ArticleJournal of chemical theory and computation2013
Importance of the ion-pair interactions in the OPEP coarse-grained force field: parametrization and validation.
Article in Journal of chemical theory and computation, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Optimized OPEP Force Field for Simulation of Crowded Protein Solutions.The journal of physical chemistry. B · 2023Article
- Dynamics of Amyloid Formation from Simplified Representation to Atomistic Simulations.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Computer Simulations Aimed at Exploring Protein Aggregation and Dissociation.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Computational Models for the Study of Protein Aggregation.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Exposure of Von Willebrand Factor Cleavage Site in A1A2A3-Fragment under Extreme Hydrodynamic Shear.Polymers · 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
- Multiscale simulation of molecular processes in cellular environments.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2016Review
- Evaluation of the coarse-grained OPEP force field for protein-protein docking.BMC biophysics · 2016Article
- Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies.Chemical reviews · 2015Review
- Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides.Journal of chemical theory and computation · 2015Article
- Protein Simulations in Fluids: Coupling the OPEP Coarse-Grained Force Field with Hydrodynamics.Journal of chemical theory and computation · 2015Article
- Are coarse-grained models apt to detect protein thermal stability? The case of OPEP force field.Journal of non-crystalline solids · 2015Article
- A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions.Journal of molecular modeling · 2014Article
- The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems.Chemical Society reviews · 2014Review
- Recent advances in transferable coarse-grained modeling of proteins.Advances in protein chemistry and structural biology · 2014Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
We have derived new effective interactions that improve the description of ion-pairs in the OPEP coarse-grained force field without introducing explicit electrostatic terms. The iterative Boltzmann inversion method was used to extract these potentials from all atom simulations by targeting the radial distribution function of the distance between the center of mass of the side-chains. The new potentials have been tested on several systems that differ in structural properties, thermodynamic stabilities and number of ion-pairs. Our modeling, by refining the packing of the charged amino-acids, impacts the stability of secondary structure motifs and the population of intermediate states during temperature folding/unfolding; it also improves the aggregation propensity of peptides. The new version of the OPEP force field has the potentiality to describe more realistically a large spectrum of situations where salt-bridges are key interactions.
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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.