ArticleProtein science : a publication of the Protein Society2012
Protein topology from predicted residue contacts.
Article in Protein science : a publication of the Protein Society, 2012. 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.
- How far can you go? Extrapolating values of catalytic activity from known protein landscapes in natural and directed evolution.Chemical Society reviews · 2026Review
- Evaluation of residue-residue contact prediction methods: From retrospective to prospective.PLoS computational biology · 2021Article
- Applications of sequence coevolution in membrane protein biochemistry.Biochimica et biophysica acta. Biomembranes · 2018Review
- COMPASS: the COMPletely Arbitrary Sequence Simulator.Bioinformatics (Oxford, England) · 2017Article
- Exploring RNA conformational space under sparse distance restraints.Scientific reports · 2017Article
- Monte Carlo simulation of a statistical mechanical model of multiple protein sequence alignment.Biophysics and physicobiology · 2017Article
- Reduction, alignment and visualisation of large diverse sequence families.BMC bioinformatics · 2016Article
- Sequence co-evolutionary information is a natural partner to minimally-frustrated models of biomolecular dynamics.F1000Research · 2016Review
- A unified statistical model of protein multiple sequence alignment integrating direct coupling and insertions.Biophysics and physicobiology · 2016Article
- An algorithm to parse segment packing in predicted protein contact maps.Algorithms for molecular biology : AMB · 2016Article
- Comparison of Algorithms for Prediction of Protein Structural Features from Evolutionary Data.PloS one · 2016Article
- Dimeric interactions and complex formation using direct coevolutionary couplings.Scientific reports · 2015Article
- Covariation Is a Poor Measure of Molecular Coevolution.Molecular biology and evolution · 2015Article
- Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently.Chemical Society reviews · 2015Review
- Improving accuracy of protein contact prediction using balanced network deconvolution.Proteins · 2015Article
- Automated procedure for contact-map-based protein structure reconstruction.The Journal of membrane biology · 2014Article
- Fast and accurate multivariate Gaussian modeling of protein families: predicting residue contacts and protein-interaction partners.PloS one · 2014Article
- Coevolutionary signals across protein lineages help capture multiple protein conformations.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Article
- A method to predict edge strands in beta-sheets from protein sequences.Computational and structural biotechnology journal · 2013Article
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Authors and funding
3 authors.
Funding
Abstract
Residue contacts predicted from correlated positions in a multiple sequence alignment are often sparse and uncertain. To some extent, these limitations in the data can be overcome by grouping the contacts by secondary structure elements and enumerating the possible packing arrangements of these elements in a combinatorial manner. Strong interactions appear frequently but inconsistent interactions are down-weighted and missing interactions up-weighted. The resulting improved consistency in the predicted interactions has allowed the method to be successfully applied to proteins up to 200 residues in length which is larger than any structure previously predicted using sequence data alone.
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