ArticleJournal of molecular modeling2016
Improvements in GROMACS plugin for PyMOL including implicit solvent simulations and displaying results of PCA analysis.
Article in Journal of molecular modeling, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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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
10 citing papers in PubMed.
- Design, synthesis, and biological evaluation of novel aryl isoxazoles as potential Hsp90 inhibitors.Research in pharmaceutical sciences · 2026Article
- In Silico Analyses of a Promising Drug Candidate for the Treatment of Amyotrophic Lateral Sclerosis Targeting Superoxide Dismutase I Protein.Pharmaceutics · 2023Article
- Baicalein Inhibits theInfection and drug resistance · 2023Article
- CHAPERONComputational and structural biotechnology journal · 2023Article
- Attacking COVID-19 Progression Using Multi-Drug Therapy for Synergetic Target Engagement.Biomolecules · 2021Article
- Silico analysis of interaction between full-length SARS-CoV2 S protein with human Ace2 receptor: Modelling, docking, MD simulation.Biophysical chemistry · 2020Article
- PyVibMS: a PyMOL plugin for visualizing vibrations in molecules and solids.Journal of molecular modeling · 2020Article
- Could the interaction between LMX1B and PAX2 influence the severity of renal symptoms?European journal of human genetics : EJHG · 2018Article
- LiGRO: a graphical user interface for protein-ligand molecular dynamics.Journal of molecular modeling · 2017Article
- Simplifying and enhancing the use of PyMOL with horizontal scripts.Protein science : a publication of the Protein Society · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In order to get the dynamic molecule model from the static one, the molecular dynamics (MD) simulation needs to be performed. Some software sets such as GROMACS are used for that purpose. Unfortunately they lack GUI. The Dynamics PyMOL plugin allows researcher to perform MD simulations directly from the PyMOL software by GUI-based interface of GROMACS tools. This paper describes many improvements introduced into the Dynamics PyMOL plugin 2.0 including: an integration with ProDy library, possibility to use the implicit solvents, an ability to interpret the MD simulations, and implementation of some more GROMACS functionality.
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Registered trials
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.