Search

Abstract Background Protein-protein interactions (PPIs) are crucial for almost all cellular processes, including metabolic cycles, DNA transcription and replication, and signaling cascades. Given the importance of PPIs, several methods have been developed to detect them. Since the experimental methods are time-consuming and expensive, developing computational methods for effectively identifying PPIs is of great practical significance. Findings Most previous methods were developed for predicting PPIs in only one species, and do not account for probability estimations. In this work, a relatively comprehensive prediction system was developed, based on a support vector machine (SVM), for predicting PPIs in five organisms, specifically humans, yeast, Drosophila, Escherichia coli, and Caenorhabditis elegans. This PPI predictor includes the probability of its prediction in the output, so it can be used to assess the confidence of each SVM prediction by the probability assignment. Using a probability of 0.5 as the threshold for assigning class labels, the method had an average accuracy for detecting protein interactions of 90.67% for humans, 88.99% for yeast, 90.09% for Drosophila, 92.73% for E. coli, and 97.51% for C. elegans. Moreover, among the correctly predicted pairs, more than 80% were predicted with a high probability of ≥0.8, indicating that this tool could predict novel PPIs with high confidence. Conclusions Based on this work, a web-based system, Pred_PPI, was constructed for predicting PPIs from the five organisms. Users can predict novel PPIs and obtain a probability value about the prediction using this tool. Pred_PPI is freely available at http://cic.scu.edu.cn/bioinformatics/predict_ppi/default.html.

Abstract: A three-stage support vector machine (SVM) was constructed to predict the state of cysteines by fusing sequence information, evolution information and annotation information of protein sequences. The first and second stages were for predicting whether the protein sequences contain disulfide bonds and whether all of the cysteines are involved in disulfide bonds. In the last stage, one SVM was constructed for predicting which cysteines are involved in disulfide bonds, among all these cysteines in proteins. The three SVMs give a good performance and the overall prediction accuracy are 90.05%, 96.36% and 80.00%, respectively, which indicates that the features selected in this work are effective for predicting the state of cysteines. In addition, current methods only paid too much attention to the prediction performance and never showed us how much important the roles of these features played in the prediction. As a result a feature importance measurement designated as F-score function was used to evaluate these features. The result shows that among these protein descriptors; evolution information is the most important feature for representing the disulfide-containing proteins. The prediction software and data sets used in this article are freely available at http://cic.scu.edu.cn/bioinformatics/Predict_Cys.zip. [ABSTRACT FROM AUTHOR]

Abstract: Protein secretion plays an important role in bacterial lifestyles. Secreted proteins are crucial for bacterial pathogenesis by making bacteria interact with their environments, particularly delivering pathogenic and symbiotic bacteria into their eukaryotic hosts. Therefore, identification of bacterial secreted proteins becomes an important process for the study of various diseases and the corresponding drugs. In this paper, fusing several new features into Chou’s pseudo-amino acid composition (PseAAC), two support vector machine (SVM)-based ternary classifiers are developed to predict secreted proteins of Gram-negative and Gram-positive bacteria. For the two types of bacteria, the high accuracy of 94.03% and 94.36% are obtained in distinguishing classically secreted, non-classically secreted and non-secreted proteins by our method. In order to compare the practical ability of our method in identifying bacterial secreted proteins with those of six published methods, proteins in Escherichia coli and Bacillus subtilis are collected to construct the test sets of Gram-negative and Gram-positive bacteria, and the prediction results of our method are comparable to those of existing methods. When performed on two public independent data sets for predicting NCSPs, it also yields satisfactory results for Gram-negative bacterial proteins. The prediction server SecretP can be accessed at http://cic.scu.edu.cn/bioinformatics/secretPV2/index.htm. [ABSTRACT FROM AUTHOR]

Background: Protein-protein interactions (PPIs) are crucial for almost all cellular processes, including metabolic cycles, DNA transcription and replication, and signaling cascades. Given the importance of PPIs, several methods have been developed to detect them. Since the experimental methods are time-consuming and expensive, developing computational methods for effectively identifying PPIs is of great practical significance., Findings: Most previous methods were developed for predicting PPIs in only one species, and do not account for probability estimations. In this work, a relatively comprehensive prediction system was developed, based on a support vector machine (SVM), for predicting PPIs in five organisms, specifically humans, yeast, Drosophila, Escherichia coli, and Caenorhabditis elegans. This PPI predictor includes the probability of its prediction in the output, so it can be used to assess the confidence of each SVM prediction by the probability assignment. Using a probability of 0.5 as the threshold for assigning class labels, the method had an average accuracy for detecting protein interactions of 90.67% for humans, 88.99% for yeast, 90.09% for Drosophila, 92.73% for E. coli, and 97.51% for C. elegans. Moreover, among the correctly predicted pairs, more than 80% were predicted with a high probability of >/=0.8, indicating that this tool could predict novel PPIs with high confidence., Conclusions: Based on this work, a web-based system, Pred_PPI, was constructed for predicting PPIs from the five organisms. Users can predict novel PPIs and obtain a probability value about the prediction using this tool. Pred_PPI is freely available at http://cic.scu.edu.cn/bioinformatics/predict_ppi/default.html.