ReviewThe journal of physical chemistry. B2024
CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.
Abstract readReview
In one paragraph
Review in The journal of physical chemistry. B, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.
0numbers the graph read from it
0cells of the map it votes in
76citing papers in PubMed
–field-weighted citation impact
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
76 citing papers in PubMed.
- Time-Dependent Voronoi Analysis of Amino Acid Side-Chain Packing in Simulations.Journal of computational chemistry · 2026Article
- Optimized M-SHAKE Constraint Implementations for GPU-Accelerated Molecular Dynamics: Balancing Precision and Performance Across Architectures.Journal of computational chemistry · 2026Article
- Molecular structure and DNA binding mode of unsymmetric cyanine dyes RiboGreen and OliGreen.Nucleic acids research · 2026Article
- Drude SILCS-Nucleic: harnessing explicit electronic polarization in targeting RNA and DNA for drug design.Nucleic acids research · 2026Article
- A Fast and Parallelized Procedure for Checking Molecular Dynamics 3D Structure.Journal of computational chemistry · 2026Article
- Substrate Recognition Analysis in an Ethyl Carbamate-Hydrolyzing Esterase and Semi-Rational Baijiu Flavor Preservation.Foods (Basel, Switzerland) · 2026Article
- Sequence-encoded determinants drive distinct early aggregation pathways and different structural outcomes in PNT1 fibrils across Henipavirus members.Protein science : a publication of the Protein Society · 2026Article
- Accurate and Time-Efficient Condensed-Phase Free Energy Simulations with Reaction Specific Δ-Machine Learning Potentials in CHARMM.Journal of chemical theory and computation · 2026Article
- Tripeptide dynamics from empirical and machine-learned energy functions.Biophysical journal · 2026Article
- Anisotropic unbinding and location-dependent hovering of a kinesin motor head over microtubule.Biophysical journal · 2026Article
- Arrhythmia risk predictions from molecular simulations of cardiac ion channel-drug interactions.Biophysical journal · 2026Article
- Systems pharmacology, structural modeling, and experimental validation reveal retinoic acid as a modulator of immune-fibrotic networks in chronic kidney disease.Naunyn-Schmiedeberg's archives of pharmacology · 2026Article
- Oosporein in Phlebia centrifuga: Prediction of Key Enzymes by a Combination of Multi-Omics and Molecular Dynamics.Journal of agricultural and food chemistry · 2026Article
- Integrating Green Process Engineering With Whole-Cell Catalysis to Intensify Sustainable Glucaric Acid Production.Biotechnology and bioengineering · 2026Article
- Computational Design and Expression of Headless Influenza Hemagglutinin Antigens Toward a Modular Universal Nanoparticle Vaccine.Antibodies (Basel, Switzerland) · 2026Article
- Comparing Enhanced Sampling Methods in Exploring the Conformational Space of β-CateninThe journal of physical chemistry. B · 2026Article
- How Medically Important Antimicrobials Bind to the 30S Ribosomal Subunit in a Bacterial Pathogen.Biochemistry · 2026Article
- Molecular basis of UV lesion binding and repair inhibition by ETS-family transcription factors.Nucleic acids research · 2026Article
- BilboMD: a web-accessible SAXS and AlphaFold-guided modeling pipeline.Nucleic acids research · 2026Article
- Predicting human mRNA isoform levels from site-specific splicing kineticsbioRxiv : the preprint server for biology · 2026Article
16 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
73 authors.
Wonmuk HwangDepartment of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States.ORCID 0000-0001-7514-3186
Steven L AustinDepartment of Chemistry, University of South Florida, Tampa, Florida 33620, United States.
Arnaud BlondelInstitut Pasteur, Université Paris Cité, CNRS UMR3825, Structural Bioinformatics Unit, 28 rue du Dr. Roux F-75015 Paris, France.ORCID 0000-0001-9586-3025
Eric D BoittierDepartment of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
Stefan BoreschFaculty of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Wahringerstrasse 17, 1090 Vienna, Austria.ORCID 0000-0002-2793-6656
Matthias BuckDepartment of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106, United States.
Joshua BucknerDepartment of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States.
Amedeo CaflischDepartment of Biochemistry, University of Zürich, CH-8057 Zürich, Switzerland.ORCID 0000-0002-2317-6792
Hao-Ting ChangInstitute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan, ROC.
Xi ChengShanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.ORCID 0000-0003-3735-645X
Yeol Kyo ChoiDepartment of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, United States.ORCID 0000-0002-4218-7139
Jhih-Wei ChuInstitute 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 (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan, ROC.ORCID 0000-0003-3842-2893
Michael F CrowleyRenewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States.ORCID 0000-0001-5163-9398
Qiang CuiDepartment of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States.ORCID 0000-0001-6214-5211
Ana DamjanovicDepartment of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States.ORCID 0000-0001-7635-2705
Yuqing DengShanghai R&D Center, DP Technology, Ltd., Shanghai 201210, China.
Mike DevereuxDepartment of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.ORCID 0000-0002-1561-1635
Xinqiang DingDepartment of Chemistry, Tufts University, Medford, Massachusetts 02155, United States.ORCID 0000-0002-4598-8732
Michael F FeigDepartment of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States.ORCID 0000-0001-9380-6422
Jiali GaoSchool of Chemical Biology & Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, China.ORCID 0000-0003-0106-7154
David R GlowackiCiTIUS Centro Singular de Investigación en Tecnoloxías Intelixentes da USC, 15705 Santiago de Compostela, Spain.ORCID 0000-0002-9608-3845
James E GonzalesDepartment of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States.ORCID 0009-0009-7696-7561
Mehdi Bagerhi HamanehDepartment of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106, United States.ORCID 0009-0000-5222-889X
Edward D HarderSchrodinger, Inc., New York, New York 10036, United States.ORCID 0000-0001-9213-787X
Ryan L HayesDepartment of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697, United States.ORCID 0000-0003-1052-6391
Jing HuangKey Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China.ORCID 0000-0001-9639-2907
Yandong HuangCollege of Computer Engineering, Jimei University, Xiamen 361021, China.ORCID 0000-0002-1452-6383
Phillip S HudsonDepartment of Chemistry, University of South Florida, Tampa, Florida 33620, United States.
Wonpil ImDepartment of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, United States.ORCID 0000-0001-5642-6041
Shahidul M IslamDepartment of Chemistry, Delaware State University, Dover, Delaware 19901, United States.ORCID 0000-0001-5769-6844
Wei JiangComputational Science Division, Argonne National Laboratory, Argonne, Illinois 60439, United States.ORCID 0000-0001-7707-6247
Michael R JonesLaboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States.ORCID 0000-0002-0542-3796
Silvan KäserDepartment of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.ORCID 0000-0002-3641-8519
Fiona L KearnsDepartment of Chemistry, University of South Florida, Tampa, Florida 33620, United States.ORCID 0000-0002-5469-9035
Nathan R KernDepartment of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, United States.ORCID 0000-0003-0936-7274
Jeffery B KlaudaDepartment of Chemical and Biomolecular Engineering, Institute for Physical Science and Technology, Biophysics Program, University of Maryland, College Park, Maryland 20742, United States.ORCID 0000-0001-8725-1870
Themis LazaridisDepartment of Chemistry, City College of New York, New York, New York 10031, United States.ORCID 0000-0003-4218-7590
Jinhyuk LeeDisease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea.
Justin A LemkulDepartment of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States.ORCID 0000-0001-6661-8653
Xiaorong LiuDepartment of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States.ORCID 0000-0002-7687-3604
Yun LuoDepartment of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, California 91766, United States.ORCID 0000-0003-3581-754X
Alexander D MacKerellDepartment of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States.ORCID 0000-0001-8287-6804
Dan T MajorDepartment of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel.ORCID 0000-0002-9231-0676
Markus MeuwlyDepartment of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.ORCID 0000-0001-7930-8806
Kwangho NamDepartment of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States.ORCID 0000-0003-0723-7839
Lennart NilssonKarolinska Institutet, Department of Biosciences and Nutrition, SE-14183 Huddinge, Sweden.ORCID 0000-0002-5067-6397
Victor OvchinnikovHarvard University, Department of Chemistry and Chemical Biology, Cambridge, Massachusetts 02138, United States.ORCID 0000-0002-1793-2352
Emanuele PaciDipartimento di Fisica e Astronomia, Universitá di Bologna, Bologna 40127, Italy.ORCID 0000-0002-4891-2768
Soohyung ParkDepartment of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, United States.ORCID 0000-0002-4883-3031
Richard W PastorLaboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States.ORCID 0000-0002-2454-5131
Amanda R PittmanDepartment of Chemistry, University of South Florida, Tampa, Florida 33620, United States.
Carol Beth PostBorch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States.ORCID 0000-0002-5233-899X
Samarjeet PrasadLaboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States.
Jingzhi PuDepartment of Chemistry and Chemical Biology, Indiana University Indianapolis, Indianapolis, Indiana 46202, United States.ORCID 0000-0002-3042-335X
Yifei QiSchool of Pharmacy, Fudan University, Shanghai 201203, China.ORCID 0000-0003-2853-7910
Thenmalarchelvi RathinavelanDepartment of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana State, 502284, India.ORCID 0000-0002-1142-0583
Daniel R RoeLaboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States.ORCID 0000-0002-5834-2447
Benoit RouxDepartment of Chemistry, University of Chicago, Chicago, Illinois 60637, United States.ORCID 0000-0002-5254-2712
Christopher N RowleyDepartment of Chemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada.ORCID 0000-0002-0205-952X
Jana ShenDepartment of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States.ORCID 0000-0002-3234-0769
Andrew C SimmonettLaboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States.ORCID 0000-0002-5921-9272
Alexander J SodtEunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States.ORCID 0000-0002-5570-8212
Kai TöpferDepartment of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.ORCID 0000-0002-4650-9641
Meenu UpadhyayDepartment of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.ORCID 0000-0003-3802-0835
Arjan van der VaartDepartment of Chemistry, University of South Florida, Tampa, Florida 33620, United States.ORCID 0000-0002-8950-1850
Luis Itza Vazquez-SalazarDepartment of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.ORCID 0000-0001-6347-5108
Richard M VenableLaboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States.
Luke C WarrensfordDepartment of Chemistry, University of South Florida, Tampa, Florida 33620, United States.ORCID 0000-0002-9206-5121
H Lee WoodcockDepartment of Chemistry, University of South Florida, Tampa, Florida 33620, United States.ORCID 0000-0003-3539-273X
Yujin WuDepartment of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States.
Charles L BrooksDepartment of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States.ORCID 0000-0002-8149-5417
Bernard R BrooksLaboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States.ORCID 0000-0002-3586-2730
Martin KarplusHarvard University, Department of Chemistry and Chemical Biology, Cambridge, Massachusetts 02138, United States.
Funding
Computer Simulations of Membranes and BiopolymersZIAHL000340 · NHLBI · NATIONAL HEART, LUNG, AND BLOOD INSTITUTE · PI PASTOR, RICHARD WALTER · 2009 to 2025
$29.1MProtein Production CoreP01AI143565 · NIAID · DANA-FARBER CANCER INST · PI Matthew J. Lang, ELLIS L REINHERZ · 2020 to 2026
$19.9MDevelopment Of Theoretical Methods For Studying Biological MacromoleculesZIAHL001051 · NHLBI · NATIONAL HEART, LUNG, AND BLOOD INSTITUTE · PI BROOKS, BERNARD R · 2009 to 2025
$16.2MTheory and Modeling of Biomolecules and their Interactions - Equipment SupplementR35GM130587 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI CHARLES L BROOKS · 2019 to 2026
$6.9MBIOMOLECULAR INTERACTIONS AND ENZYMATIC PROCESSESR01GM046736 · NIGMS · UNIVERSITY OF MINNESOTA TWIN CITIES · PI JIALI GAO · 1993 to 2026
$6.5MNMR Structure of Peptide and Protein Complexes SupplementR01GM039478 · NIGMS · PURDUE UNIVERSITY WEST LAFAYETTE · PI POST, CAROL B. · 1997 to 2024
$6.5MMacromolecular Conformational HeterogeneityR35GM131710 · NIGMS · UNIVERSITY OF MARYLAND BALTIMORE · PI ALEXANDER D MACKERELL · 2019 to 2026
$6.2MUnderstanding the structural basis of T cell receptor (TCR) and preTCR mechanosensing: single molecule, NMR and molecular dynamics studiesR01AI136301 · NIAID · VANDERBILT UNIVERSITY · PI LANG, MATTHEW J. · 2018 to 2022
$3.9MModeling and dynamics of biomolecules on cellular scalesR35GM126948 · NIGMS · MICHIGAN STATE UNIVERSITY · PI Michael Feig · 2018 to 2026
$3.2MComputational Analysis of Enzyme Catalysis and RegulationR35GM141930 · NIGMS · BOSTON UNIVERSITY (CHARLES RIVER CAMPUS) · PI Qiang Cui · 2021 to 2026
$2.7MExploring Electronic Polarization in Biomolecular Folding and InteractionsR35GM133754 · NIGMS · VIRGINIA POLYTECHNIC INST AND ST UNIV · PI Justin Alan Lemkul · 2019 to 2026
$2.2MToward Understanding the Chemistry and Biology of Microbial DXP SynthaseR01GM143810 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI Caren L. Freel Meyers · 2021 to 2026
$2.0MIntramural NIH HHS Z01 HL001052Intramural NIH HHS ZIA HL000340Intramural NIH HHS ZIA HL001051NIAID NIH HHS P01 AI143565NIAID NIH HHS R01 AI136301NIGMS NIH HHS R01 GM039478NIGMS NIH HHS R01 GM046736NIGMS NIH HHS R01 GM127723NIGMS NIH HHS R01 GM129519NIGMS NIH HHS R01 GM132481NIGMS NIH HHS R01 GM135392NIGMS NIH HHS R01 GM138472NIGMS NIH HHS R01 GM140316NIGMS NIH HHS R01 GM143810NIGMS NIH HHS R21 GM148895NIGMS NIH HHS R35 GM126948NIGMS NIH HHS R35 GM130587NIGMS NIH HHS R35 GM131710NIGMS NIH HHS R35 GM133754NIGMS NIH HHS R35 GM141930NIGMS NIH HHS R35 GM148261
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.
Indexed as
Quantum TheoryMolecular Dynamics SimulationSoftware
Identifiers
What OpenQuestion holds
Textmetadata
LicenceCC BY
Read underepoch 390
Registered trials
None linked
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.