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Sun A, Li H, Dong G, Zhao Y, Zhang D. DBPboost:A method of classification of DNA-binding proteins based on improved differential evolution algorithm and feature extraction. Methods 2024; 223:56-64. [PMID: 38237792 DOI: 10.1016/j.ymeth.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 12/29/2023] [Accepted: 01/13/2024] [Indexed: 02/01/2024] Open
Abstract
DNA-binding proteins are a class of proteins that can interact with DNA molecules through physical and chemical interactions. Their main functions include regulating gene expression, maintaining chromosome structure and stability, and more. DNA-binding proteins play a crucial role in cellular and molecular biology, as they are essential for maintaining normal cellular physiological functions and adapting to environmental changes. The prediction of DNA-binding proteins has been a hot topic in the field of bioinformatics. The key to accurately classifying DNA-binding proteins is to find suitable feature sources and explore the information they contain. Although there are already many models for predicting DNA-binding proteins, there is still room for improvement in mining feature source information and calculation methods. In this study, we created a model called DBPboost to better identify DNA-binding proteins. The innovation of this study lies in the use of eight feature extraction methods, the improvement of the feature selection step, which involves selecting some features first and then performing feature selection again after feature fusion, and the optimization of the differential evolution algorithm in feature fusion, which improves the performance of feature fusion. The experimental results show that the prediction accuracy of the model on the UniSwiss dataset is 89.32%, and the sensitivity is 89.01%, which is better than most existing models.
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Affiliation(s)
- Ailun Sun
- College of Computer and Control Engineering, Northeast Forestry University, Harbin 150040, China
| | - Hongfei Li
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Guanghui Dong
- College of Computer and Control Engineering, Northeast Forestry University, Harbin 150040, China
| | - Yuming Zhao
- College of Computer and Control Engineering, Northeast Forestry University, Harbin 150040, China
| | - Dandan Zhang
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China.
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Lu L, Wang J, Wang C, Zhu J, Wang H, Liao L, Zhao Y, Wang X, Yang C, He Z, Li M. Plant-derived virulence arresting drugs as novel antimicrobial agents: Discovery, perspective, and challenges in clinical use. Phytother Res 2024; 38:727-754. [PMID: 38014754 DOI: 10.1002/ptr.8072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/23/2023] [Accepted: 11/05/2023] [Indexed: 11/29/2023]
Abstract
Antimicrobial resistance (AMR) emerges as a severe crisis to public health and requires global action. The occurrence of bacterial pathogens with multi-drug resistance appeals to exploring alternative therapeutic strategies. Antivirulence treatment has been a positive substitute in seeking to circumvent AMR, which aims to target virulence factors directly to combat bacterial infections. Accumulated evidence suggests that plant-derived natural products, which have been utilized to treat infectious diseases for centuries, can be abundant sources for screening potential virulence-arresting drugs (VADs) to develop advanced therapeutics for infectious diseases. This review sums up some virulence factors and their actions in various species of bacteria, as well as recent advances pertaining to plant-derived natural products as VAD candidates. Furthermore, we also discuss natural VAD-related clinical trials and patents, the perspective of VAD-based advanced therapeutics for infectious diseases and critical challenges hampering clinical use of VADs, and genomics-guided identification for VAD therapeutic. These newly discovered natural VADs will be encouraging and optimistic candidates that may sustainably combat AMR.
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Affiliation(s)
- Lan Lu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, Sichuan, P.R. China
| | - Jingya Wang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, Sichuan, P.R. China
| | - Chongrui Wang
- Faculty of Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, P.R. China
| | - Jie Zhu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, Sichuan, P.R. China
| | - Hongping Wang
- Safety Evaluation Center, Sichuan Institute for Drug Control (Sichuan Testing Center of Medical Devices), Chengdu, Sichuan, P.R. China
| | - Li Liao
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, Sichuan, P.R. China
| | - Yuting Zhao
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, Sichuan, P.R. China
| | - Xiaobo Wang
- Department of Hepatobiliary Surgery, Langzhong People's Hospital, Langzhong, Sichuan, P.R. China
| | - Chen Yang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, Sichuan, P.R. China
| | - Zhengyou He
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, Sichuan, P.R. China
| | - Mingxing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, Sichuan, China
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Samantray D, Tanwar AS, Murali TS, Brand A, Satyamoorthy K, Paul B. A Comprehensive Bioinformatics Resource Guide for Genome-Based Antimicrobial Resistance Studies. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:445-460. [PMID: 37861712 DOI: 10.1089/omi.2023.0140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
The use of high-throughput sequencing technologies and bioinformatic tools has greatly transformed microbial genome research. With the help of sophisticated computational tools, it has become easier to perform whole genome assembly, identify and compare different species based on their genomes, and predict the presence of genes responsible for proteins, antimicrobial resistance, and toxins. These bioinformatics resources are likely to continuously improve in quality, become more user-friendly to analyze the multiple genomic data, efficient in generating information and translating it into meaningful knowledge, and enhance our understanding of the genetic mechanism of AMR. In this manuscript, we provide an essential guide for selecting the popular resources for microbial research, such as genome assembly and annotation, antibiotic resistance gene profiling, identification of virulence factors, and drug interaction studies. In addition, we discuss the best practices in computer-oriented microbial genome research, emerging trends in microbial genomic data analysis, integration of multi-omics data, the appropriate use of machine-learning algorithms, and open-source bioinformatics resources for genome data analytics.
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Affiliation(s)
- Debyani Samantray
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Ankit Singh Tanwar
- United Nations University-Maastricht Economic and Social Research Institute on Innovation and Technology (UNU-MERIT), Maastricht, The Netherlands
- Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
| | - Thokur Sreepathy Murali
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Angela Brand
- United Nations University-Maastricht Economic and Social Research Institute on Innovation and Technology (UNU-MERIT), Maastricht, The Netherlands
- Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
- Department of Health Information, Prasanna School of Public Health (PSPH), Manipal Academy of Higher Education, Manipal, India
| | - Kapaettu Satyamoorthy
- SDM College of Medical Sciences and Hospital, Shri Dharmasthala Manjunatheshwara (SDM) University, Dharwad, India
| | - Bobby Paul
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
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