ArticleJournal of computer-aided molecular design2011
Molecular motions in drug design: the coming age of the metadynamics method.
Article in Journal of computer-aided molecular design, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 42 citations in OpenAlex.
- Unlocking the chemistry facilitated by enzymes that process nucleic acids using quantum mechanical and combined quantum mechanics-molecular mechanics techniques.Pure and applied chemistry. Chimie pure et appliquee · 2025Review
- Advances in methods and concepts provide new insight into antibiotic fluxes across the bacterial membrane.Communications biology · 2024Article
- Pathways for the formation of ice polymorphs from water predicted by a metadynamics method.Scientific reports · 2020Article
- Interplay of cysteine exposure and global protein dynamics in small-molecule recognition by a regulator of G-protein signaling protein.Proteins · 2019Article
- In Silico Studies in Drug Research Against Neurodegenerative Diseases.Current neuropharmacology · 2018Review
- Interaction of antibacterial compounds with RND efflux pumps in Pseudomonas aeruginosa.Frontiers in microbiology · 2015Review
- Serpin latency transition at atomic resolution.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- In silico and in vivo studies of molecular structures and mechanisms of AtPCS1 protein involved in binding arsenite and/or cadmium in plant cells.Journal of molecular modeling · 2014Article
- Computational methods in drug discovery.Pharmacological reviews · 2014Review
- Some ligands enhance the efflux of other ligands by the Escherichia coli multidrug pump AcrB.Biochemistry · 2013Article
- Molecular recognition of DNA by ligands: roughness and complexity of the free energy profile.The Journal of chemical physics · 2013Article
- Conformational free-energy landscapes for a peptide in saline environments.Biophysical journal · 2012Article
- In silico and in vivo studies of an Arabidopsis thaliana gene, ACR2, putatively involved in arsenic accumulation in plants.Journal of molecular modeling · 2012Article
- Molecular simulation methods in drug discovery: a prospective outlook.Journal of computer-aided molecular design · 2012Article
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Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metadynamics is emerging as a useful free energy method in physics, chemistry and biology. Recently, it has been applied also to investigate ligand binding to biomolecules of pharmacological interest. Here, after introducing the basic idea of the method, we review applications to challenging targets for pharmaceutical intervention. We show that this methodology, especially when combined with a variety of other computational approaches such as molecular docking and/or molecular dynamics simulation, may be useful to predict structure and energetics of ligand/target complexes even when the targets lack a deep binding cavity, such as DNA and proteins undergoing fibrillation in neurodegenerative diseases. Furthermore, the method allows investigating the routes of molecular recognition and the associated binding energy profiles, providing a molecular interpretation to experimental data.
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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.