ArticleProteins2009
Multiscale characterization of protein conformational ensembles.
Article in Proteins, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 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
14 citing papers in PubMed.
- EnGens: a computational framework for generation and analysis of representative protein conformational ensembles.Briefings in bioinformatics · 2023Article
- Dynamical network of residue-residue contacts reveals coupled allosteric effects in recognition, catalysis, and mutation.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.PLoS computational biology · 2016Review
- The power of coarse graining in biomolecular simulations.Wiley interdisciplinary reviews. Computational molecular science · 2014Article
- Rapid sampling of local minima in protein energy surface and effective reduction through a multi-objective filter.Proteome science · 2013Article
- A population-based evolutionary search approach to the multiple minima problem in de novo protein structure prediction.BMC structural biology · 2013Article
- Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method.BMC structural biology · 2013Article
- Evolutionary-inspired probabilistic search for enhancing sampling of local minima in the protein energy surface.Proteome science · 2012Article
- Article
- Order parameters for macromolecules: application to multiscale simulation.The Journal of chemical physics · 2011Article
- Ensemble-based methods for describing protein dynamics.Current opinion in pharmacology · 2010Review
- Tracing conformational changes in proteins.BMC structural biology · 2010Article
- Multi-scale characterization of the energy landscape of proteins with application to the C3D/Efb-C complex.Proteins · 2010Article
- Restriction versus guidance in protein structure prediction.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
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
We propose a multiscale exploration method to characterize the conformational space populated by a protein at equilibrium. The method efficiently obtains a large set of equilibrium conformations in two stages: first exploring the entire space at a coarse-grained level of detail, then narrowing a refined exploration to selected low-energy regions. The coarse-grained exploration periodically adds all-atom detail to selected conformations to ensure that the search leads to regions which maintain low energies in all-atom detail. The second stage reconstructs selected low-energy coarse-grained conformations in all-atom detail. A low-dimensional energy landscape associated with all-atom conformations allows focusing the exploration to energy minima and their conformational ensembles. The lowest energy ensembles are enriched with additional all-atom conformations through further multiscale exploration. The lowest energy ensembles obtained from the application of the method to three different proteins correctly capture the known functional states of the considered systems.
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.