iDPF-PseRAAAC: A Web-Server for Identifying the Defensin Peptide Family and Subfamily Using Pseudo Reduced Amino Acid Alphabet Composition

Abstract

Defensins as one of the most abundant classes of antimicrobial peptides are an essential part of the innate immunity that has evolved in most living organisms from lower organisms to humans. To identify specific defensins as interesting antifungal leads, in this study, we constructed a more rigorous benchmark dataset and the iDPF-PseRAAAC server was developed to predict the defensin family and subfamily. Using reduced dipeptide compositions were used, the overall accuracy of proposed method increased to 95.10% for the defensin family, and 98.39% for the vertebrate subfamily, which is higher than the accuracy from other methods. The jackknife test shows that more than 4% improvement was obtained comparing with the previous method. A free online server was further established for the convenience of most experimental scientists at http://wlxy.imu.edu.cn/college/biostation/fuwu/iDPF-PseRAAAC/index.asp. A friendly guide is provided to describe how to use the web server. We anticipate that iDPF-PseRAAAC may become a useful high-throughput tool for both basic research and drug design.

Competence Classification of Cumulus and Granulosa Cell Transcriptome in Embryos Matched by Morphology and Female Age

“…After completion of a large independent validation by a prospective randomized study comparing standard morphological evaluation with non-invasive classification of LB probability using CC expression profiling for embryo selection, we are aiming at establishing a web-server application allowing the public to perform CC expression profile classification (as exemplified in [ 23 , 60 ]).…”

“…Based on these data sets, three different classification algorithms (diagonal linear discriminant analysis (dLDA) [ 19 , 20 ], k-nearest neighbors (K-NN) [ 20 , 21 ] and support vector machines (SVM) with linear kernel [ 22 , 23 ] were generated and tested. In order to formulate and select the best model for classification of LB, the misclassification rate for each classifier was estimated using leave-one-out cross-validation (LOOCV), during which we applied uni-variate t-tests with a grit of p-values (p < 0.001, p < 0.005, p < 0.01, p < 0.05) for selection of the optimal number of probe sets to include in each model.…”

Predicting Protein Submitochondrial Locations: The 10th Anniversary

“…We collect the jackknife test results in (Table 3 ). Three commonly applied performance measures [ 6 , 12 - 14 , 17 , 39 - 41 ] can be defined as follows:…”

Simplification of complexity in protein molecular systems by grouping amino acids: a view from physics

“…In bioinformatics, the simplified amino acid alphabets are also widely used. The simplified alphabets are used, but not limited, in the prediction of protein-protein interaction and interface [126][127][128], nuclear receptors [129], DNA-binding proteins [130], defensin family and subfamily [131], heat shock protein family [132], residue flexibility [133,134], ability of protein crystallization [135] and various kinds of applications [136,137]. For example, the simplified alphabet (six groups) could be used to detect the sequence conservation related to the super-families of proteins [138,139].…”