iUmami-SCM:一种新颖的基于序列的预测器,用于使用基于二肽倾向分数的评分卡方法预测和分析鲜味肽。

iUmami-SCM: A Novel Sequence-Based Predictor for Prediction and Analysis of Umami Peptides Using a Scoring Card Method with Propensity Scores of Dipeptides.

机构信息

Modern Management and Information Technology, College of Arts, Media and Technology, Chiang Mai University, Chiang Mai 50200, Thailand.

Department of Chemistry, Faculty of Science and Technology, Chiang Mai Rajabhat University, Chiang Mai 50300, Thailand.

出版信息

J Chem Inf Model. 2020 Dec 28;60(12):6666-6678. doi: 10.1021/acs.jcim.0c00707. Epub 2020 Oct 23.

Abstract

Umami or the taste of monosodium glutamate represents one of the major attractive taste modalities in humans. Therefore, knowledge about biophysical and biochemical properties of the umami taste is important for both scientific research and the food industry. Experimental approaches for predicting umami peptides are labor intensive, time consuming, and expensive. To date, computational models for the prediction and analysis of umami peptides as a function of sequence information have not been developed yet. In this study, we have proposed the first sequence-based predictor named iUmami-SCM using primary sequence information for the identification and characterization of umami peptides. iUmami-SCM utilized a newly developed scoring card method (SCM) in conjunction with the propensity scores of amino acids and dipeptide. Our predictor demonstrated excellent prediction performance ability for predicting umami peptides as well as outperforming other commonly used machine learning classifiers. Particularly, iUmami-SCM afforded the highest accuracy and Matthews correlation coefficient of 0.865 and 0.679, respectively, on an independent data set. Furthermore, the analysis of SCM-derived propensity scores was performed so as to provide a more in-depth understanding and knowledge of biophysical and biochemical properties of umami intensities of peptides. To develop a convenient bioinformatics tool, the best model is deployed as a web server that is made publicly available at http://camt.pythonanywhere.com/iUmami-SCM. The iUmami-SCM, as presented herein, serves as a powerful computational technique for large-scale umami peptide identification as well as facilitating the interpretation of umami peptides.

摘要

鲜味或谷氨酸钠的味道代表了人类主要的吸引力味道模式之一。因此,了解鲜味的生物物理和生化特性对于科学研究和食品工业都很重要。预测鲜味肽的实验方法既费力又耗时,而且成本高昂。迄今为止,尚未开发出用于预测和分析鲜味肽作为序列信息函数的计算模型。在这项研究中,我们提出了第一个基于序列的预测器,命名为 iUmami-SCM,它使用基本序列信息来识别和描述鲜味肽。iUmami-SCM 利用了一种新开发的评分卡方法 (SCM),结合了氨基酸和二肽的倾向性得分。我们的预测器在预测鲜味肽方面表现出了出色的预测性能,并且优于其他常用的机器学习分类器。特别是,iUmami-SCM 在独立数据集上的准确率和 Matthews 相关系数分别达到了 0.865 和 0.679。此外,还进行了 SCM 衍生的倾向性得分分析,以提供对鲜味肽强度的生物物理和生化特性的更深入理解和认识。为了开发一个方便的生物信息学工具,最佳模型被部署为一个网络服务器,可在 http://camt.pythonanywhere.com/iUmami-SCM 上公开获取。本文提出的 iUmami-SCM 是一种用于大规模鉴定鲜味肽的强大计算技术,同时也有助于解释鲜味肽。

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