ArticleJournal of computational chemistry2014
Implicit treatment of solvent dispersion forces in protein simulations.
Article in Journal of computational chemistry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
8 citing papers in PubMed, 12 citations in OpenAlex.
- Modulation of free energy landscapes as a strategy for the design of antimicrobial peptides.Journal of biological physics · 2022Article
- Stereoelectronic effects in stabilizing protein-N-glycan interactions revealed by experiment and machine learning.Nature chemistry · 2021Article
- Strong dependence of the nano-bio interactions on core morphology and layer composition of ultrasmall nanostructures.The Journal of chemical physics · 2019Article
- Peptide and Protein Structure Prediction with a Simplified Continuum Solvent Model.The journal of physical chemistry. B · 2018Article
- Self-adaptive multiscaling algorithm for efficient simulations of many-protein systems in crowded conditions.Physical chemistry chemical physics : PCCP · 2018Article
- Computational study of the inhibitory mechanism of the kinase CDK5 hyperactivity by peptide p5 and derivation of a pharmacophore.Journal of computer-aided molecular design · 2016Article
- Detection and characterization of nonspecific, sparsely populated binding modes in the early stages of complexation.Journal of computational chemistry · 2015Article
- Role of Albumin in the Formation and Stabilization of Nanoparticle Aggregates in Serum Studied by Continuous Photon Correlation Spectroscopy and Multiscale Computer Simulations.The journal of physical chemistry. C, Nanomaterials and interfaces · 2014Article
Corrections and comments
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Authors and funding
1 author at 1 institution in 1 country.
Funding
Abstract
A model is proposed for the evaluation of dispersive forces in a continuum solvent representation for use in large-scale computer simulations. The model captures the short- and long-range effects of water-exclusion in conditions of partial and anisotropic hydration. The model introduces three parameters, one of which represents the degree of hydration (water occupancy) at any point in the system, which depends on the solute conformation, and two that represent the strength of water-water and water-solute dispersive interactions. The model is optimized for proteins, using hydration data of a suboptimally hydrated binding site and results from dynamics simulations in explicit water. The model is applied to a series of aliphatic-alcohol/protein complexes and a set of binary and ternary complexes of various sizes. Implications for weak and ultra-weak protein-protein association and for simulation in crowded media are discussed.
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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.