PRED-TMBB2: Improved topology prediction and detection of beta-barrel outer membrane proteins
Date
2016Language
en
Sujet
Résumé
Motivation: The PRED-TMBB method is based on Hidden Markov Models and is capable of predicting the topology of beta-barrel outer membrane proteins and discriminate them from water-soluble ones. Here, we present an updated version of the method, PRED-TMBB2, with several newly developed features that improve its performance. The inclusion of a properly defined end state allows for better modeling of the beta-barrel domain, while different emission probabilities for the adjacent residues in strands are used to incorporate knowledge concerning the asymmetric amino acid distribution occurring there. Furthermore, the training was performed using newly developed algorithms in order to optimize the labels of the training sequences. Moreover, the method is retrained on a larger, non-redundant dataset which includes recently solved structures, and a newly developed decoding method was added to the already available options. Finally, the method now allows the incorporation of evolutionary information in the form of multiple sequence alignments. Results: The results of a strict cross-validation procedure show that PRED-TMBB2 with homology information performs significantly better compared to other available prediction methods. It yields 76% in correct topology predictions and outperforms the best available predictor by 7%, with an overall SOV of 0.9. Regarding detection of beta-barrel proteins, PRED-TMBB2, using just the query sequence as input, achieves an MCC value of 0.92, outperforming even predictors designed for this task and are much slower. Availability and Implementation: The method, along with all datasets used, is freely available for academic users at http://www.compgen.org/tools/PRED-TMBB2. © 2016 The Author 2016. Published by Oxford University Press. All rights reserved.
Collections
Related items
Showing items related by title, author, creator and subject.
-
Investigating Molecular Determinants of Cancer Cell Resistance to Ionizing Radiation Through an Integrative Bioinformatics Approach
Toy H.I., Karakülah G., Kontou P.I., Alotaibi H., Georgakilas A.G., Pavlopoulou A. (2021)Eradication of cancer cells through exposure to high doses of ionizing radiation (IR) is a widely used therapeutic strategy in the clinical setting. However, in many cases, cancer cells can develop remarkable resistance ... -
Enhancer of rudimentary homologue interacts with scaffold attachment factor B at the nuclear matrix to regulate SR protein phosphorylation
Drakouli S., Lyberopoulou A., Papathanassiou M., Mylonis I., Georgatsou E. (2017)Scaffold attachment factor B1 (SAFB1) is an integral component of the nuclear matrix of vertebrate cells. It binds to DNA on scaffold/matrix attachment region elements, as well as to RNA and a multitude of different proteins, ... -
Proteomic analysis of the mitochondrial glucocorticoid receptor interacting proteins reveals pyruvate dehydrogenase and mitochondrial 60 kDa heat shock protein as potent binding partners
Karra A.G., Sioutopoulou A., Gorgogietas V., Samiotaki M., Panayotou G., Psarra A.-M.G. (2022)Glucocorticoids are steroid hormones that regulate plethora biological actions such as growth and metabolism, immune response, and apoptosis. Glucocorticoids actions are mediated via glucocorticoid receptors which act ...