Abstract
Antimicrobial peptides (AMPs) are considered as potential substitutes of antibiotics in the field of new anti-infective drug design. There have been several machine learning algorithms and web servers in identifying AMPs and their functional activities. However, there is still room for improvement in prediction algorithms and feature extraction methods. The reduced amino acid (RAA) alphabet effectively solved the problems of simplifying protein complexity and recognizing the structure conservative region. This article goes into details about evaluating the performances of more than 5,000 amino acid reduced descriptors generated from 74 types of amino acid reduced alphabet in the first stage and the second stage to construct an excellent two-stage classifier, Identification of Antimicrobial Peptides by Reduced Amino Acid Cluster (iAMP-RAAC), for identifying AMPs and their functional activities, respectively. The results show that the first stage AMP classifier is able to achieve the accuracy of 97.21 and 97.11% for the training data set and independent test dataset. In the second stage, our classifier still shows good performance. At least three of the four metrics, sensitivity (SN), specificity (SP), accuracy (ACC), and Matthews correlation coefficient (MCC), exceed the calculation results in the literature. Further, the ANOVA with incremental feature selection (IFS) is used for feature selection to further improve prediction performance. The prediction performance is further improved after the feature selection of each stage. At last, a user-friendly web server, iAMP-RAAC, is established at http://bioinfor.imu.edu. cn/iampraac.
Highlights
Antimicrobial peptides (AMPs) are a kind of special polypeptide substance which exists in living organisms (Bahar and Ren, 2013; Khamis et al, 2015; Lv et al, 2021a)
It can be seen that iAMP-RAAC obtains the maximum SP, ACC, and Matthews correlation coefficient (MCC) of 98.94, 97.21, and 82.84% with 361 features respectively, while AMPfun got the ACC of 95.09% with 9,367 features
Since the highest ACC appears in type 5 and cluster size 19, only the Method iAMP-RAAC RF iAMP-RAAC RF iAMP-RAAC RF iAMP-RAAC RF iAMP-RAAC RF iAMP-RAAC RF iAMP-RAAC RF
Summary
Antimicrobial peptides (AMPs) are a kind of special polypeptide substance which exists in living organisms (Bahar and Ren, 2013; Khamis et al, 2015; Lv et al, 2021a). It has a wide range of biological functions, such as broad antibacterial spectrum, high antibacterial activity and difficult to produce drug resistance (O’Brien-Simpson et al, 2018; Shoombuatong et al, 2018; Qin et al, 2019). AMPs have become research focus in the fields of animal and human medicine (Hancock and Sahl, 2006; Popovic et al, 2012; O’Brien-Simpson et al, 2018; Lv et al, 2021a), nutrition, food science, and immunology. The utilization of biological AMPs is expected to become an ideal way to solve the problem of drug-resistant bacteria
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