AmberTools.

Journal

Journal of chemical information and modeling
ISSN: 1549-960X
Titre abrégé: J Chem Inf Model
Pays: United States
ID NLM: 101230060

Informations de publication

Date de publication:
23 Oct 2023
Historique:
medline: 8 10 2023
pubmed: 8 10 2023
entrez: 8 10 2023
Statut: ppublish

Résumé

AmberTools is a free and open-source collection of programs used to set up, run, and analyze molecular simulations. The newer features contained within AmberTools23 are briefly described in this Application note.

Identifiants

DOI: 10.1021/acs.jcim.3c01153 PMID: 37805934 PMC: PMC10598796
pubmed: 37805934
doi: 10.1021/acs.jcim.3c01153
pmc: PMC10598796
mid: NIHMS1940356
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

6183-6191

Subventions

Organisme : NIGMS NIH HHS
ID : R35 GM144089
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM107485
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM107104
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM062248
Pays : United States
Organisme : Intramural NIH HHS
ID : Z01 HL001051
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM108583
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM149874
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM130367
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM144596
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM130641
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM147673
Pays : United States
Organisme : NIGMS NIH HHS
ID : RM1 GM135136
Pays : United States
Organisme : NIGMS NIH HHS
ID : R16 GM146633
Pays : United States

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Auteurs

David A Case (DA)

Department of Chemistry and Chemical Biology, Rutgers University, Piscataway 08854, New Jersey, United States.
ORCID: 0000-0003-2314-2346

Hasan Metin Aktulga (HM)

Department of Computer Science and Engineering, Michigan State University, East Lansing 48824-1322, Michigan, United States.

Kellon Belfon (K)

FOG Pharmaceuticals Inc., Cambridge 02140, Massachusetts, United States.

David S Cerutti (DS)

Psivant, 451 D Street, Suite 205, Boston 02210, Massachusetts, United States.

G Andrés Cisneros (GA)

Department of Physics, Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson 75801, Texas, United States.
ORCID: 0000-0001-6629-3430

Vinícius Wilian D Cruzeiro (VWD)

Department of Chemistry and The PULSE Institute, Stanford University, Stanford 94305, California, United States.
ORCID: 0000-0002-4739-5447

Negin Forouzesh (N)

Department of Computer Science, California State University, Los Angeles 90032, California, United States.

Timothy J Giese (TJ)

Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway 08854, New Jersey, United States.
ORCID: 0000-0002-0653-9168

Andreas W Götz (AW)

San Diego Supercomputer Center, University of California San Diego, La Jolla 92093-0505, California, United States.
ORCID: 0000-0002-8048-6906

Holger Gohlke (H)

Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany.
Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich 52425, Germany.
ORCID: 0000-0001-8613-1447

Saeed Izadi (S)

Pharmaceutical Development, Genentech, Inc., South San Francisco 94080, California, United States.

Koushik Kasavajhala (K)

Laufer Center for Physical and Quantitative Biology, Department of Chemistry, Stony Brook University, Stony Brook 11794, New York, United States.

Mehmet C Kaymak (MC)

Department of Computer Science and Engineering, Michigan State University, East Lansing 48824-1322, Michigan, United States.

Edward King (E)

Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, Graduate Program in Chemical and Materials Physics, University of California, Irvine 92697, California, United States.

Tom Kurtzman (T)

Ph.D. Programs in Chemistry, Biochemistry, and Biology, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York 10016, New York, United States.
Department of Chemistry, Lehman College, 250 Bedford Park Blvd West, Bronx 10468, New York, United States.

Tai-Sung Lee (TS)

Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway 08854, New Jersey, United States.
ORCID: 0000-0003-2110-2279

Pengfei Li (P)

Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago 60660, Illinois, United States.
ORCID: 0000-0002-2572-5935

Jian Liu (J)

Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
ORCID: 0000-0002-2906-5858

Tyler Luchko (T)

Department of Physics and Astronomy, California State University, Northridge, Northridge 91330, California, United States.
ORCID: 0000-0001-6737-6019

Ray Luo (R)

Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, Graduate Program in Chemical and Materials Physics, University of California, Irvine 92697, California, United States.

Madushanka Manathunga (M)

Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing 48824-1322, Michigan, United States.
ORCID: 0000-0002-3594-8112

Matias R Machado (MR)

Institut Pasteur de Montevideo, Montevideo 11400, Uruguay.
ORCID: 0000-0002-9971-4710

Hai Minh Nguyen (HM)

Department of Chemistry and Chemical Biology, Rutgers University, Piscataway 08854, New Jersey, United States.
ORCID: 0000-0002-0814-1364

Kurt A O'Hearn (KA)

Department of Computer Science and Engineering, Michigan State University, East Lansing 48824-1322, Michigan, United States.

Alexey V Onufriev (AV)

Departments of Computer Science and Physics, Virginia Tech, Blacksburg 24061, Virginia, United States.
ORCID: 0000-0002-4930-6612

Feng Pan (F)

Department of Statistics, Florida State University, Tallahassee 32304, Florida, United States.

Sergio Pantano (S)

Institut Pasteur de Montevideo, Montevideo 11400, Uruguay.
ORCID: 0000-0001-6435-4543

Ruxi Qi (R)

Cryo-EM Center, Southern University of Science and Technology, Shenzhen 518055, China.

Ali Rahnamoun (A)

Department of Computer Science and Engineering, Michigan State University, East Lansing 48824-1322, Michigan, United States.

Ali Risheh (A)

Department of Computer Science, California State University, Los Angeles 90032, California, United States.

Stephan Schott-Verdugo (S)

Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich 52425, Germany.

Akhil Shajan (A)

Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing 48824-1322, Michigan, United States.

Jason Swails (J)

Entos, 4470 W Sunset Blvd, Suite 107, Los Angeles 90027, California, United States.

Junmei Wang (J)

Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh 15261, Pennsylvania, United States.
ORCID: 0000-0002-9607-8229

Haixin Wei (H)

Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, Graduate Program in Chemical and Materials Physics, University of California, Irvine 92697, California, United States.
ORCID: 0000-0002-0954-4560

Xiongwu Wu (X)

Laboratory of Computational Biology, NHLBI, NIH, Bethesda 20892, Maryland, United States.

Yongxian Wu (Y)

Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, Graduate Program in Chemical and Materials Physics, University of California, Irvine 92697, California, United States.
ORCID: 0000-0003-1497-2444

Shi Zhang (S)

Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway 08854, New Jersey, United States.

Shiji Zhao (S)

Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, Graduate Program in Chemical and Materials Physics, University of California, Irvine 92697, California, United States.
Nurix Therapeutics, Inc., San Francisco 94158, California, United States.
ORCID: 0000-0002-4514-0897

Qiang Zhu (Q)

Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, Graduate Program in Chemical and Materials Physics, University of California, Irvine 92697, California, United States.
ORCID: 0000-0002-5612-0728

Thomas E Cheatham (TE)

Department of Medicinal Chemistry, The University of Utah, 30 South 2000 East, Salt Lake City 84112, Utah, United States.
ORCID: 0000-0003-0298-3904

Daniel R Roe (DR)

Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda 20892, Maryland, United States.

Adrian Roitberg (A)

Department of Chemistry, The University of Florida, 440 Leigh Hall, Gainesville 32611-7200, Florida, United States.
ORCID: 0000-0003-3963-8784

Carlos Simmerling (C)

Laufer Center for Physical and Quantitative Biology, Department of Chemistry, Stony Brook University, Stony Brook 11794, New York, United States.
ORCID: 0000-0002-7252-4730

Darrin M York (DM)

Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway 08854, New Jersey, United States.
ORCID: 0000-0002-9193-7055

Maria C Nagan (MC)

Department of Chemistry, Stony Brook University, Stony Brook 11794, New York, United States.
ORCID: 0000-0003-2678-6825

Kenneth M Merz (KM)

Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing 48824-1322, Michigan, United States.
ORCID: 0000-0001-9139-5893

Classifications MeSH