ArticleJournal of chemical information and modeling2025
Recent Developments in Amber Biomolecular Simulations.
Abstract read
In one paragraph
Article in Journal of chemical information and modeling, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 89 papers.
0numbers the graph read from it
0cells of the map it votes in
89citing 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
89 citing papers in PubMed.
- Anti-proliferative and anti-inflammatory potential of 2-chloro-3-((4-hydroxyphenyl)amino)naphthalene-1,4-dione through targeting TNF-α/IL-8 and NF-κB signaling in HCT116 cancer cells: a comprehensiveBiochemistry and biophysics reports · 2026Article
- Assessment of the Binding Affinity of Covalent Inhibitors of Cruzain and Cathepsin L Using Relative Binding Free Energy.ChemMedChem · 2026Article
- Transposon end recognition and pairing by I-F3 CRISPR-associated transposase.Science advances · 2026Article
- STING agonist profiling by nucleotide library defines structural determinants of cyclic dinucleotide recognition.iScience · 2026Article
- Training a force field for proteins and small molecules from scratch.Chemical science · 2026Article
- High-throughput physics-based enzyme engineering.bioRxiv : the preprint server for biology · 2026Article
- Covalent Targeting and Thermostabilization of Oncogenic R280K and R273H Mutants p53 by Small Molecule RVJB59.ChemMedChem · 2026Article
- Scorpiand Pyrazole Azacyclophanes: Synthesis, Protonation Behavior, and Cu2+ Coordination Chemistry.Inorganic chemistry · 2026Article
- Kinetic assembly tuning NIR-II cyanine aggregated states: Remarkable photothermal-mediated sustained retention in orthotopic hepatoma.Science advances · 2026Article
- Development of m6A Readers for Enhanced Recognition In Vitro via Genetic Code Expansion.ACS chemical biology · 2026Article
- Pre-activation and gating pathway of AMPA receptors revealed by full and partial agonists.Nature structural & molecular biology · 2026Article
- Lineage-Specific CagA Binding Mechanics and Microenvironmental Rewiring in East Asian Gastric Carcinogenesis.Molecules (Basel, Switzerland) · 2026Article
- Methods for the establishment of enzymatic mechanisms - from QM to ML.Chemical science · 2026Review
- Machine learning-driven identification of PIM2 kinase inhibitors through QSAR modeling and molecular dynamics simulations.Journal, genetic engineering & biotechnology · 2026Article
- A glycosaminoglycan microarray identifies galectin-4 binding to sulfated glycosaminoglycans.Biochemistry and biophysics reports · 2026Article
- The conformation of the complementary strand and the deformation of the DNA groove upon DDB2 binding justifies the different repair rates for cyclobutane pyrimidine dimers.Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology · 2026Article
- The nematode Caenorhabditis elegans has a cationic amphiphilic drug (CAD) defense system.PLoS biology · 2026Article
- Agonist Binding Reshapes the Kinetic Landscape and Allosteric Communication of APLNR Toward Activation-Competent States.International journal of molecular sciences · 2026Article
- Modeling Peptides in Aqueous Ionic Liquid Mixtures: A Quantum Mechanics/Molecular Dynamics Study of Structural and NMR Properties.Journal of chemical theory and computation · 2026Article
- Article
29 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
31 authors.
David A CaseDepartment of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States.
David S CeruttiDepartment of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States.
Vinícius Wilian D CruzeiroDepartment of Chemistry, The University of Florida, 440 Leigh Hall, Gainesville, Florida 32611-7200, United States.
Thomas A DardenNational Institute of Environmental Health Sciences, 111 TW Alexander Dr., Durham, North Carolina 27709, United States.
Robert E DukeNational Institute of Environmental Health Sciences, 111 TW Alexander Dr., Durham, North Carolina 27709, United States.
Mahdieh GhazimirsaeedAdvanced Micro Devices Inc., Austin, Texas 78735, United States.
George M GiambaşuLaboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States.ORCID 0000-0003-0581-8605
Timothy J GieseLaboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States.ORCID 0000-0002-0653-9168
Andreas W GötzSan Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093-0505, United States.ORCID 0000-0002-8048-6906
Julie A HarrisDepartment of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States.ORCID 0000-0002-1130-6457
Koushik KasavajhalaLaufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States.
Tai-Sung LeeLaboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States.ORCID 0000-0003-2110-2279
Zhen LiDepartment of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1322, United States.ORCID 0000-0001-7947-3887
Charles LinCold Start Therapeutics, San Diego, California 92126, United States.
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
Yinglong MiaoDepartment of Pharmacology and Computational Medicine Program, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina 27599, United States.ORCID 0000-0003-3714-1395
Romelia Salomon-FerrrerSan Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093-0505, United States.
Jana ShenDepartment of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States.ORCID 0000-0002-3234-0769
Ryan SnyderLaboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States.
Jason SwailsIambic Therapeutics, 5627 Oberlin Drive, Suite 120, San Diego, California 92121, United States.
Ross C WalkerSan Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093-0505, United States.
Jinan WangDepartment of Pharmacology and Computational Medicine Program, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina 27599, United States.
Xiongwu WuLaboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, Maryland 20892, United States.
Jinzhe ZengLaboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States.ORCID 0000-0002-1515-8172
Thomas E Cheatham IiiDepartment of Medicinal Chemistry, The University of Utah, 30 South 2000 East, Salt Lake City, Utah 84112, United States.ORCID 0000-0003-0298-3904
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
Adrian RoitbergDepartment of Chemistry, The University of Florida, 440 Leigh Hall, Gainesville, Florida 32611-7200, United States.ORCID 0000-0003-3963-8784
Carlos SimmerlingLaufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, 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, New Jersey 08854, United States.ORCID 0000-0002-9193-7055
Maria C NaganDepartment of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States.ORCID 0000-0003-2678-6825
Kenneth M MerzDepartment of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1322, United States.
Funding
Multi-Scale Quantum Models for Ribozyme CatalysisR01GM062248 · NIGMS · UNIVERSITY OF MINNESOTA TWIN CITIES · PI Darrin M York · 2001 to 2026
$7.1MNext-generation integrated quantum force fields for biomedical applicationsR01GM107485 · NIGMS · RUTGERS, THE STATE UNIV OF N.J. · PI Darrin M York · 2015 to 2026
$3.8MElectrostatic modulation of protein stability and foldingR01GM098818 · NIGMS · UNIVERSITY OF OKLAHOMA · PI SHEN, JANA · 2011 to 2021
$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
$2.4MTheoretical 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
$1.3MMetals in Medicine Gordon Research ConferenceR13GM066248 · NIGMS · GORDON RESEARCH CONFERENCES · PI FARRELL, NICHOLAS P · 2002 to 2004
$10kIntramural NIH HHS Z01 HL001051Intramural NIH HHS Z99 HL999999NIGMS NIH HHS R01 GM062248NIGMS NIH HHS R01 GM098818NIGMS NIH HHS R01 GM107104NIGMS NIH HHS R01 GM107485NIGMS NIH HHS R01 GM130641NIGMS NIH HHS R01 GM149874NIGMS NIH HHS R13 GM066248
Abstract
Amber is a molecular dynamics (MD) software package first conceived by Peter Kollman, his lab and collaborators to simulate biomolecular systems. The
Indexed as
Molecular Dynamics SimulationSoftwareProteinsThermodynamicsProteins
Identifiers
What OpenQuestion holds
Textmetadata
LicenceTDM
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.