ArticleBMC bioinformatics2005
Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method.
Article in BMC bioinformatics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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42 citing papers in PubMed.
- Computational approaches for molecular characterization and structure-based functional elucidation of a hypothetical protein from Mycobacterium tuberculosis.Genomics & informatics · 2023Article
- Computational prediction of secreted proteins in gram-negative bacteria.Computational and structural biotechnology journal · 2021Review
- Prediction of Transmembrane Regions, Cholesterol, and Ganglioside Binding Sites in Amyloid-Forming Proteins Indicate Potential for Amyloid Pore Formation.Frontiers in molecular neuroscience · 2021Article
- Integrative approach for detecting membrane proteins.BMC bioinformatics · 2020Article
- Comparative Analysis of TM and Cytoplasmic β-barrel Conformations Using Joint Descriptor.Scientific reports · 2018Article
- Efflux Pumps Represent Possible Evolutionary Convergence onto the β-Barrel Fold.Structure (London, England : 1993) · 2018Article
- Measuring the Conformational Distance of GPCR-related Proteins Using a Joint-based Descriptor.Scientific reports · 2017Article
- Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase.Computational and structural biotechnology journal · 2017Review
- Evolution of the Translocation and Assembly Module (TAM).Genome biology and evolution · 2015Article
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- Weakly stable regions and protein-protein interactions in beta-barrel membrane proteins.Current pharmaceutical design · 2014Review
- Inmembrane, a bioinformatic workflow for annotation of bacterial cell-surface proteomes.Source code for biology and medicine · 2013Article
- A 3-dimensional trimeric β-barrel model for Chlamydia MOMP contains conserved and novel elements of Gram-negative bacterial porins.PloS one · 2013Article
- In silico determination and validation of baumannii acinetobactin utilization a structure and ligand binding site.BioMed research international · 2013Article
- TMBB-DB: a transmembrane β-barrel proteome database.Bioinformatics (Oxford, England) · 2012Article
- Ranking models of transmembrane β-barrel proteins using Z-coordinate predictions.Bioinformatics (Oxford, England) · 2012Article
- Predicting the outer membrane proteome of Pasteurella multocida based on consensus prediction enhanced by results integration and manual confirmation.BMC bioinformatics · 2012Article
- A graph-theoretic approach for classification and structure prediction of transmembrane β-barrel proteins.BMC genomics · 2012Article
- Mutational analyses reveal overall topology and functional regions of NilB, a bacterial outer membrane protein required for host association in a model of animal-microbe mutualism.Journal of bacteriology · 2012Article
- Legionella pneumophila LbtU acts as a novel, TonB-independent receptor for the legiobactin siderophore.Journal of bacteriology · 2011Article
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3 authors.
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Abstract
backgroundPrediction of the transmembrane strands and topology of beta-barrel outer membrane proteins is of interest in current bioinformatics research. Several methods have been applied so far for this task, utilizing different algorithmic techniques and a number of freely available predictors exist. The methods can be grossly divided to those based on Hidden Markov Models (HMMs), on Neural Networks (NNs) and on Support Vector Machines (SVMs). In this work, we compare the different available methods for topology prediction of beta-barrel outer membrane proteins. We evaluate their performance on a non-redundant dataset of 20 beta-barrel outer membrane proteins of gram-negative bacteria, with structures known at atomic resolution. Also, we describe, for the first time, an effective way to combine the individual predictors, at will, to a single consensus prediction method.
resultsWe assess the statistical significance of the performance of each prediction scheme and conclude that Hidden Markov Model based methods, HMM-B2TMR, ProfTMB and PRED-TMBB, are currently the best predictors, according to either the per-residue accuracy, the segments overlap measure (SOV) or the total number of proteins with correctly predicted topologies in the test set. Furthermore, we show that the available predictors perform better when only transmembrane beta-barrel domains are used for prediction, rather than the precursor full-length sequences, even though the HMM-based predictors are not influenced significantly. The consensus prediction method performs significantly better than each individual available predictor, since it increases the accuracy up to 4% regarding SOV and up to 15% in correctly predicted topologies.
conclusionsThe consensus prediction method described in this work, optimizes the predicted topology with a dynamic programming algorithm and is implemented in a web-based application freely available to non-commercial users at http://bioinformatics.biol.uoa.gr/ConBBPRED.
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