ArticleJournal of chemical information and modeling2023
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Article in Journal of chemical information and modeling, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 948 papers.
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0cells of the map it votes in
948citing papers in PubMed
–field-weighted citation impact
What it found
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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.
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Who cites it
948 citing papers in PubMed.
- Reassigning an amber codon to selenocysteine using a functional cysteine suppression pair inSynthetic and systems biotechnology · 2027Article
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- Are QM/MM models systematically improvable? A case study on carbonic anhydrase binding affinities.Journal of computer-aided molecular design · 2026Article
- AntiLipo: A Comprehensive Database, Deep Learning-Based Prediction Model, and Computational Study of Anti-Hyperlipidemic Peptides.Interdisciplinary sciences, computational life sciences · 2026Article
- Synthesis and evaluation of 3,5-disubstituted isothiazolo[4,5-b]pyridines, pyrazolo[4,3-b]pyridines and isothiazolo[3,4-b]pyrazines as inhibitors of PIKfyve.Bioorganic chemistry · 2026Article
- Cysteine Thioaldehydes: Photolytic Generation, Reactivity, and Biological Implications.Angewandte Chemie (International ed. in English) · 2026Article
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- Structural and Functional Characterisation of a Metagenome-Derived CYP108D18 Reveals an Unusual Dioxygen-Bound State and Selective Hydrocarbon Hydroxylation.Microbial biotechnology · 2026Article
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- DFT and TD-DFT insights into the conformational, electronic, and spectral properties of purine-based glycol nucleic acid (GNA) monophosphates and their Zn(II) coordination effects.Journal of computer-aided molecular design · 2026Article
- Conserved and divergent mitochondrial assemblies in kinetoplastid parasites.Molecular cell · 2026Article
- High-throughput screening and structure-guided design of small molecules enable modulation of SAL-PAP stress signaling.Journal of experimental botany · 2026Article
- Mechanism of GPR84 allosteric modulation at a helix 8-proximate site.Science advances · 2026Article
- Characterization of the pH-Dependent Stabilizing Forces of Insulin's Native and Fibril States.ACS physical chemistry Au · 2026Article
- Repurposing HIV Protease Inhibitors against West Nile Virus: Insights from Molecular Docking and Molecular Dynamics Simulations.ACS physical chemistry Au · 2026Article
- FoldaVirus, a knowledge-based icosahedral capsid prediction tool using AlphaFold.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Generative AI designs functional thiolation domains for reprogramming non-ribosomal peptide synthetases.Nature communications · 2026Article
888 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
47 authors.
David A CaseDepartment of Chemistry and Chemical Biology, Rutgers University, Piscataway 08854, New Jersey, United States.ORCID 0000-0003-2314-2346
Hasan Metin AktulgaDepartment of Computer Science and Engineering, Michigan State University, East Lansing 48824-1322, Michigan, United States.
Kellon BelfonFOG Pharmaceuticals Inc., Cambridge 02140, Massachusetts, United States.
David S CeruttiPsivant, 451 D Street, Suite 205, Boston 02210, Massachusetts, United States.
G Andrés CisnerosDepartment 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 CruzeiroDepartment of Chemistry and The PULSE Institute, Stanford University, Stanford 94305, California, United States.ORCID 0000-0002-4739-5447
Negin ForouzeshDepartment of Computer Science, California State University, Los Angeles 90032, California, United States.
Timothy J GieseLaboratory 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 GötzSan Diego Supercomputer Center, University of California San Diego, La Jolla 92093-0505, California, United States.ORCID 0000-0002-8048-6906
Holger GohlkeInstitute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany.ORCID 0000-0001-8613-1447
Saeed IzadiPharmaceutical Development, Genentech, Inc., South San Francisco 94080, California, United States.
Koushik KasavajhalaLaufer Center for Physical and Quantitative Biology, Department of Chemistry, Stony Brook University, Stony Brook 11794, New York, United States.
Mehmet C KaymakDepartment of Computer Science and Engineering, Michigan State University, East Lansing 48824-1322, Michigan, United States.
Edward KingDepartments 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 KurtzmanPh.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.
Tai-Sung LeeLaboratory 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 LiDepartment of Chemistry and Biochemistry, Loyola University Chicago, Chicago 60660, Illinois, United States.ORCID 0000-0002-2572-5935
Jian LiuBeijing 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 LuchkoDepartment of Physics and Astronomy, California State University, Northridge, Northridge 91330, California, United States.ORCID 0000-0001-6737-6019
Ray LuoDepartments 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 ManathungaDepartment 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 MachadoInstitut Pasteur de Montevideo, Montevideo 11400, Uruguay.ORCID 0000-0002-9971-4710
Hai Minh NguyenDepartment of Chemistry and Chemical Biology, Rutgers University, Piscataway 08854, New Jersey, United States.ORCID 0000-0002-0814-1364
Kurt A O'HearnDepartment of Computer Science and Engineering, Michigan State University, East Lansing 48824-1322, Michigan, United States.
Alexey V OnufrievDepartments of Computer Science and Physics, Virginia Tech, Blacksburg 24061, Virginia, United States.ORCID 0000-0002-4930-6612
Feng PanDepartment of Statistics, Florida State University, Tallahassee 32304, Florida, United States.
Sergio PantanoInstitut Pasteur de Montevideo, Montevideo 11400, Uruguay.ORCID 0000-0001-6435-4543
Ruxi QiCryo-EM Center, Southern University of Science and Technology, Shenzhen 518055, China.
Ali RahnamounDepartment of Computer Science and Engineering, Michigan State University, East Lansing 48824-1322, Michigan, United States.
Ali RishehDepartment of Computer Science, California State University, Los Angeles 90032, California, United States.
Stephan Schott-VerdugoInstitute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich 52425, Germany.
Akhil ShajanDepartment of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing 48824-1322, Michigan, United States.
Jason SwailsEntos, 4470 W Sunset Blvd, Suite 107, Los Angeles 90027, California, United States.
Junmei WangDepartment of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh 15261, Pennsylvania, United States.ORCID 0000-0002-9607-8229
Haixin WeiDepartments 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 WuLaboratory of Computational Biology, NHLBI, NIH, Bethesda 20892, Maryland, United States.
Yongxian WuDepartments 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 ZhangLaboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway 08854, New Jersey, United States.
Shiji ZhaoDepartments 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 0000-0002-4514-0897
Qiang ZhuDepartments 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 CheathamDepartment 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 RoeLaboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda 20892, Maryland, United States.
Adrian RoitbergDepartment of Chemistry, The University of Florida, 440 Leigh Hall, Gainesville 32611-7200, Florida, United States.ORCID 0000-0003-3963-8784
Carlos SimmerlingLaufer 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 YorkLaboratory 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 NaganDepartment of Chemistry, Stony Brook University, Stony Brook 11794, New York, United States.ORCID 0000-0003-2678-6825
Kenneth M MerzDepartment of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing 48824-1322, Michigan, United States.ORCID 0000-0001-9139-5893
Funding
Multi-Scale Quantum Models for Ribozyme CatalysisR01GM062248 · NIGMS · UNIVERSITY OF MINNESOTA TWIN CITIES · PI Darrin M York · 2001 to 2026
$7.1MSolvation modeling for next-gen biomolecule simulationsRM1GM135136 · NIGMS · STATE UNIVERSITY NEW YORK STONY BROOK · PI COUTSIAS, EVANGELOS A., DILL, KEN A · 2020 to 2024
$6.0MNext-generation integrated quantum force fields for biomedical applicationsR01GM107485 · NIGMS · RUTGERS, THE STATE UNIV OF N.J. · PI Darrin M York · 2015 to 2026
$3.8MMulti-scaled Modeling of Electrostatic and Polarization Effects in BiomoleculesR35GM130367 · NIGMS · UNIVERSITY OF CALIFORNIA-IRVINE · PI RAY LUO · 2019 to 2026
$3.0MTheory and Simulation of DNA Repair Enzymes; Mechanism, Structure and FunctionR01GM108583 · NIGMS · WAYNE STATE UNIVERSITY · PI CISNEROS, GERARDO ANDRES · 2014 to 2022
$2.9MModeling Transition Metal Ion Binding to ProteinsR01GM130641 · NIGMS · MICHIGAN STATE UNIVERSITY · PI KENNETH M. MERZ · 2019 to 2026
$2.5MNew Solvent Models, Sampling Methods and Maintenance of Amber SoftwareR01GM107104 · NIGMS · STATE UNIVERSITY NEW YORK STONY BROOK · PI SIMMERLING, CARLOS · 2013 to 2020
$2.4MSolvation directed drug design: from molecular physics to lead optimizationR35GM144089 · NIGMS · HERBERT H. LEHMAN COLLEGE · PI Thomas Philip Kurtzman · 2022 to 2026
$1.9MNew Generation of General AMBER Force Field for Biomedical ResearchR01GM147673 · NIGMS · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI WANG, JUNMEI, YANG, WEI · 2022 to 2025
$1.5MTheoretical Methods to Study Biological MacromoleculesZ01HL001051 · NHLBI · NATIONAL HEART, LUNG, AND BLOOD INSTITUTE · PI BROOKS, BERNARD R · 1998 to 2008
$1.4MA next-generation extendable simulation environment for affordable, accurate, and efficient free energy simulationsR01GM149874 · NIGMS · RUTGERS, THE STATE UNIV OF N.J. · PI TAI-SUNG LEE · 2023 to 2026
$1.3MNext generation implicit solvation for atomistic modelingR01GM144596 · NIGMS · VIRGINIA POLYTECHNIC INST AND ST UNIV · PI ONUFRIEV, ALEXEY VLAD · 2022 to 2025
$1.2MIntramural NIH HHS Z01 HL001051NIGMS NIH HHS R01 GM062248NIGMS NIH HHS R01 GM107104NIGMS NIH HHS R01 GM107485NIGMS NIH HHS R01 GM108583NIGMS NIH HHS R01 GM130641NIGMS NIH HHS R01 GM144596NIGMS NIH HHS R01 GM147673NIGMS NIH HHS R01 GM149874NIGMS NIH HHS R16 GM146633NIGMS NIH HHS R35 GM130367NIGMS NIH HHS R35 GM144089NIGMS NIH HHS R35 GM151951NIGMS NIH HHS RM1 GM135136
Abstract
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.
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What OpenQuestion holds
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LicenceCC BY-NC-ND
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.