ArticleThe journal of physical chemistry. B2018
AWSEM-IDP: A Coarse-Grained Force Field for Intrinsically Disordered Proteins.
Article in The journal of physical chemistry. B, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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Who cites it
69 citing papers in PubMed.
- Article
- Article
- Valency-Limited Molecular Dynamics Simulations of Stickers-and-Spacers Polymers Reveal a Tradeoff Between Condensation and Organization.bioRxiv : the preprint server for biology · 2026Article
- HyRes: Accurate Physics-Based Simulation of Dynamic Protein Structures and Interactions in Complex Environments at Scale.bioRxiv : the preprint server for biology · 2026Article
- MOFF2: A Transferable Coarse-Grained Protein Force Field for Predictive Condensate Simulations.bioRxiv : the preprint server for biology · 2026Article
- In Search of Shape in the Unshaped: Constructing Ensembles of Intrinsically Disordered Proteins.Biophysics reviews · 2026Article
- Bridging Scales: Coarse-Grained Protein Models in Computational Biology.Advances in experimental medicine and biology · 2026Review
- Neurodegeneration Through the Lens of Bioinformatics Approaches: Computational Mechanisms of Protein Misfolding.International journal of molecular sciences · 2025Review
- Sequence-Dependent Conformational Landscapes of Intrinsically Disordered Proteins Reveal Asymmetric Chain Compaction.Journal of chemical theory and computation · 2025Article
- Targeting protein disorder: the next hurdle in drug discovery.Nature reviews. Drug discovery · 2025Review
- Biomolecular Condensates as Emerging Biomaterials: Functional Mechanisms and Advances in Computational and Experimental Approaches.Advanced materials (Deerfield Beach, Fla.) · 2025Review
- Energy Landscapes and Structural Plasticity of Intrinsically Disordered Histones.Journal of chemical information and modeling · 2025Article
- Toward understanding biomolecular materials comprising intrinsically disordered proteinsMolecular systems design & engineering · 2025Review
- Conformational dynamics and multimodal interaction of Paxillin with the focal adhesion targeting domain.Science advances · 2025Article
- Conformational dynamics and multi-modal interaction of Paxillin with the Focal Adhesion Targeting Domain.bioRxiv : the preprint server for biology · 2025Article
- Toward Predictive Coarse-Grained Simulations of Biomolecular Condensates.Biochemistry · 2025Review
- Sizes, conformational fluctuations, and SAXS profiles for intrinsically disordered proteins.Protein science : a publication of the Protein Society · 2025Article
- Use of AI-methods over MD simulations in the sampling of conformational ensembles in IDPs.Frontiers in molecular biosciences · 2025Review
- Wild-Type α-Synuclein Structure and Aggregation: A Comprehensive Coarse-Grained and All-Atom Molecular Dynamics Study.Journal of chemical information and modeling · 2024Article
- A Practical Guide to All-Atom and Coarse-Grained Molecular Dynamics Simulations Using Amber and Gromacs: A Case Study of Disulfide-Bond Impact on the Intrinsically Disordered Amyloid Beta.International journal of molecular sciences · 2024Article
9 more citing papers are in PubMed but not listed here.
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3 authors.
Funding
Abstract
The associative memory, water-mediated, structure and energy model (AWSEM) has been successfully used to study protein folding, binding, and aggregation problems. In this work, we introduce AWSEM-IDP, a new AWSEM branch for simulating intrinsically disordered proteins (IDPs), where the weights of the potentials determining secondary structure formation have been finely tuned, and a novel potential is introduced that helps to precisely control both the average extent of protein chain collapse and the chain's fluctuations in size. AWSEM-IDP can efficiently sample large conformational spaces, while retaining sufficient molecular accuracy to realistically model proteins. We applied this new model to two IDPs, demonstrating that AWSEM-IDP can reasonably well reproduce higher-resolution reference data, thus providing the foundation for a transferable IDP force field. Finally, we used thermodynamic perturbation theory to show that, in general, the conformational ensembles of IDPs are highly sensitive to fine-tuning of force field parameters.
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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.