ArticleProteins2006
Multipass membrane protein structure prediction using Rosetta.
Article in Proteins, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 187 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
187 citing papers in PubMed.
- Structural and immunogenic evaluation of silk proteins from Bombyx mori using advanced bioinformatics and deep learning for biomaterials applications.Journal, genetic engineering & biotechnology · 2026Article
- Designer artificial environments for membrane protein synthesis.Nature communications · 2025Article
- Atomistic mechanisms of the regulation of small-conductance CaProceedings of the National Academy of Sciences of the United States of America · 2024Article
- The chemistry of electrical signaling in sodium channels from bacteria and beyond.Cell chemical biology · 2024Review
- A multiscale predictive digital twin for neurocardiac modulation.The Journal of physiology · 2023Article
- Phosphatidylserine-dependent structure of synaptogyrin remodels the synaptic vesicle membrane.Nature structural & molecular biology · 2023Article
- General trends in the effects of VX-661 and VX-445 on the plasma membrane expression of clinical CFTR variants.Cell chemical biology · 2023Article
- Recent Advances in NMR Protein Structure Prediction with ROSETTA.International journal of molecular sciences · 2023Review
- Elucidation of a dynamic interplay between a beta-2 adrenergic receptor, its agonist, and stimulatory G protein.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Article
- The Role of Transmembrane Proteins in Plant Growth, Development, and Stress Responses.International journal of molecular sciences · 2022Review
- Integrated AlphaFold2 and DEER investigation of the conformational dynamics of a pH-dependent APC antiporter.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Modeling of protein conformational changes with Rosetta guided by limited experimental data.Structure (London, England : 1993) · 2022Article
- The seizure-inducing plastic explosive RDX inhibits the α1β2γ2 GABAAnnals of clinical and translational neurology · 2022Article
- Mapping the Binding Sites of UDP and Prostaglandin E2 Glyceryl Ester in the Nucleotide Receptor P2YChemMedChem · 2022Article
- Structural Comparative Modeling of Multi-Domain F508del CFTR.Biomolecules · 2022Article
- Differential Activation of TRPM8 by the Stereoisomers of Menthol.Frontiers in pharmacology · 2022Article
- Molecular determinants of pro-arrhythmia proclivity of d- and l-sotalol via a multi-scale modeling pipeline.Journal of molecular and cellular cardiology · 2021Article
- Diverse Scientific Benchmarks for Implicit Membrane Energy Functions.Journal of chemical theory and computation · 2021Article
- Computational structure prediction provides a plausible mechanism for electron transfer by the outer membrane protein Cyc2 from Acidithiobacillus ferrooxidans.Protein science : a publication of the Protein Society · 2021Article
127 more citing papers are in PubMed but not listed here.
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
We describe the adaptation of the Rosetta de novo structure prediction method for prediction of helical transmembrane protein structures. The membrane environment is modeled by embedding the protein chain into a model membrane represented by parallel planes defining hydrophobic, interface, and polar membrane layers for each energy evaluation. The optimal embedding is determined by maximizing the exposure of surface hydrophobic residues within the membrane and minimizing hydrophobic exposure outside of the membrane. Protein conformations are built up using the Rosetta fragment assembly method and evaluated using a new membrane-specific version of the Rosetta low-resolution energy function in which residue-residue and residue-environment interactions are functions of the membrane layer in addition to amino acid identity, distance, and density. We find that lower energy and more native-like structures are achieved by sequential addition of helices to a growing chain, which may mimic some aspects of helical protein biogenesis after translocation, rather than folding the whole chain simultaneously as in the Rosetta soluble protein prediction method. In tests on 12 membrane proteins for which the structure is known, between 51 and 145 residues were predicted with root-mean-square deviation <4 A from the native structure.
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.