ArticleScientific reports2013
Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment.
Article in Scientific reports, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 48 citations in OpenAlex.
- Recent Progress of Protein Tertiary Structure Prediction.Molecules (Basel, Switzerland) · 2024Review
- Enhancement of novel Endo-polygalacturonase expression in Rhodotorula mucilaginosa PY18: insights from mutagenesis and molecular docking.Microbial cell factories · 2023Article
- Development of anti-PD-L1 antibody based on structure prediction of AlphaFold2.Frontiers in immunology · 2023Article
- Proteome-wide landscape of solubility limits in a bacterial cell.Scientific reports · 2022Article
- Article
- Toward the solution of the protein structure prediction problem.The Journal of biological chemistry · 2021Review
- Protein structure, amino acid composition and sequence determine proteome vulnerability to oxidation-induced damage.The EMBO journal · 2020Article
- Selenoprotein N is an endoplasmic reticulum calcium sensor that links luminal calcium levels to a redox activity.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models.Nature communications · 2018Article
- Multiple Optimal Phenotypes Overcome Redox and Glycolytic Intermediate Metabolite Imbalances in Escherichia coli pgi Knockout Evolutions.Applied and environmental microbiology · 2018Article
- Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism.Nature communications · 2018Article
- Recon3D enables a three-dimensional view of gene variation in human metabolism.Nature biotechnology · 2018Article
- Molecular Modeling of ClonedIndian journal of microbiology · 2017Article
- Approaches to ab initio molecular replacement of α-helical transmembrane proteins.Acta crystallographica. Section D, Structural biology · 2017Article
- Comparative genomics and expression levels of hydrophobins from eight mycorrhizal genomes.Mycorrhiza · 2017Article
- Purification, Biochemical Characterization, and Amino Acid Sequence of a Novel Type of Lectin from Aplysia dactylomela Eggs with Antibacterial/Antibiofilm Potential.Marine biotechnology (New York, N.Y.) · 2017Article
- Systems biology of the structural proteome.BMC systems biology · 2016Article
- Alignment behaviors of short peptides provide a roadmap for functional profiling of metagenomic data.BMC genomics · 2015Article
- Accurate disulfide-bonding network predictions improve ab initio structure prediction of cysteine-rich proteins.Bioinformatics (Oxford, England) · 2015Article
- General overview on structure prediction of twilight-zone proteins.Theoretical biology & medical modelling · 2015Review
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2 authors at 2 institutions in 1 country.
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Abstract
Genome-wide protein structure prediction and structure-based function annotation have been a long-term goal in molecular biology but not yet become possible due to difficulties in modeling distant-homology targets. We developed a hybrid pipeline combining ab initio folding and template-based modeling for genome-wide structure prediction applied to the Escherichia coli genome. The pipeline was tested on 43 known sequences, where QUARK-based ab initio folding simulation generated models with TM-score 17% higher than that by traditional comparative modeling methods. For 495 unknown hard sequences, 72 are predicted to have a correct fold (TM-score > 0.5) and 321 have a substantial portion of structure correctly modeled (TM-score > 0.35). 317 sequences can be reliably assigned to a SCOP fold family based on structural analogy to existing proteins in PDB. The presented results, as a case study of E. coli, represent promising progress towards genome-wide structure modeling and fold family assignment using state-of-the-art ab initio folding algorithms.
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