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Wu J, Liu B, Zhang J, Wang Z, Li J. DL-PPI: a method on prediction of sequenced protein-protein interaction based on deep learning. BMC Bioinformatics 2023; 24:473. [PMID: 38097937 PMCID: PMC10722729 DOI: 10.1186/s12859-023-05594-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/01/2023] [Indexed: 12/17/2023] Open
Abstract
PURPOSE Sequenced Protein-Protein Interaction (PPI) prediction represents a pivotal area of study in biology, playing a crucial role in elucidating the mechanistic underpinnings of diseases and facilitating the design of novel therapeutic interventions. Conventional methods for extracting features through experimental processes have proven to be both costly and exceedingly complex. In light of these challenges, the scientific community has turned to computational approaches, particularly those grounded in deep learning methodologies. Despite the progress achieved by current deep learning technologies, their effectiveness diminishes when applied to larger, unfamiliar datasets. RESULTS In this study, the paper introduces a novel deep learning framework, termed DL-PPI, for predicting PPIs based on sequence data. The proposed framework comprises two key components aimed at improving the accuracy of feature extraction from individual protein sequences and capturing relationships between proteins in unfamiliar datasets. 1. Protein Node Feature Extraction Module: To enhance the accuracy of feature extraction from individual protein sequences and facilitate the understanding of relationships between proteins in unknown datasets, the paper devised a novel protein node feature extraction module utilizing the Inception method. This module efficiently captures relevant patterns and representations within protein sequences, enabling more informative feature extraction. 2. Feature-Relational Reasoning Network (FRN): In the Global Feature Extraction module of our model, the paper developed a novel FRN that leveraged Graph Neural Networks to determine interactions between pairs of input proteins. The FRN effectively captures the underlying relational information between proteins, contributing to improved PPI predictions. DL-PPI framework demonstrates state-of-the-art performance in the realm of sequence-based PPI prediction.
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Affiliation(s)
- Jiahui Wu
- Faculty of Information Technology, Beijing University of Technology, Beijing, 100124, China
| | - Bo Liu
- School of Mathematical and Computational Sciences, Massey University, Auckland, 0745, New Zealand.
| | - Jidong Zhang
- Faculty of Information Technology, Beijing University of Technology, Beijing, 100124, China
| | - Zhihan Wang
- Faculty of Information Technology, Beijing University of Technology, Beijing, 100124, China
| | - Jianqiang Li
- Faculty of Information Technology, Beijing University of Technology, Beijing, 100124, China
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Umemura M, Tamano K. How to improve the production of peptidyl compounds in filamentous fungi. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:1085624. [PMID: 37746201 PMCID: PMC10512285 DOI: 10.3389/ffunb.2022.1085624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/02/2022] [Indexed: 09/26/2023]
Abstract
Peptidyl compounds produced by filamentous fungi, which are nonribosomal peptides (NRPs) and ribosomally synthesized and post-translationally modified peptides (RiPPs), are rich sources of bioactive compounds with a wide variety of structures. Some of these peptidyl compounds are useful as pharmaceuticals and pesticides. However, for industrial use, their low production often becomes an obstacle, and various approaches have been challenged to overcome this weakness. In this article, we summarize the successful attempts to increase the production of NRPs and RiPPs in filamentous fungi and present our perspectives on how to improve it further.
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Affiliation(s)
- Maiko Umemura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Koichi Tamano
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
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Li S, Wu S, Wang L, Li F, Jiang H, Bai F. Recent advances in predicting protein-protein interactions with the aid of artificial intelligence algorithms. Curr Opin Struct Biol 2022; 73:102344. [PMID: 35219216 DOI: 10.1016/j.sbi.2022.102344] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 01/02/2022] [Accepted: 01/17/2022] [Indexed: 12/15/2022]
Abstract
Protein-protein interactions (PPIs) are essential in the regulation of biological functions and cell events, therefore understanding PPIs have become a key issue to understanding the molecular mechanism and investigating the design of drugs. Here we highlight the major developments in computational methods developed for predicting PPIs by using types of artificial intelligence algorithms. The first part introduces the source of experimental PPI data. The second part is devoted to the PPI prediction methods based on sequential information. The third part covers representative methods using structural information as the input feature. The last part is methods designed by combining different types of features. For each part, the state-of-the-art computational PPI prediction methods are reviewed in an inclusive view. Finally, we discuss the flaws existing in this area and future directions of next-generation algorithms.
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Affiliation(s)
- Shiwei Li
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Sanan Wu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Lin Wang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Fenglei Li
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; School of Information Science and Technology, ShanghaiTech University, Shanghai, China
| | - Hualiang Jiang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai, 201203, China
| | - Fang Bai
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; School of Information Science and Technology, ShanghaiTech University, Shanghai, China.
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Guo C. Research on pre-competition emotion recognition of student athletes based on improved machine learning. JOURNAL OF INTELLIGENT & FUZZY SYSTEMS 2020. [DOI: 10.3233/jifs-189047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
There are currently few studies on the stress of athletes, so it is impossible to provide effective stadium guidance for athletes. Based on this, this study combines machine learning algorithms to identify athletes’ pre-game emotions. At the same time, this study obtains the data related to the research through the survey access form and obtains the physiological parameters of the athletes under stress in the experimental way and processes the physiological parameters of the athletes with the machine learning algorithm. In order to improve the efficiency of data processing, this study improves the traditional machine learning algorithm, and combines the particle optimization algorithm with the support vector machine to realize the effective recognition of the athlete’s physiological state. In addition, through the experimental method combined with the contrast method, this paper compares the performance of the improved algorithm with the traditional algorithm and combines the data analysis to analyze the test results. Finally, this study analyzes the effectiveness of the proposed algorithm by example analysis. The research shows that the proposed algorithm has better performance than the traditional algorithm and has certain practical significance and can provide theoretical reference for subsequent related research.
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Affiliation(s)
- Chunfeng Guo
- College of Physical Education, Northeast Agricultural University, Harbin Heilongjiang, China
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Mei S, Zhang K. Neglog: Homology-Based Negative Data Sampling Method for Genome-Scale Reconstruction of Human Protein-Protein Interaction Networks. Int J Mol Sci 2019; 20:ijms20205075. [PMID: 31614890 PMCID: PMC6829266 DOI: 10.3390/ijms20205075] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 10/11/2019] [Indexed: 12/11/2022] Open
Abstract
Rapid reconstruction of genome-scale protein-protein interaction (PPI) networks is instrumental in understanding the cellular processes and disease pathogenesis and drug reactions. However, lack of experimentally verified negative data (i.e., pairs of proteins that do not interact) is still a major issue that needs to be properly addressed in computational modeling. In this study, we take advantage of the very limited experimentally verified negative data from Negatome to infer more negative data for computational modeling. We assume that the paralogs or orthologs of two non-interacting proteins also do not interact with high probability. We coin an assumption as "Neglog" this assumption is to some extent supported by paralogous/orthologous structure conservation. To reduce the risk of bias toward the negative data from Negatome, we combine Neglog with less biased random sampling according to a certain ratio to construct training data. L2-regularized logistic regression is used as the base classifier to counteract noise and train on a large dataset. Computational results show that the proposed Neglog method outperforms pure random sampling method with sound biological interpretability. In addition, we find that independent test on negative data is indispensable for bias control, which is usually neglected by existing studies. Lastly, we use the Neglog method to validate the PPIs in STRING, which are supported by gene ontology (GO) enrichment analyses.
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Affiliation(s)
- Suyu Mei
- Software College, Shenyang Normal University, Shenyang 110034, China.
| | - Kun Zhang
- Bioinformatics facility of Xavier NIH RCMI Cancer Research Center, Department of Computer Science, Xavier University of Louisiana, New Orleans, LA 70125, USA.
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Blanco JL, Porto-Pazos AB, Pazos A, Fernandez-Lozano C. Prediction of high anti-angiogenic activity peptides in silico using a generalized linear model and feature selection. Sci Rep 2018; 8:15688. [PMID: 30356060 PMCID: PMC6200741 DOI: 10.1038/s41598-018-33911-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 10/06/2018] [Indexed: 12/22/2022] Open
Abstract
Screening and in silico modeling are critical activities for the reduction of experimental costs. They also speed up research notably and strengthen the theoretical framework, thus allowing researchers to numerically quantify the importance of a particular subset of information. For example, in fields such as cancer and other highly prevalent diseases, having a reliable prediction method is crucial. The objective of this paper is to classify peptide sequences according to their anti-angiogenic activity to understand the underlying principles via machine learning. First, the peptide sequences were converted into three types of numerical molecular descriptors based on the amino acid composition. We performed different experiments with the descriptors and merged them to obtain baseline results for the performance of the models, particularly of each molecular descriptor subset. A feature selection process was applied to reduce the dimensionality of the problem and remove noisy features – which are highly present in biological problems. After a robust machine learning experimental design under equal conditions (nested resampling, cross-validation, hyperparameter tuning and different runs), we statistically and significantly outperformed the best previously published anti-angiogenic model with a generalized linear model via coordinate descent (glmnet), achieving a mean AUC value greater than 0.96 and with an accuracy of 0.86 with 200 molecular descriptors, mixed from the three groups. A final analysis with the top-40 discriminative anti-angiogenic activity peptides is presented along with a discussion of the feature selection process and the individual importance of each molecular descriptors According to our findings, anti-angiogenic activity peptides are strongly associated with amino acid sequences SP, LSL, PF, DIT, PC, GH, RQ, QD, TC, SC, AS, CLD, ST, MF, GRE, IQ, CQ and HG.
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Affiliation(s)
- Jose Liñares Blanco
- Department of Computer Science, Faculty of Computer Science, University of A Coruña, A Coruña, 15071, Spain
| | - Ana B Porto-Pazos
- Department of Computer Science, Faculty of Computer Science, University of A Coruña, A Coruña, 15071, Spain.,Instituto de Investigación Biomédica de A Coruña (INIBIC). Complexo Hospitalario Universitario de A Coruña, A Coruña, Spain
| | - Alejandro Pazos
- Department of Computer Science, Faculty of Computer Science, University of A Coruña, A Coruña, 15071, Spain.,Instituto de Investigación Biomédica de A Coruña (INIBIC). Complexo Hospitalario Universitario de A Coruña, A Coruña, Spain
| | - Carlos Fernandez-Lozano
- Department of Computer Science, Faculty of Computer Science, University of A Coruña, A Coruña, 15071, Spain. .,Instituto de Investigación Biomédica de A Coruña (INIBIC). Complexo Hospitalario Universitario de A Coruña, A Coruña, Spain.
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Tatjewski M, Kierczak M, Plewczynski D. Predicting Post-Translational Modifications from Local Sequence Fragments Using Machine Learning Algorithms: Overview and Best Practices. Methods Mol Biol 2017; 1484:275-300. [PMID: 27787833 DOI: 10.1007/978-1-4939-6406-2_19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Here, we present two perspectives on the task of predicting post translational modifications (PTMs) from local sequence fragments using machine learning algorithms. The first is the description of the fundamental steps required to construct a PTM predictor from the very beginning. These steps include data gathering, feature extraction, or machine-learning classifier selection. The second part of our work contains the detailed discussion of more advanced problems which are encountered in PTM prediction task. Probably the most challenging issues which we have covered here are: (1) how to address the training data class imbalance problem (we also present statistics describing the problem); (2) how to properly set up cross-validation folds with an approach which takes into account the homology of protein data records, to address this problem we present our folds-over-clusters algorithm; and (3) how to efficiently reach for new sources of learning features. Presented techniques and notes resulted from intense studies in the field, performed by our and other groups, and can be useful both for researchers beginning in the field of PTM prediction and for those who want to extend the repertoire of their research techniques.
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Affiliation(s)
- Marcin Tatjewski
- Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097, Warsaw, Poland
| | - Marcin Kierczak
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Dariusz Plewczynski
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, Warsaw, 02-097, Poland.
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Raza K. Protein Features Identification for Machine Learning-Based Prediction of Protein-Protein Interactions. COMMUNICATIONS IN COMPUTER AND INFORMATION SCIENCE 2017:305-317. [DOI: 10.1007/978-981-10-6544-6_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
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Chang JW, Zhou YQ, Ul Qamar MT, Chen LL, Ding YD. Prediction of Protein-Protein Interactions by Evidence Combining Methods. Int J Mol Sci 2016; 17:ijms17111946. [PMID: 27879651 PMCID: PMC5133940 DOI: 10.3390/ijms17111946] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/15/2016] [Accepted: 11/15/2016] [Indexed: 12/27/2022] Open
Abstract
Most cellular functions involve proteins' features based on their physical interactions with other partner proteins. Sketching a map of protein-protein interactions (PPIs) is therefore an important inception step towards understanding the basics of cell functions. Several experimental techniques operating in vivo or in vitro have made significant contributions to screening a large number of protein interaction partners, especially high-throughput experimental methods. However, computational approaches for PPI predication supported by rapid accumulation of data generated from experimental techniques, 3D structure definitions, and genome sequencing have boosted the map sketching of PPIs. In this review, we shed light on in silico PPI prediction methods that integrate evidence from multiple sources, including evolutionary relationship, function annotation, sequence/structure features, network topology and text mining. These methods are developed for integration of multi-dimensional evidence, for designing the strategies to predict novel interactions, and for making the results consistent with the increase of prediction coverage and accuracy.
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Affiliation(s)
- Ji-Wei Chang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yan-Qing Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Muhammad Tahir Ul Qamar
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Ling-Ling Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yu-Duan Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
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