ArticleProteins2018
Structure refinement of membrane proteins via molecular dynamics simulations.
Article in Proteins, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
13 citing papers in PubMed.
- Multi-Target Neuroprotective Compound Exhibits EAAT2-Modulating and Alzheimer's Pathology-Attenuating Effects in In Vitro and In Vivo Models.ACS chemical neuroscience · 2026Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- HLA-EpiCheck: novel approach for HLA B-cell epitope prediction using 3D-surface patch descriptors derived from molecular dynamic simulations.Bioinformatics advances · 2024Article
- Membrane-mediated interaction of non-conventional snake three-finger toxins with nicotinic acetylcholine receptors.Communications biology · 2022Article
- Computational discovery of binding mode of anti-TRBC1 antibody and predicted key amino acids of TRBC1.Scientific reports · 2022Article
- Diverse Scientific Benchmarks for Implicit Membrane Energy Functions.Journal of chemical theory and computation · 2021Article
- Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?PLoS computational biology · 2021Article
- Molecular Dynamics Simulations of Mitochondrial Uncoupling Protein 2.International journal of molecular sciences · 2021Article
- Guardians of the Cell: State-of-the-Art of Membrane Proteins from a Computational Point-of-View.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Article
- Methods for the Refinement of Protein Structure 3D Models.International journal of molecular sciences · 2019Review
- Generalized Born Implicit Solvent Models for Biomolecules.Annual review of biophysics · 2019Review
- Experimental accuracy in protein structure refinement via molecular dynamics simulations.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
A refinement protocol based on physics-based techniques established for water soluble proteins is tested for membrane protein structures. Initial structures were generated by homology modeling and sampled via molecular dynamics simulations in explicit lipid bilayer and aqueous solvent systems. Snapshots from the simulations were selected based on scoring with either knowledge-based or implicit membrane-based scoring functions and averaged to obtain refined models. The protocol resulted in consistent and significant refinement of the membrane protein structures similar to the performance of refinement methods for soluble proteins. Refinement success was similar between sampling in the presence of lipid bilayers and aqueous solvent but the presence of lipid bilayers may benefit the improvement of lipid-facing residues. Scoring with knowledge-based functions (DFIRE and RWplus) was found to be as good as scoring using implicit membrane-based scoring functions suggesting that differences in internal packing is more important than orientations relative to the membrane during the refinement of membrane protein homology models.
Indexed as
Identifiers
What OpenQuestion holds
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.