ArticleJournal of chemical information and modeling2011
Predictive power of molecular dynamics receptor structures in virtual screening.
Article in Journal of chemical information and modeling, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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
36 citing papers in PubMed.
- Chemical and Genetic Validation of an Essential Calcium Entry Channel ofACS infectious diseases · 2025Article
- Article
- Molecular Dynamics as a Tool for Virtual Ligand Screening.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Virtual screening of substances used in the treatment of SARS-CoV-2 infection and analysis of compounds with known action on structurally similar proteins from other viruses.Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie · 2022Review
- Development of tBu-phenyl Acetamide Appended Thiacalix[4]arene as "Turn-ON" Fluorescent Probe for Selective Recognition of Hg(II) Ions.Journal of fluorescence · 2022Article
- Molecular Structure-Based Screening of the Constituents ofCurrent issues in molecular biology · 2022Article
- Ensemble learning from ensemble docking: revisiting the optimum ensemble size problem.Scientific reports · 2022Article
- Supervised molecular dynamics for exploring the druggability of the SARS-CoV-2 spike protein.Journal of computer-aided molecular design · 2021Article
- Decrypting a Cryptic Allosteric Pocket inCommunications chemistry · 2021Article
- Chemical-Shift Perturbations Reflect Bile Acid Binding to Norovirus Coat Protein: Recognition Comes in Different Flavors.Chembiochem : a European journal of chemical biology · 2020Article
- Cellular and Molecular Targets of Waterbuck Repellent Blend Odors in Antennae ofFrontiers in cellular neuroscience · 2020Article
- Application ofFrontiers in chemistry · 2020Review
- Using parallelized incremental meta-docking can solve the conformational sampling issue when docking large ligands to proteins.BMC molecular and cell biology · 2019Article
- Computational Strategy for Bound State Structure Prediction in Structure-Based Virtual Screening: A Case Study of Protein Tyrosine Phosphatase Receptor Type O Inhibitors.Journal of chemical information and modeling · 2018Article
- High-performance virtual screening by targeting a high-resolution RNA dynamic ensemble.Nature structural & molecular biology · 2018Article
- Virtual screening for potential inhibitors of Mcl-1 conformations sampled by normal modes, molecular dynamics, and nuclear magnetic resonance.Drug design, development and therapy · 2017Article
- Enhancing Virtual Screening Performance of Protein Kinases with Molecular Dynamics Simulations.Journal of chemical information and modeling · 2016Article
- Knowledge-Based Methods To Train and Optimize Virtual Screening Ensembles.Journal of chemical information and modeling · 2016Article
- Computational drug design strategies applied to the modelling of human immunodeficiency virus-1 reverse transcriptase inhibitors.Memorias do Instituto Oswaldo Cruz · 2015Review
- Molecular dynamics to enhance structure-based virtual screening on cathepsin B.Journal of computer-aided molecular design · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Molecular dynamics (MD) simulation is a well-established method for understanding protein dynamics. Conformations from unrestrained MD simulations have yet to be assessed for blind virtual screening (VS) by docking. This study presents a critical analysis of the predictive power of MD snapshots to this regard, evaluating two well-characterized systems of varying flexibility in ligand-bound and unbound configurations. Results from such VS predictions are discussed with respect to experimentally determined structures. In all cases, MD simulations provide snapshots that improve VS predictive power over known crystal structures, possibly due to sampling more relevant receptor conformations. Additionally, MD can move conformations previously not amenable to docking into the predictive range.
Indexed as
Identifiers
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.