ArticleProceedings of the National Academy of Sciences of the United States of America2012
Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 99 papers.
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Who cites it
99 citing papers in PubMed.
- How far can you go? Extrapolating values of catalytic activity from known protein landscapes in natural and directed evolution.Chemical Society reviews · 2026Review
- From systems to structure - using genetic data to model protein structures.Nature reviews. Genetics · 2022Review
- SPARC: Structural properties associated with residue constraints.Computational and structural biotechnology journal · 2022Article
- Improved Protein Structure Prediction Using a New Multi-Scale Network and Homologous Templates.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2021Article
- COMTOP: Protein Residue-Residue Contact Prediction through Mixed Integer Linear Optimization.Membranes · 2021Article
- Evaluation of residue-residue contact prediction methods: From retrospective to prospective.PLoS computational biology · 2021Article
- Hybrid methods for combined experimental and computational determination of protein structure.The Journal of chemical physics · 2020Review
- Deep learning enables the atomic structure determination of the Fanconi Anemia core complex from cryoEM.IUCrJ · 2020Article
- Structure determination of the HgcAB complex using metagenome sequence data: insights into microbial mercury methylation.Communications biology · 2020Article
- Deep Analysis of Residue Constraints (DARC): identifying determinants of protein functional specificity.Scientific reports · 2020Article
- Protein contact prediction using metagenome sequence data and residual neural networks.Bioinformatics (Oxford, England) · 2020Article
- Obtaining extremely large and accurate protein multiple sequence alignments from curated hierarchical alignments.Database : the journal of biological databases and curation · 2020Article
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- Advances in protein structure prediction and design.Nature reviews. Molecular cell biology · 2019Review
- Deep learning extends de novo protein modelling coverage of genomes using iteratively predicted structural constraints.Nature communications · 2019Article
- A lipophilicity-based energy function for membrane-protein modelling and design.PLoS computational biology · 2019Article
- Evolutionary couplings of amino acid residues reveal structure and function of bacterial signaling proteins.Molecular microbiology · 2019Article
- Statistical investigations of protein residue direct couplings.PLoS computational biology · 2018Article
- Synthetic protein alignments by CCMgen quantify noise in residue-residue contact prediction.PLoS computational biology · 2018Article
39 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
A new de novo protein structure prediction method for transmembrane proteins (FILM3) is described that is able to accurately predict the structures of large membrane proteins domains using an ensemble of two secondary structure prediction methods to guide fragment selection in combination with a scoring function based solely on correlated mutations detected in multiple sequence alignments. This approach has been validated by generating models for 28 membrane proteins with a diverse range of complex topologies and an average length of over 300 residues with results showing that TM-scores > 0.5 can be achieved in almost every case following refinement using MODELLER. In one of the most impressive results, a model of mitochondrial cytochrome c oxidase polypeptide I was obtained with a TM-score > 0.75 and an rmsd of only 5.7 Å over all 514 residues. These results suggest that FILM3 could be applicable to a wide range of transmembrane proteins of as-yet-unknown 3D structure given sufficient homologous sequences.
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