ArticleBioinformatics (Oxford, England)2013
High-accuracy prediction of transmembrane inter-helix contacts and application to GPCR 3D structure modeling.
Article in Bioinformatics (Oxford, England), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 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
21 citing papers in PubMed.
- GM-lncLoc: LncRNAs subcellular localization prediction based on graph neural network with meta-learning.BMC genomics · 2023Article
- ISSEC: inferring contacts among protein secondary structure elements using deep object detection.BMC bioinformatics · 2020Article
- A Comparative Study of Modern Homology Modeling Algorithms for Rhodopsin Structure Prediction.ACS omega · 2018Article
- Measuring the Conformational Distance of GPCR-related Proteins Using a Joint-based Descriptor.Scientific reports · 2017Article
- Folding Membrane Proteins by Deep Transfer Learning.Cell systems · 2017Article
- EPSILON-CP: using deep learning to combine information from multiple sources for protein contact prediction.BMC bioinformatics · 2017Article
- Co-evolution techniques are reshaping the way we do structural bioinformatics.F1000Research · 2017Review
- Characterization of Ghrelin O-Acyltransferase (GOAT) in goldfish (Carassius auratus).PloS one · 2017Article
- Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase.Computational and structural biotechnology journal · 2017Review
- Article
- Evolution of the α-Subunit of Na/K-ATPase from Paramecium to Homo sapiens: Invariance of Transmembrane Helix Topology.Journal of molecular evolution · 2016Article
- GPCR-I-TASSER: A Hybrid Approach to G Protein-Coupled Receptor Structure Modeling and the Application to the Human Genome.Structure (London, England : 1993) · 2015Article
- Improving homology modeling of G-protein coupled receptors through multiple-template derived conserved inter-residue interactions.Journal of computer-aided molecular design · 2015Article
- Improving accuracy of protein contact prediction using balanced network deconvolution.Proteins · 2015Article
- A new ensemble coevolution system for detecting HIV-1 protein coevolution.Biology direct · 2015Article
- Computational modeling of membrane proteins.Proteins · 2015Review
- A Gly-zipper motif mediates homodimerization of the transmembrane domain of the mitochondrial kinase ADCK3.Journal of the American Chemical Society · 2014Article
- Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges.Structure (London, England : 1993) · 2014Article
- In silico evaluation of the influence of the translocon on partitioning of membrane segments.BMC bioinformatics · 2014Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
motivationResidue-residue contacts across the transmembrane helices dictate the three-dimensional topology of alpha-helical membrane proteins. However, contact determination through experiments is difficult because most transmembrane proteins are hard to crystallize.
resultsWe present a novel method (MemBrain) to derive transmembrane inter-helix contacts from amino acid sequences by combining correlated mutations and multiple machine learning classifiers. Tested on 60 non-redundant polytopic proteins using a strict leave-one-out cross-validation protocol, MemBrain achieves an average accuracy of 62%, which is 12.5% higher than the current best method from the literature. When applied to 13 recently solved G protein-coupled receptors, the MemBrain contact predictions helped increase the TM-score of the I-TASSER models by 37% in the transmembrane region. The number of foldable cases (TM-score >0.5) increased by 100%, where all G protein-coupled receptor templates and homologous templates with sequence identity >30% were excluded. These results demonstrate significant progress in contact prediction and a potential for contact-driven structure modeling of transmembrane proteins. AVAILABILITY: www.csbio.sjtu.edu.cn/bioinf/MemBrain/
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.