ArticleNucleic acids research2016
CoinFold: a web server for protein contact prediction and contact-assisted protein folding.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Protein structure prediction with in-cell photo-crosslinking mass spectrometry and deep learning.Nature biotechnology · 2023Article
- A computational approach to design a polyvalent vaccine against human respiratory syncytial virus.Scientific reports · 2023Article
- Article
- Contact-Assisted Threading in Low-Homology Protein Modeling.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Identification of key amino acid residues in AtUMAMIT29 for transport of glucosinolates.Frontiers in plant science · 2023Article
- Design of novel cyanovirin-N variants by modulation of binding dynamics through distal mutations.eLife · 2022Article
- LPTD: a novel linear programming-based topology determination method for cryo-EM maps.Bioinformatics (Oxford, England) · 2022Article
- Designing of a Chimeric Vaccine Using EIS (Rv2416c) Protein Against Mycobacterium tuberculosis H37Rv: an Immunoinformatics Approach.Applied biochemistry and biotechnology · 2022Article
- Customized chitooligosaccharide production-controlling their lengthFrontiers in bioengineering and biotechnology · 2022Article
- Three-Dimensional Graph Matching to Identify Secondary Structure Correspondence of Medium-Resolution Cryo-EM Density Maps.Biomolecules · 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
- An in silico deep learning approach to multi-epitope vaccine design: a SARS-CoV-2 case study.Scientific reports · 2021Article
- Hybridized distance- and contact-based hierarchical structure modeling for folding soluble and membrane proteins.PLoS computational biology · 2021Article
- Recent Advances in Protein Homology Detection Propelled by Inter-Residue Interaction Map Threading.Frontiers in molecular biosciences · 2021Review
- Chasing coevolutionary signals in intrinsically disordered proteins complexes.Scientific reports · 2020Article
- A single-model quality assessment method for poor quality protein structure.BMC bioinformatics · 2020Article
- Structural basis of ER-associated protein degradation mediated by the Hrd1 ubiquitin ligase complex.Science (New York, N.Y.) · 2020Article
- Evaluating the significance of contact maps in low-homology protein modeling using contact-assisted threading.Scientific reports · 2020Article
- Structure of the human BBSome core complex.eLife · 2020Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
CoinFold (http://raptorx2.uchicago.edu/ContactMap/) is a web server for protein contact prediction and contact-assisted de novo structure prediction. CoinFold predicts contacts by integrating joint multi-family evolutionary coupling (EC) analysis and supervised machine learning. This joint EC analysis is unique in that it not only uses residue coevolution information in the target protein family, but also that in the related families which may have divergent sequences but similar folds. The supervised learning further improves contact prediction accuracy by making use of sequence profile, contact (distance) potential and other information. Finally, this server predicts tertiary structure of a sequence by feeding its predicted contacts and secondary structure to the CNS suite. Tested on the CASP and CAMEO targets, this server shows significant advantages over existing ones of similar category in both contact and tertiary structure prediction.
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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.