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CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.

Autor: Hwang W; 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., Austin SL; Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States., Blondel A; Institut Pasteur, Université Paris Cité, CNRS UMR3825, Structural Bioinformatics Unit, 28 rue du Dr. Roux F-75015 Paris, France., Boittier ED; Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland., Boresch S; Faculty of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Wahringerstrasse 17, 1090 Vienna, Austria., Buck M; Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106, United States., Buckner J; Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States., Caflisch A; Department of Biochemistry, University of Zürich, CH-8057 Zürich, Switzerland., Chang HT; Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan, ROC., Cheng X; Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China., Choi YK; Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, United States., Chu JW; 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., Crowley MF; Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States., Cui Q; 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., Damjanovic A; 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., Deng Y; Shanghai R&D Center, DP Technology, Ltd., Shanghai 201210, China., Devereux M; Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland., Ding X; Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States., Feig MF; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States., Gao J; 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., Glowacki DR; CiTIUS Centro Singular de Investigación en Tecnoloxías Intelixentes da USC, 15705 Santiago de Compostela, Spain., Gonzales JE 2nd; 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., Hamaneh MB; Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106, United States., Harder ED; Schrodinger, Inc., New York, New York 10036, United States., Hayes RL; 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., Huang J; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China., Huang Y; College of Computer Engineering, Jimei University, Xiamen 361021, China., Hudson PS; Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States.; Medicine Design, Pfizer Inc., Cambridge, Massachusetts 02139, United States., Im W; Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, United States., Islam SM; Department of Chemistry, Delaware State University, Dover, Delaware 19901, United States., Jiang W; Computational Science Division, Argonne National Laboratory, Argonne, Illinois 60439, 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 Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland., Kearns FL; Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States., Kern NR; Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, United States., Klauda JB; Department of Chemical and Biomolecular Engineering, Institute for Physical Science and Technology, Biophysics Program, University of Maryland, College Park, Maryland 20742, United States., Lazaridis T; Department of Chemistry, City College of New York, New York, New York 10031, United States., Lee J; 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., Lemkul JA; Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States., Liu X; Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States., Luo Y; Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, California 91766, United States., MacKerell AD Jr; Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States., Major DT; Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel., Meuwly M; Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.; Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States., Nam K; Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States., Nilsson L; Karolinska Institutet, Department of Biosciences and Nutrition, SE-14183 Huddinge, Sweden., Ovchinnikov V; Harvard University, Department of Chemistry and Chemical Biology, Cambridge, Massachusetts 02138, United States., Paci E; Dipartimento di Fisica e Astronomia, Universitá di Bologna, Bologna 40127, Italy., Park S; Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, United States., Pastor RW; Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States., Pittman AR; Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States., Post CB; Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States., Prasad S; Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States., Pu J; Department of Chemistry and Chemical Biology, Indiana University Indianapolis, Indianapolis, Indiana 46202, United States., Qi Y; School of Pharmacy, Fudan University, Shanghai 201203, China., Rathinavelan T; Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana State, 502284, India., Roe DR; Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States., Roux B; Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States., Rowley CN; Department of Chemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada., Shen J; Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States., Simmonett AC; Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States., Sodt AJ; Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States., Töpfer K; Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland., Upadhyay M; Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland., van der Vaart A; Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States., Vazquez-Salazar LI; Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland., Venable RM; Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States., Warrensford LC; Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States., Woodcock HL; Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States., Wu Y; Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States., Brooks CL 3rd; Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States., Brooks BR; Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States., Karplus M; Harvard University, Department of Chemistry and Chemical Biology, Cambridge, Massachusetts 02138, United States.; Laboratoire de Chimie Biophysique, ISIS, Université de Strasbourg, 67000 Strasbourg, France.

Publikováno v: The journal of physical chemistry. B [J Phys Chem B] 2024 Oct 17; Vol. 128 (41), pp. 9976-10042. Date of Electronic Publication: 2024 Sep 20.

Exploring induced pluripotency in human fibroblasts via construction, validation, and application of a gene regulatory network.

Autor: Hamaneh MB; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America., Yu YK; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America.

Publikováno v: PloS one [PLoS One] 2019 Aug 02; Vol. 14 (8), pp. e0220742. Date of Electronic Publication: 2019 Aug 02 (Print Publication: 2019).

Mechanism-based disease similarity.

Autor: Hamaneh MB; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA., Yu YK; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.

Publikováno v: Journal of rare diseases research & treatment [J Rare Dis Res Treat] 2016; Vol. 1 (3), pp. 1-4. Date of Electronic Publication: 2016 Oct 18.