ArticleThe journal of physical chemistry. B2017
Protein Folding and Structure Prediction from the Ground Up II: AAWSEM for α/β Proteins.
Article in The journal of physical chemistry. B, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Biophysical modeling for accurate T cell specificity prediction of viral and tumor antigens.Nature communications · 2026Article
- FINCHES: A Computational Framework for Predicting Intermolecular Interactions in Intrinsically Disordered Proteins.International journal of molecular sciences · 2025Review
- Generating the polymorph landscapes of amyloid fibrils using AI: RibbonFold.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- RACER-m leverages structural features for sparse T cell specificity prediction.Science advances · 2024Article
- Illuminating Intrinsically Disordered Proteins with Integrative Structural Biology.Biomolecules · 2023Review
- BAP1 forms a trimer with HMGB1 and HDAC1 that modulates gene × environment interaction with asbestos.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems.Biomolecules · 2021Article
- From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules.Frontiers in molecular biosciences · 2021Review
- Article
- Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level.Biomolecules · 2019Article
- AWSEM-IDP: A Coarse-Grained Force Field for Intrinsically Disordered Proteins.The journal of physical chemistry. B · 2018Article
- Surveying the Energy Landscapes of Aβ Fibril Polymorphism.The journal of physical chemistry. B · 2018Article
- Template-Guided Protein Structure Prediction and Refinement Using Optimized Folding Landscape Force Fields.Journal of chemical theory and computation · 2018Article
- PAGE4 and Conformational Switching: Insights from Molecular Dynamics Simulations and Implications for Prostate Cancer.Journal of molecular biology · 2018Article
- Protein structure prediction: making AWSEM AWSEM-ER by adding evolutionary restraints.Proteins · 2017Article
- Aggregation landscapes of Huntingtin exon 1 protein fragments and the critical repeat length for the onset of Huntington's disease.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
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Authors and funding
5 authors.
Funding
Abstract
The atomistic associative memory, water mediated, structure and energy model (AAWSEM) is an efficient coarse-grained force field with transferable tertiary interactions that incorporates local in sequence energetic biases using structural information derived from all-atom simulations of long segments of the protein. For α helical proteins, the accuracy of structure prediction using AAWSEM has been established previously. In this article, we examine the capability of AAWSEM to predict the structure of α/β proteins. We also elaborate on an iterative approach that uses the structures from a first round of AAWSEM simulation as fragment memories. This iterative scheme improves the quality of the structure prediction and makes the free energy profile more funneled toward native configurations. We explore the use of clustering analyses as a way of evaluating the confidence in various structure prediction models. Clustering using a local relative order parameter (mutual Q) of the predicted structural ensemble turns out to be optimal. The tightest cluster according to mutual Q generally has the most correctly folded structure. Since there is no bioinformatic input, AAWSEM amounts to an ab initio protein structure prediction method that combines the efficiency of coarse-grained simulations with the local structural accuracy that can be achieved from all-atom simulations.
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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.