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Paper · 36949402

Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS.

Vieira IHP and 5 others. BMC Bioinformatics, 2023. Cited by 94 papers, by iCite.

11 sourcespapers-2026-11-12-0.1.0

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ConductScience Library. Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS. Papers, record 36949402. Release papers-2026-11-12-0.1.0, 12 Nov 2026. https://conductscience.org/library/papers/36949402

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Paper

PubMed's record of the paper, with iCite's citation figures. No abstract is shown.

Title
Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS.
PubMed
Journal
BMC Bioinformatics
PubMed
Year
2023
PubMed
Publication types
Journal Article
PubMed
Citations, by iCite
94
iCite
Relative citation ratio, by iCite
14
iCite
Revised in PubMed
2023-03-25
PubMed

Authors6

The authors in the order PubMed's record lists them, with the ORCID iDs it states.

OrderAuthorForenameKindORCID iD
1Vieira IHPIvo Henrique Provensi
2Botelho EBEduardo Buganemi
3de Souza Gomes TJThales Junior
4Kist RRoger
5Caceres RARafael Andrade
6Zanchi FBFernando Bertonhttps://orcid.org/0000-0003-3386-0069

Source PubMed

Topics5

NLM's MeSH indexing of the paper, its major topics first.

MeSH termMajor
Molecular Dynamics SimulationMajor topic
SoftwareMajor topic
Proteins
Kinetics
Web Browser

Source PubMed

Grants3

Each grant PubMed's record writes, matched to the NIH project NIH's grant and paper links name for this paper, and each of those links the record does not write.

Grant, as the record writes itAgencyCountryNIH projectStated by
VOGDI-008-FIO-21Fundação para o Desenvolvimento Científico e Tecnológico em Saúde (Fiotec)PubMed
VOGDI-008-FIO-21Fundação para o Desenvolvimento Científico e Tecnológico em Saúde (Fiotec)PubMed
PAP-UNIVERSALFundação Rondônia de Amparo ao Desenvolvimento das Ações Científicas e Tecnológicas e à Pesquisa do Estado de Rondônia (FAPERO)PubMed

Source PubMed

Trials0

The trials whose ClinicalTrials.gov record lists the paper, and the trial numbers the paper's PubMed record names.

None in this release.

Comments and corrections0

PubMed's comments and corrections, NLM's own indexing: retractions first, then expressions of concern, errata and updates, and comments last.

None in this release.

References18

The papers the reference list in PubMed's record names, those in our copy of PubMed, in the list's order.

OrderPMIDTitleJournalYearIn PapersSource
18,744,570VMD: visual molecular dynamics.J Mol Graph1996https://conductscience.org/library/papers/8744570PubMed
219,399,780AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility.J Comput Chem2009https://conductscience.org/library/papers/19399780PubMed
315,272,157PRODRG: a tool for high-throughput crystallography of protein-ligand complexes.Acta Crystallogr D Biol Crystallogr2004https://conductscience.org/library/papers/15272157PubMed
416,381,869MODBASE: a database of annotated comparative protein structure models and associated resources.Nucleic Acids Res2006https://conductscience.org/library/papers/16381869PubMed
521,624,888SwissDock, a protein-small molecule docking web service based on EADock DSS.Nucleic Acids Res2011https://conductscience.org/library/papers/21624888PubMed
622,824,207ACPYPE - AnteChamber PYthon Parser interfacE.BMC Res Notes2012https://conductscience.org/library/papers/22824207PubMed
718,931,379The SWISS-MODEL Repository and associated resources.Nucleic Acids Res2009https://conductscience.org/library/papers/18931379PubMed
827,216,779QwikMD - Integrative Molecular Dynamics Toolkit for Novices and Experts.Sci Rep2016https://conductscience.org/library/papers/27216779PubMed
922,437,851MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.Bioinformatics2012https://conductscience.org/library/papers/22437851PubMed
1015,264,259A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6.J Comput Chem2004https://conductscience.org/library/papers/15264259PubMed

1 to 10 of 18

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Cited by60

The papers in our copy of PubMed whose reference list names this one, newest first. iCite, which reads more sources, counts 94 citations.

PMIDTitleJournalYearIn PapersSource
42,989,094Effects of cadmium stress on phenolic composition and biological activities of rosemary (Salvia rosmarinus Spenn., syn. Rosmarinus officinalis L.): LC-HRMS and in-silico insights.BMC Plant Biol2026https://conductscience.org/library/papers/42989094PubMed
42,964,753GFRAL genetic variations and circulating GFRAL in hyperemesis gravidarum.iScience2026https://conductscience.org/library/papers/42964753PubMed
42,920,563Exploring molecular interactions between yeast topoisomerase I and RNA polymerase III subunit, Rpc82 using an in-silico approach.Front Bioinform2026https://conductscience.org/library/papers/42920563PubMed
42,766,180Structural analysis of Sphingobium yanoikuyae P4 carboxylesterase reveals conformational and catalytic determinants for PET biodegradation.World J Microbiol Biotechnol2026https://conductscience.org/library/papers/42766180PubMed
42,764,332TTC33 forms a complex with WDR61 and PHF5A to recruit factors relevant to genomic integrity.Nat Commun2026https://conductscience.org/library/papers/42764332PubMed
42,733,058A glycolytic intermediate gatekeeps global mRNA decay in Escherichia coli.Nat Commun2026https://conductscience.org/library/papers/42733058PubMed
42,577,411Network reorganization of a cold-adapted β-glucosidase couples conformational flexibility to catalytic efficiency under low-temperature conditions.Front Microbiol2026https://conductscience.org/library/papers/42577411PubMed
42,576,455Integrated Molecular Docking and Dynamic Simulations Reveal Glycyrrhizic Acid Alleviates Allergic Rhinitis in Rats by Inhibiting the TLR4/NF-κB/IL-1β Pathway.J Immunol Res2026https://conductscience.org/library/papers/42576455PubMed
42,568,669Virtual Screening of Bacteriocins From Lactic Acid Bacteria Against Monkeypox DNA Polymerase: Sakacin P and Mundticin KS Emerge as Promising Candidates.Food Sci Nutr2026https://conductscience.org/library/papers/42568669PubMed
42,450,119Improving the Photostability and Antioxidant Activity of Resveratrol via Incorporation in Two Types of Polymeric Nanoparticles.Int J Mol Sci2026https://conductscience.org/library/papers/42450119PubMed

1 to 10 of 60

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Genes0

The genes the Gene search release ties to the paper: Swiss-Prot's references first, then PubTator's text mining.

None in this release.

Drugs0

The drugs whose trials, in the Pipelines release, list the paper.

None in this release.

Data0

The data bank entries PubMed's record names. Trial numbers are under Trials.

None in this release.

Data dates

The date of each source this release read.

PubMed
2026-11-06
PubMed
iCite
2026-11-05
iCite
PMC's ID file
2026-11-05
PMC's ID file
NIH RePORTER's grant and paper links
2026-11-01
NIH RePORTER's grant and paper links
Trials
2026-11-12
Gene search
2026-11-11
Pipelines
2026-09-18

Sources 11

  • ChEMBL, through Open TargetsCC BY-SA 3.0
  • ClinicalTrials.govNo license stated
  • HGNCCC0
  • iCiteCC BY 4.0
  • NCBI GenePublic domain (US government)
  • NIH RePORTER's grant and paper linksPublic domain
  • Open TargetsCC0 1.0
  • PMC's ID filePublic domain (US government)
  • PubMedNLM's terms
  • PubTator 3Public domain
  • UniProtCC BY 4.0
Each source's terms
  • ChEMBL, through Open TargetsCC BY-SA 3.0, for the parts from ChEMBL. Read on 8 Nov 2026 at https://platform-docs.opentargets.org/licence
  • ClinicalTrials.govnone stated
  • HGNCCC0: https://www.genenames.org/about/license/
  • iCiteCC BY 4.0
  • NCBI GeneNone named for the file. NCBI says information created by or for the US government on its site is in the public domain, and asks that NLM be acknowledged: https://www.ncbi.nlm.nih.gov/home/about/policies/
  • NIH RePORTER's grant and paper linksPublic domain (NIH RePORTER)
  • Open TargetsCC0 1.0. Open Targets asks that users cite its latest paper: Buniello et al. 2025, Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery, Nucleic Acids Research 53(D1):D1467, PMID 39657122. Read on 8 Nov 2026 at https://platform-docs.opentargets.org/licence
  • PMC's ID fileNone named for the file. NCBI says information created by or for the US government on its site is in the public domain, and asks that NLM be acknowledged: https://www.ncbi.nlm.nih.gov/home/about/policies/
  • PubMedNLM's terms
  • PubTator 3Public domain
  • UniProtCC BY 4.0. UniProt's licence file: "All databases and documents in the UniProt FTP directory may be copied and redistributed freely, without advance permission, provided that this copyright statement is reproduced with each copy." UniProt asks that users cite its latest paper: The UniProt Consortium, UniProt: the Universal Protein Knowledgebase in 2025, Nucleic Acids Research 53:D609-D617, https://doi.org/10.1093/nar/gkae1010. Read on 9 Nov 2026 at https://www.uniprot.org/help/license

ClinicalTrials.gov's data carry an international copyright outside the United States: https://clinicaltrials.gov/about-site/terms-conditions.

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