ArticleProceedings of the National Academy of Sciences of the United States of America2015
All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Intrinsic dataset features drive mutational effect prediction by protein language models.bioRxiv : the preprint server for biology · 2026Article
- Pan-cancer structurome reveals overrepresentation of beta sandwiches and underrepresentation of alpha helical domains.Scientific reports · 2023Article
- Machine learning in computational modelling of membrane protein sequences and structures: From methodologies to applications.Computational and structural biotechnology journal · 2023Review
- Exploring microbial functional biodiversity at the protein family level-From metagenomic sequence reads to annotated protein clusters.Frontiers in bioinformatics · 2023Review
- Improved Protein Structure Prediction Using a New Multi-Scale Network and Homologous Templates.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 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
- Modeling aspects of the language of life through transfer-learning protein sequences.BMC bioinformatics · 2019Article
- Refinement of evolutionary medicine predictions based on clinical evidence for the manifestations of Mendelian diseases.Scientific reports · 2019Article
- Article
- Synthetic protein alignments by CCMgen quantify noise in residue-residue contact prediction.PLoS computational biology · 2018Article
- Co-Evolution of Intrinsically Disordered Proteins with Folded Partners Witnessed by Evolutionary Couplings.International journal of molecular sciences · 2018Article
- Comparative Analysis of TM and Cytoplasmic β-barrel Conformations Using Joint Descriptor.Scientific reports · 2018Article
- Characterization of C-ring component assembly in flagellar motors from amino acid coevolution.Royal Society open science · 2018Article
- Applications of sequence coevolution in membrane protein biochemistry.Biochimica et biophysica acta. Biomembranes · 2018Review
- High-resolution structure prediction ofProceedings of the National Academy of Sciences of the United States of America · 2018Article
- Patterns of coevolving amino acids unveil structural and dynamical domains.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Origins of coevolution between residues distant in protein 3D structures.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Large-scale structure prediction by improved contact predictions and model quality assessment.Bioinformatics (Oxford, England) · 2017Article
- Correlated positions in protein evolution and engineering.Journal of industrial microbiology & biotechnology · 2017Review
- Potts Hamiltonian models of protein co-variation, free energy landscapes, and evolutionary fitness.Current opinion in structural biology · 2017Review
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4 authors.
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Abstract
Transmembrane β-barrels (TMBs) carry out major functions in substrate transport and protein biogenesis but experimental determination of their 3D structure is challenging. Encouraged by successful de novo 3D structure prediction of globular and α-helical membrane proteins from sequence alignments alone, we developed an approach to predict the 3D structure of TMBs. The approach combines the maximum-entropy evolutionary coupling method for predicting residue contacts (EVfold) with a machine-learning approach (boctopus2) for predicting β-strands in the barrel. In a blinded test for 19 TMB proteins of known structure that have a sufficient number of diverse homologous sequences available, this combined method (EVfold_bb) predicts hydrogen-bonded residue pairs between adjacent β-strands at an accuracy of ∼70%. This accuracy is sufficient for the generation of all-atom 3D models. In the transmembrane barrel region, the average 3D structure accuracy [template-modeling (TM) score] of top-ranked models is 0.54 (ranging from 0.36 to 0.85), with a higher (44%) number of residue pairs in correct strand-strand registration than in earlier methods (18%). Although the nonbarrel regions are predicted less accurately overall, the evolutionary couplings identify some highly constrained loop residues and, for FecA protein, the barrel including the structure of a plug domain can be accurately modeled (TM score = 0.68). Lower prediction accuracy tends to be associated with insufficient sequence information and we therefore expect increasing numbers of β-barrel families to become accessible to accurate 3D structure prediction as the number of available sequences increases.
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