ArticleProteins2018
Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12.
Article in Proteins, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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48 citing papers in PubMed.
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- DeepFold: enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function.Bioinformatics (Oxford, England) · 2023Article
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- I-TASSER-MTD: a deep-learning-based platform for multi-domain protein structure and function prediction.Nature protocols · 2022Review
- Protein Function Analysis through Machine Learning.Biomolecules · 2022Review
- cpxDeepMSA: A Deep Cascade Algorithm for Constructing Multiple Sequence Alignments of Protein-Protein Interactions.International journal of molecular sciences · 2022Article
- Application of the MAHDS Method for Multiple Alignment of Highly Diverged Amino Acid Sequences.International journal of molecular sciences · 2022Article
- Effect of human secretory calcium-binding phosphoprotein proline-glutamine rich 1 protein on Porphyromonas gingivalis and identification of its active portions.Scientific reports · 2021Article
- A Deep-Learning Proteomic-Scale Approach for Drug Design.Pharmaceuticals (Basel, Switzerland) · 2021Article
- A computational evaluation of targeted oxidation strategy (TOS) for potential inhibition of SARS-CoV-2 by disulfiram and analogues.Biophysical chemistry · 2021Article
- Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations.Cell reports methods · 2021Article
- Deep learning techniques have significantly impacted protein structure prediction and protein design.Current opinion in structural biology · 2021Review
- CD9 inhibition reveals a functional connection of extracellular vesicle secretion with mitophagy in melanoma cells.Journal of extracellular vesicles · 2021Article
- Membrane Environment Modulates Ligand-Binding Propensity of P2Y12 Receptor.Pharmaceutics · 2021Article
- Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks.PLoS computational biology · 2021Article
- A proline rich protein from the gingival seal around teeth exhibits antimicrobial properties against Porphyromonas gingivalis.Scientific reports · 2021Article
- Hybrid methods for combined experimental and computational determination of protein structure.The Journal of chemical physics · 2020Review
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5 authors.
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Abstract
We develop two complementary pipelines, "Zhang-Server" and "QUARK", based on I-TASSER and QUARK pipelines for template-based modeling (TBM) and free modeling (FM), and test them in the CASP12 experiment. The combination of I-TASSER and QUARK successfully folds three medium-size FM targets that have more than 150 residues, even though the interplay between the two pipelines still awaits further optimization. Newly developed sequence-based contact prediction by NeBcon plays a critical role to enhance the quality of models, particularly for FM targets, by the new pipelines. The inclusion of NeBcon predicted contacts as restraints in the QUARK simulations results in an average TM-score of 0.41 for the best in top five predicted models, which is 37% higher than that by the QUARK simulations without contacts. In particular, there are seven targets that are converted from non-foldable to foldable (TM-score >0.5) due to the use of contact restraints in the simulations. Another additional feature in the current pipelines is the local structure quality prediction by ResQ, which provides a robust residue-level modeling error estimation. Despite the success, significant challenges still remain in ab initio modeling of multi-domain proteins and folding of β-proteins with complicated topologies bound by long-range strand-strand interactions. Improvements on domain boundary and long-range contact prediction, as well as optimal use of the predicted contacts and multiple threading alignments, are critical to address these issues seen in the CASP12 experiment.
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