ReviewCurrent topics in medicinal chemistry2012
Rational prediction with molecular dynamics for hit identification.
Review in Current topics in medicinal chemistry, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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.
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.
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Who cites it
10 citing papers in PubMed.
- Interference of small compounds and MgScientific reports · 2024Article
- Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field.Journal of chemical theory and computation · 2023Article
- Emerging Computational Methods for the Rational Discovery of Allosteric Drugs.Chemical reviews · 2016Review
- Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations.PLoS computational biology · 2016Review
- Knowledge-Based Methods To Train and Optimize Virtual Screening Ensembles.Journal of chemical information and modeling · 2016Article
- All-Atom Molecular Dynamics of Virus Capsids as Drug Targets.The journal of physical chemistry letters · 2016Article
- Discovery of Novel ROCK1 Inhibitors via Integrated Virtual Screening Strategy and Bioassays.Scientific reports · 2015Article
- Clustering molecular dynamics trajectories for optimizing docking experiments.Computational intelligence and neuroscience · 2015Article
- POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics.Journal of chemical theory and computation · 2014Article
- Exploring the role of receptor flexibility in structure-based drug discovery.Biophysical chemistry · 2014Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Although the motions of proteins are fundamental for their function, for pragmatic reasons, the consideration of protein elasticity has traditionally been neglected in drug discovery and design. This review details protein motion, its relevance to biomolecular interactions and how it can be sampled using molecular dynamics simulations. Within this context, two major areas of research in structure-based prediction that can benefit from considering protein flexibility, binding site detection and molecular docking, are discussed. Basic classification metrics and statistical analysis techniques, which can facilitate performance analysis, are also reviewed. With hardware and software advances, molecular dynamics in combination with traditional structure-based prediction methods can potentially reduce the time and costs involved in the hit identification pipeline.
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What OpenQuestion holds
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.