ArticleProteins2017
Protein structure prediction: making AWSEM AWSEM-ER by adding evolutionary restraints.
Article in Proteins, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Exploring Abeta42 monomer diffusion dynamics on fibril surfaces through molecular simulations.Protein science : a publication of the Protein Society · 2025Article
- Generating the polymorph landscapes of amyloid fibrils using AI: RibbonFold.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Machine learning in biological physics: From biomolecular prediction to design.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- The physical and evolutionary energy landscapes of devolved protein sequences corresponding to pseudogenes.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Early-Stage Oligomerization of Prion-like Polypeptides Reveals the Molecular Mechanism of Amyloid-Disrupting Capacity by Proline Residues.The journal of physical chemistry. B · 2023Article
- Illuminating Intrinsically Disordered Proteins with Integrative Structural Biology.Biomolecules · 2023Review
- Coevolution-derived native and non-native contacts determine the emergence of a novel fold in a universally conserved family of transcription factors.Protein science : a publication of the Protein Society · 2022Article
- Metamorphic proteins under a computational microscope: Lessons from a fold-switching RfaH protein.Computational and structural biotechnology journal · 2022Review
- The N-terminal domain of RfaH plays an active role in protein fold-switching.PLoS computational biology · 2021Article
- OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations.PLoS computational biology · 2021Article
- Fibril Surface-Dependent Amyloid Precursors Revealed by Coarse-Grained Molecular Dynamics Simulation.Frontiers in molecular biosciences · 2021Article
- Article
- Exploring the F-actin/CPEB3 interaction and its possible role in the molecular mechanism of long-term memory.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- AWSEM-Suite: a protein structure prediction server based on template-guided, coevolutionary-enhanced optimized folding landscapes.Nucleic acids research · 2020Article
- Forging tools for refining predicted protein structures.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level.Biomolecules · 2019Article
- Template-Guided Protein Structure Prediction and Refinement Using Optimized Folding Landscape Force Fields.Journal of chemical theory and computation · 2018Article
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3 authors.
Funding
Abstract
Protein sequences have evolved to fold into functional structures, resulting in families of diverse protein sequences that all share the same overall fold. One can harness protein family sequence data to infer likely contacts between pairs of residues. In the current study, we combine this kind of inference from coevolutionary information with a coarse-grained protein force field ordinarily used with single sequence input, the Associative memory, Water mediated, Structure and Energy Model (AWSEM), to achieve improved structure prediction. The resulting Associative memory, Water mediated, Structure and Energy Model with Evolutionary Restraints (AWSEM-ER) yields a significant improvement in the quality of protein structure prediction over the single sequence prediction from AWSEM when a sufficiently large number of homologous sequences are available. Free energy landscape analysis shows that the addition of the evolutionary term shifts the free energy minimum to more native-like structures, which explains the improvement in the quality of structures when performing predictions using simulated annealing. Simulations using AWSEM without coevolutionary information have proved useful in elucidating not only protein folding behavior, but also mechanisms of protein function. The success of AWSEM-ER in de novo structure prediction suggests that the enhanced model opens the door to functional studies of proteins even when no experimentally solved structures are available.
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