ArticleBMC structural biology2011
A conformation ensemble approach to protein residue-residue contact.
Article in BMC structural biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Importance of Inter-residue Contacts for Understanding Protein Folding and Unfolding Rates, Remote Homology, and Drug Design.Molecular biotechnology · 2025Review
- EPSILON-CP: using deep learning to combine information from multiple sources for protein contact prediction.BMC bioinformatics · 2017Article
- Article
- UniCon3D: de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling.Bioinformatics (Oxford, England) · 2016Article
- Residue-level global and local ensemble-ensemble comparisons of protein domains.Protein science : a publication of the Protein Society · 2015Article
- Sequence-based Gaussian network model for protein dynamics.Bioinformatics (Oxford, England) · 2014Article
- Combining physicochemical and evolutionary information for protein contact prediction.PloS one · 2014Article
- On the importance of the distance measures used to train and test knowledge-based potentials for proteins.PloS one · 2014Article
- A study and benchmark of DNcon: a method for protein residue-residue contact prediction using deep networks.BMC bioinformatics · 2013Article
- Predicting protein residue-residue contacts using deep networks and boosting.Bioinformatics (Oxford, England) · 2012Article
- Recursive protein modeling: a divide and conquer strategy for Protein Structure Prediction and its case study in CASP9.Journal of bioinformatics and computational biology · 2012Article
- Article
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3 authors.
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Abstract
backgroundProtein residue-residue contact prediction is important for protein model generation and model evaluation. Here we develop a conformation ensemble approach to improve residue-residue contact prediction. We collect a number of structural models stemming from a variety of methods and implementations. The various models capture slightly different conformations and contain complementary information which can be pooled together to capture recurrent, and therefore more likely, residue-residue contacts.
resultsWe applied our conformation ensemble approach to free modeling targets from both CASP8 and CASP9. Given a diverse ensemble of models, the method is able to achieve accuracies of. 48 for the top L/5 medium range contacts and. 36 for the top L/5 long range contacts for CASP8 targets (L being the target domain length). When applied to targets from CASP9, the accuracies of the top L/5 medium and long range contact predictions were. 34 and. 30 respectively.
conclusionsWhen operating on a moderately diverse ensemble of models, the conformation ensemble approach is an effective means to identify medium and long range residue-residue contacts. An immediate benefit of the method is that when tied with a scoring scheme, it can be used to successfully rank models.
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