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InterPep2: global p...
InterPep2: global peptide-protein docking using interaction surface templates
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- Johansson-Åkhe, Isak (författare)
- Linköpings universitet,Bioinformatik,Tekniska fakulteten
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- Mirabello, Claudio (författare)
- Linköpings universitet,Bioinformatik,Tekniska fakulteten
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- Wallner, Björn (författare)
- Linköpings universitet,Bioinformatik,Tekniska fakulteten
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(creator_code:org_t)
- 2020-01-09
- 2020
- Engelska.
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Ingår i: Bioinformatics. - : OXFORD UNIV PRESS. - 1367-4803 .- 1367-4811. ; 36:8, s. 2458-2465
- Relaterad länk:
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https://liu.diva-por... (primary) (Raw object)
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visa fler...
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https://academic.oup...
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Ämnesord
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- Motivation: Interactions between proteins and peptides or peptide-like intrinsically disordered regions are involved in many important biological processes, such as gene expression and cell life-cycle regulation. Experimentally determining the structure of such interactions is time-consuming and difficult because of the inherent flexibility of the peptide ligand. Although several prediction-methods exist, most are limited in performance or availability. Results: InterPep2 is a freely available method for predicting the structure of peptide-protein interactions. Improved performance is obtained by using templates from both peptide-protein and regular protein-protein interactions, and by a random forest trained to predict the DockQ-score for a given template using sequence and structural features. When tested on 252 bound peptide-protein complexes from structures deposited after the complexes used in the construction of the training and templates sets of InterPep2, InterPep2-Refined correctly positioned 67 peptides within 4.0 angstrom LRMSD among top10, similar to another state-of-the-art template-based method which positioned 54 peptides correctly. However, InterPep2 displays a superior ability to evaluate the quality of its own predictions. On a previously established set of 27 non-redundant unbound-to-bound peptide-protein complexes, InterPep2 performs on-par with leading methods. The extended InterPep2-Refined protocol managed to correctly model 15 of these complexes within 4.0 angstrom LRMSD among top10, without using templates from homologs. In addition, combining the template-based predictions from InterPep2 with ab initio predictions from PIPER-FlexPepDock resulted in 22% more near-native predictions compared to the best single method (22 versus 18).
Ämnesord
- NATURVETENSKAP -- Biologi -- Biofysik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biophysics (hsv//eng)
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- ref (ämneskategori)
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