringerstrasse 17, 1090 Vienna, Austria
| | - Matthias Buck
- Department
of Physiology and Biophysics, Case Western
Reserve University, School of Medicine, Cleveland, Ohio 44106, United States
| | - Joshua Buckner
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Amedeo Caflisch
- Department
of Biochemistry, University of Zürich, CH-8057 Zürich, Switzerland
| | - Hao-Ting Chang
- Institute
of Bioinformatics and Systems Biology, National
Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan, ROC
| | - Xi Cheng
- Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yeol Kyo Choi
- Department
of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Jhih-Wei Chu
- Institute
of Bioinformatics and Systems Biology, Department of Biological Science
and Technology, Institute of Molecular Medicine and Bioengineering,
and Center for Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung
University, Hsinchu 30010, Taiwan,
ROC
| | - Michael F. Crowley
- Renewable
Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Qiang Cui
- Department
of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department
of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department
of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
| | - Ana Damjanovic
- Department
of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department
of Physics and Astronomy, Johns Hopkins
University, Baltimore, Maryland 21218, United States
- Laboratory
of Computational Biology, National Heart
Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Yuqing Deng
- Shanghai
R&D Center, DP Technology, Ltd., Shanghai 201210, China
| | - Mike Devereux
- Department
of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Xinqiang Ding
- Department
of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Michael F. Feig
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
| | - Jiali Gao
- School
of Chemical Biology & Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, China
- Institute
of Systems and Physical Biology, Shenzhen
Bay Laboratory, Shenzhen, Guangdong 518055, China
- Department
of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - David R. Glowacki
- CiTIUS
Centro Singular de Investigación en Tecnoloxías Intelixentes
da USC, 15705 Santiago de Compostela, Spain
| | - James E. Gonzales
- Department
of Biomedical Engineering, Texas A&M
University, College
Station, Texas 77843, United States
- Laboratory
of Computational Biology, National Heart
Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Mehdi Bagerhi Hamaneh
- Department
of Physiology and Biophysics, Case Western
Reserve University, School of Medicine, Cleveland, Ohio 44106, United States
| | | | - Ryan L. Hayes
- Department
of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697, United States
- Department
of Pharmaceutical Sciences, University of
California, Irvine, Irvine, California 92697, United States
| | - Jing Huang
- Key Laboratory
of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
| | - Yandong Huang
- College
of Computer Engineering, Jimei University, Xiamen 361021, China
| | - Phillip S. Hudson
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
- Medicine
Design, Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | - Wonpil Im
- Department
of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Shahidul M. Islam
- Department
of Chemistry, Delaware State University, Dover, Delaware 19901, United States
| | - Wei Jiang
- Computational
Science Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Michael R. Jones
- Laboratory
of Computational Biology, National Heart
Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Silvan Käser
- Department
of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Fiona L. Kearns
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Nathan R. Kern
- Department
of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Jeffery B. Klauda
- Department
of Chemical and Biomolecular Engineering, Institute for Physical Science
and Technology, Biophysics Program, University
of Maryland, College Park, Maryland 20742, United States
| | - Themis Lazaridis
- Department
of Chemistry, City College of New York, New York, New York 10031, United States
| | - Jinhyuk Lee
- Disease
Target Structure Research Center, Korea
Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
- Department
of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34141, Republic of Korea
| | - Justin A. Lemkul
- Department
of Biochemistry, Virginia Polytechnic Institute
and State University, Blacksburg, Virginia 24061, United States
| | - Xiaorong Liu
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yun Luo
- Department
of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, California 91766, United States
| | - Alexander D. MacKerell
- Department
of Pharmaceutical Sciences, University of
Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Dan T. Major
- Department
of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Markus Meuwly
- Department
of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
- Department
of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Kwangho Nam
- Department
of Chemistry and Biochemistry, University
of Texas at Arlington, Arlington, Texas 76019, United States
| | - Lennart Nilsson
- Karolinska
Institutet, Department of Biosciences and
Nutrition, SE-14183 Huddinge, Sweden
| | - Victor Ovchinnikov
- Harvard
University, Department of Chemistry
and Chemical Biology, Cambridge, Massachusetts 02138, United States
| | - Emanuele Paci
- Dipartimento
di Fisica e Astronomia, Universitá
di Bologna, Bologna 40127, Italy
| | - Soohyung Park
- Department
of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Richard W. Pastor
- Laboratory
of Computational Biology, National Heart
Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Amanda R. Pittman
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Carol Beth Post
- Borch Department
of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Samarjeet Prasad
- Laboratory
of Computational Biology, National Heart
Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Jingzhi Pu
- Department
of Chemistry and Chemical Biology, Indiana
University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Yifei Qi
- School
of Pharmacy, Fudan University, Shanghai 201203, China
| | | | - Daniel R. Roe
- Laboratory
of Computational Biology, National Heart
Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Benoit Roux
- Department
of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | | | - Jana Shen
- Department
of Pharmaceutical Sciences, University of
Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Andrew C. Simmonett
- Laboratory
of Computational Biology, National Heart
Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Alexander J. Sodt
- Eunice
Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Kai Töpfer
- Department
of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Meenu Upadhyay
- Department
of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Arjan van der Vaart
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | | | - Richard M. Venable
- Laboratory
of Computational Biology, National Heart
Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Luke C. Warrensford
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - H. Lee Woodcock
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Yujin Wu
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Charles L. Brooks
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bernard R. Brooks
- Laboratory
of Computational Biology, National Heart
Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Martin Karplus
- Harvard
University, Department of Chemistry
and Chemical Biology, Cambridge, Massachusetts 02138, United States
- Laboratoire
de Chimie Biophysique, ISIS, Université
de Strasbourg, 67000 Strasbourg, France
| |
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