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CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.
Hwang, Wonmuk; Austin, Steven L; Blondel, Arnaud; Boittier, Eric D; Boresch, Stefan; Buck, Matthias; Buckner, Joshua; Caflisch, Amedeo; Chang, Hao-Ting; Cheng, Xi; Choi, Yeol Kyo; Chu, Jhih-Wei; Crowley, Michael F; Cui, Qiang; Damjanovic, Ana; Deng, Yuqing; Devereux, Mike; Ding, Xinqiang; Feig, Michael F; Gao, Jiali; Glowacki, David R; Gonzales, James E; Hamaneh, Mehdi Bagerhi; Harder, Edward D; Hayes, Ryan L; Huang, Jing; Huang, Yandong; Hudson, Phillip S; Im, Wonpil; Islam, Shahidul M; Jiang, Wei; Jones, Michael R; Käser, Silvan; Kearns, Fiona L; Kern, Nathan R; Klauda, Jeffery B; Lazaridis, Themis; Lee, Jinhyuk; Lemkul, Justin A; Liu, Xiaorong; Luo, Yun; MacKerell, Alexander D; Major, Dan T; Meuwly, Markus; Nam, Kwangho; Nilsson, Lennart; Ovchinnikov, Victor; Paci, Emanuele; Park, Soohyung; Pastor, Richard W.
Affiliation
  • Hwang W; Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States.
  • Austin SL; Department of Materials Science and Engineering, Texas A&M University, College Station, Texas 77843, United States.
  • Blondel A; Department of Physics and Astronomy, Texas A&M University, College Station, Texas 77843, United States.
  • Boittier ED; Center for AI and Natural Sciences, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea.
  • Boresch S; Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States.
  • Buck M; Institut Pasteur, Université Paris Cité, CNRS UMR3825, Structural Bioinformatics Unit, 28 rue du Dr. Roux F-75015 Paris, France.
  • Buckner J; Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
  • Caflisch A; Faculty of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Wahringerstrasse 17, 1090 Vienna, Austria.
  • Chang HT; Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106, United States.
  • Cheng X; Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States.
  • Choi YK; Department of Biochemistry, University of Zürich, CH-8057 Zürich, Switzerland.
  • Chu JW; Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan, ROC.
  • Crowley MF; Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
  • Cui Q; Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, United States.
  • Damjanovic A; 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 (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan, ROC.
  • Deng Y; Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States.
  • Devereux M; Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States.
  • Ding X; Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States.
  • Feig MF; Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States.
  • Gao J; Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States.
  • Glowacki DR; Department of Physics and Astronomy, Johns Hopkins University, Baltimore, Maryland 21218, United States.
  • Gonzales JE; Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States.
  • Hamaneh MB; Shanghai R&D Center, DP Technology, Ltd., Shanghai 201210, China.
  • Harder ED; Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
  • Hayes RL; Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States.
  • Huang J; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States.
  • Huang Y; School of Chemical Biology & Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, China.
  • Hudson PS; Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518055, China.
  • Im W; Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States.
  • Islam SM; CiTIUS Centro Singular de Investigación en Tecnoloxías Intelixentes da USC, 15705 Santiago de Compostela, Spain.
  • Jiang W; Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States.
  • Jones MR; Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States.
  • Käser S; Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106, United States.
  • Kearns FL; Schrodinger, Inc., New York, New York 10036, United States.
  • Kern NR; Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697, United States.
  • Klauda JB; Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697, United States.
  • Lazaridis T; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China.
  • Lee J; College of Computer Engineering, Jimei University, Xiamen 361021, China.
  • Lemkul JA; Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States.
  • Liu X; Medicine Design, Pfizer Inc., Cambridge, Massachusetts 02139, United States.
  • Luo Y; Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, United States.
  • MacKerell AD; Department of Chemistry, Delaware State University, Dover, Delaware 19901, United States.
  • Major DT; Computational Science Division, Argonne National Laboratory, Argonne, Illinois 60439, United States.
  • Meuwly M; Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States.
  • Nam K; Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
  • Nilsson L; Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States.
  • Ovchinnikov V; Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, United States.
  • Paci E; Department of Chemical and Biomolecular Engineering, Institute for Physical Science and Technology, Biophysics Program, University of Maryland, College Park, Maryland 20742, United States.
  • Park S; Department of Chemistry, City College of New York, New York, New York 10031, United States.
  • Pastor RW; Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea.
J Phys Chem B ; 128(41): 9976-10042, 2024 Oct 17.
Article in En | MEDLINE | ID: mdl-39303207
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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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Quantum Theory Language: En Journal: J Phys Chem B Journal subject: QUIMICA Year: 2024 Document type: Article Affiliation country: United States Country of publication: United States
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Quantum Theory Language: En Journal: J Phys Chem B Journal subject: QUIMICA Year: 2024 Document type: Article Affiliation country: United States Country of publication: United States