ArticleJournal of chemical theory and computation2016
Using Local States To Drive the Sampling of Global Conformations in Proteins.
Article in Journal of chemical theory and computation, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 16 citations in OpenAlex.
- Toward the Prediction of Binding Events in Very Flexible, Allosteric, Multidomain Proteins.Journal of chemical information and modeling · 2025Article
- Predicting binding events in very flexible, allosteric, multi-domain proteins.bioRxiv : the preprint server for biology · 2024Article
- Protein conformational ensembles in function: roles and mechanisms.RSC chemical biology · 2023Review
- The conformational and mutational landscape of the ubiquitin-like marker for autophagosome formation in cancer.Autophagy · 2021Article
- In silico identification of rescue sites by double force scanning.Bioinformatics (Oxford, England) · 2018Article
- SAFlex: A structural alphabet extension to integrate protein structural flexibility and missing data information.PloS one · 2018Article
- Temperature evolution of Trp-cage folding pathways: An analysis by dividing the probability flux field into stream tubes.Journal of biological physics · 2017Article
- Allosteric modulation of cardiac myosin dynamics by omecamtiv mecarbil.PLoS computational biology · 2017Article
- Exploring the potential of a structural alphabet-based tool for mining multiple target conformations and target flexibility insight.PloS one · 2017Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
Conformational changes associated with protein function often occur beyond the time scale currently accessible to unbiased molecular dynamics (MD) simulations, so that different approaches have been developed to accelerate their sampling. Here we investigate how the knowledge of backbone conformations preferentially adopted by protein fragments, as contained in precalculated libraries known as structural alphabets (SA), can be used to explore the landscape of protein conformations in MD simulations. We find that (a) enhancing the sampling of native local states in both metadynamics and steered MD simulations allows the recovery of global folded states in small proteins; (b) folded states can still be recovered when the amount of information on the native local states is reduced by using a low-resolution version of the SA, where states are clustered into macrostates; and (c) sequences of SA states derived from collections of structural motifs can be used to sample alternative conformations of preselected protein regions. The present findings have potential impact on several applications, ranging from protein model refinement to protein folding and design.
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Registered trials
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