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Geological and Mining Engineering

Geological and Mining Engineering (GME), published by Scineer Publishing PTE. LTD, is an open-access journal. GME is devoted to publish geological and mining engineering related articles in the form of original papers, review papers and case studies. It also provides a platform for scholars to exchange the latest information in the related fields and aim to promote the research on geological and mining engineering throughout the world. GME welcomes all original

ISSN: 3029-1887(P)

3029-2034(O)

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Food Safety and Quality

Food Safety and Quality (FSQ), published by Scineer Publishing PTE. LTD, is an open-access journal. FSQ is devoted to publish food safety and quality related articles in the form of original papers, review papers and case studies. It also provides a platform for scholars to exchange the latest information in the related fields and aim to promote the research on food safety and quality throughout the world. FSQ welcomes all original manuscripts that do not be published in any other journals.

ISSN: 3029-2115(P)

3029-2123(O)

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Hydraulic Engineering and Power Research

Hydraulic Engineering and Power Research (HEPR), published by Scineer Publishing PTE. LTD, is an open-access journal. HEPR is devoted to publish hydraulic engineering and power related articles in the form of original papers, review papers and case studies. It also provides a platform for scholars to exchange the latest information in the related fields and aim to promote the research on hydraulic engineering and power throughout the world. HEPR welcomes all original manuscripts that do not be published in any other journals.Â

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Â Â Â Â ISSN: 3029-2158(P)

Â Â Â Â Â Â Â Â Â 3029-2166(O)

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Medical and Health Research

Medical and Health Research (MHR), published by Scineer Publishing PTE. LTD, is an open-access journal. MHR is devoted to publish medicine related articles in the form of original papers, review papers and case studies. It also provides a platform for scholars to exchange the latest information in the related fields and aim to promote the research on medicine throughout the world. MHR welcomes all original manuscripts that do not be published in any other journals.Â

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Â Â Â Â ISSN: 3029-2190(P)

Â Â Â Â Â Â Â Â Â 3029-2204(O)

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Practical Medical Research

Practical Medical Research (PMR), published by Scineer Publishing PTE. LTD, is an open-access journal. PMR is devoted to publish medicine related articles in the form of original papers, review papers and case studies. It also provides a platform for scholars to exchange the latest information in the related fields and aim to promote the research on medicine throughout the world. PMR welcomes all original manuscripts that do not be published in any other journals.Â

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Â Â Â Â ISSN: 3029-2085(P)

Â Â Â Â Â Â Â Â Â Â 3029-2093(O)

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Forum on Research and Innovation Management

Forum on Research and Innovation Management (FRIM), published by Scineer Publishing PTE. LTD, is an open-access journal. FRIM is devoted to publish research and innovation management related articles in the form of original papers, review papers and case studies. It also provides a platform for scholars to exchange the latest information in the related fields and aim to promote the research on research and innovation management throughout the world. FRIM welcomes all original manuscripts that do not be published in any other journals.Â

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Â Â Â Â ISSN: 3029-1933(P)

Â Â Â Â Â Â Â Â Â 3029-1984(O)

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Construction Safety Technology and Management

Construction Safety Technology and Management (CSTM), published by Scineer Publishing PTE. LTD, is an open-access journal. CSTM is devoted to publish construction safety technology and management related articles in the form of original papers, review papers and case studies. It also provides a platform for scholars to exchange the latest information in the related fields and aim to promote the research on construction safety technology and management throughout the world. CSTM welcomes all original manuscripts that do not be published in any other journals.Â

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Â Â Â Â Â ISSN: 3029-2069(P)

Â Â Â Â Â Â Â Â Â Â Â 3029-2077(O)

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Industrial Technology Research

Industrial Technology Research (ITR), published by Scineer Publishing PTE. LTD, is an open-access journal. ITR is devoted to publish industrial technology related articles in the form of original papers, review papers and case studies. It also provides a platform for scholars to exchange the latest information in the related fields and aim to promote the research on industrial technology throughout the world. ITR welcomes all original manuscripts that do not be published in any other journals.

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Â Â Â Â ISSN: 3029-1895(P)

Â Â Â Â Â Â Â Â Â Â 3029-2026(O)

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Environmental Protection and Health

Environmental Protection and Health (EPH), published by Scineer Publishing PTE. LTD, is an open-access journal. EPH is devoted to publish environmental protection and health related articles in the form of original papers, review papers and case studies. It also provides a platform for scholars to exchange the latest information in the related fields and aim to promote the research on environmental protection and health throughout the world. EPH welcomes all original manuscripts that do not be published in any other journals.Â

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Â Â Â Â ISSN: 3029-1909(P)

Â Â Â Â Â Â Â Â Â 3029-2018(O)

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Artificial Intelligence Technology Research

Artificial Intelligence Technology Research (AITR), published by Scineer Publishing PTE. LTD, is an open-access journal. AITR is devoted to publish artificial intelligence technology related articles in the form of original papers, review papers and case studies. It also provides a platform for scholars to exchange the latest information in the related fields and aim to promote the research on artificial intelligence technology throughout the world. AITR welcomes all original manuscripts that do not be published in any other journals.Â

Â Â Â Â ISSN: 3029-1968(O)

Â Â Â Â Â Â Â Â Â 3029-195X(P)
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Curriculum Learning and Exploration

Curriculum Learning and Exploration (CLE), published by Scineer Publishing PTE. LTD, is an open-access journal. CLE is devoted to publish curriculum related articles in the form of original papers, review papers and case studies. It also provides a platform for scholars to exchange the latest information in the related fields and aim to promote the research on curriculum throughout the world. CLE welcomes all original manuscripts that do not be published in any other journals.Â

Â Â Â Â ISSN: 3029-1976(O)

Â Â Â Â Â Â Â Â Â 3029-1941(P)
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Evaluation of Educational Research

Evaluation of Educational Research (EER), published by Scineer Publishing PTE. LTD, is an open-access journal. EER is devoted to publish education related articles in the form of original papers, review papers and case studies. It also provides a platform for scholars to exchange the latest information in the related fields and aim to promote the research on education throughout the world. EER welcomes all original manuscripts that do not be published in any other journals.

Â Â Â Â ISSN: 3029-1992(O)

Â Â Â Â Â Â Â Â Â 3029-1925(P)
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World Education Forum

World Education Forum (WEF), published by Scineer Publishing PTE. LTD, is an open-access journal. WEF is devoted to publish education related articles in the form of original papers, review papers and case studies. It also provides a platform for scholars to exchange the latest information in the related fields and aim to promote the research on education throughout the world. WEF welcomes all original manuscripts that do not be published in any other journals.

Â Â Â Â ISSN: 3029-214X(O)

Â Â Â Â Â Â Â Â Â 3029-2131(P)

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New Explorations in Education and Teaching

New Explorations in Education and Teaching (NEET), published by Scineer Publishing PTE. LTD, is an open-access journal. NEET is devoted to publish education related articles in the form of original papers, review papers and case studies. It also provides a platform for scholars to exchange the latest information in the related fields and aim to promote the research on education throughout the world. NEET welcomes all original manuscripts that do not be published in any other journals.Â

Â Â Â Â ISSN: 3029-200X(O)

Â Â Â Â Â Â Â Â Â 3029-1917(P)

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Modern Economic Management Forum

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Modern Economic Management Forum (MEMF), published by Scineer Publishing PTE. LTD, is an open-access journal. MEMF is devoted to publish modern economic management related articles in the form of original papers, review papers and case studies. It also provides a platform for scholars to exchange the latest information in the related fields and aim to promote the research on economic management throughout the world. MEMF welcomes all original manuscripts that do not be published in any other journals.Â

Â Â Â Â ISSN: 3029-2182(O)

Â Â Â Â Â Â Â Â Â 3029-2174(P)

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Research and Commentary on Humanities and Arts

Research and Commentary on Humanities and ArtsÂ (RCHA), published by Scineer Publishing PTE. LTD, is an open-access journal. RCHA is devoted to publish humanities and arts related articles in the form of original papers, review papers and case studies. It also provides a platform for scholars to exchange the latest information in the related fields and aim to promote the research on humanities and arts throughout the world. RCHA welcomes all original manuscripts that do not be published in any other journals.Â

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Â Â Â Â Â Â ISSN: 3029-2050(O)

Â Â Â Â Â Â Â Â Â Â Â 3029-2042(P)

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Scineer Publishing is a publisher of open access journals. Covering various disciplines and promoting interdisciplinary development, Scineer Publishing adheres to a principle of respecting academics, and publishes insightful and rigorous academic research contents.

12 Eu Tong Sen Street, #07-168, Singapore 059819

E-mail: scineerpub@126.com

Copyright © 2023 Scineer Publishing Pte. Ltd.

iAMPM: A Deep Learning Approach for Improved Recognition of Antimicrobial Peptides

Chuxin Han, Jiale Lu, Ji Qiu

Abstract

Antimicrobial peptides (AMPs) naturally produced by diverse living organisms, exhibit potent antimicrobial activity characterized
by swift killing capabilities, low toxicity profiles, and broad-spectrum activity. These attributes render AMPs as promising candidates for addressing the pressing issue of escalating antibiotic resistance. In comparison to the labor-intensive wet-laboratory techniques and machine
learning approaches for antimicrobial peptide identification, deep learning-based methodologies offer a more streamlined and convenient
alternative that obviates the need for intricate feature engineering processes. This study presents a novel deep learning framework, designated
as iAMPM, for the identification of antimicrobial peptides. This model makes predictions by extracting the spatial structural features of peptides in the global dimension. A graph neural network module, comprising a MixHop layer, a global average pooling layer, and a self-attentive
module, is employed for the extraction of peptide spatial information. The three-dimensional peptide structure was initially calculated with
atomic precision using the AlphaFold protein structure prediction module. Thereafter, the peptide residue contact maps were generated
computationally based on this peptide structure. Subsequently, the pre-trained model (ESM) is employed to extract peptide residue features,
thereby generating peptide residue contact map embeddings. The data utilized in this experiment were obtained from a number of databases,
including dbAMP, APD3, CAMP, DRAMP, and UniProt. In the independent dataset, the Sn metrics and AUC values of iAMPM demonstrated
superior performance compared to the best-performing sequence-based iAMPCN, with an improvement of 9.08% and 4.2%, respectively.

Keywords

Antimicrobial peptide; Deep learning; Graph neural network; Contact map

Full Text:

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References

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[2] Erdem B¨uy¨ukkiraz M, Kesmen Z. Antimicrobial peptides (AMPs): A promising class of antimicrobial compounds. Journal of applied

microbiology 2022; 132(3): 1573-1596.

[3] Zhang L, Gallo RL. Antimicrobial peptides. Current biology 2016; 26(1): R14-R19.

[4] Bahar AA, Ren D. Antimicrobial peptides. Pharmaceuticals 2013; 6(12): 1543-1575.

[5] Magana M, Pushpanathan M, Santos AL, et al. The value of antimicrobial peptides in the age of resistance. The lancet infectious diseases 2020; 20(9): e216-e230.

[6] Veltri D, Kamath U, Shehu A. Deep learning improves antimicrobial peptide recognition. Bioinformatics 2018; 34(16): 2740-2747.

[7] Su X, Xu J, Yin Y, Quan X, Zhang H. Antimicrobial peptide identification using multi-scale convolutional network. BMC bioinformatics

2019; 20: 1-10.

[8] Xu J, Li F, Li C, et al. iAMPCN: a deep-learning approach for identifying antimicrobial peptides and their functional activities. Briefings

in Bioinformatics 2023; 24(4): bbad240.

[9] Jumper J, Evans R, Pritzel A, et al. Highly accurate protein structure prediction with AlphaFold. nature 2021; 596(7873): 583-589.

[10] Lin Z, Akin H, Rao R, et al. Evolutionary-scale prediction of atomic-level protein structure with a language model. Science 2023;

379(6637): 1123-1130.

[11] Abu-El-Haija S, Perozzi B, Kapoor A, et al. Mixhop: Higher-order graph convolutional architectures via sparsified neighborhood mixing. In: international conference on machine learning; 2019. pp. 21-29

[12] Vaswani A. Attention is all you need. arXiv preprint arXiv:1706.03762 2017.

[13] Chicco D, Jurman G. The advantages of the Matthews correlation coefficient (MCC) over F1 score and accuracy in binary classification

evaluation. BMC genomics 2020; 21: 1-13.

[14] Jhong JH, Yao L, Pang Y, et al. dbAMP 2.0: updated resource for antimicrobial peptides with an enhanced scanning method for genomic

and proteomic data. Nucleic acids research 2022; 50(D1): D460-D470.

[15] Wang G, Li X, Wang Z. APD3: the antimicrobial peptide database as a tool for research and education. Nucleic acids research 2016;

44(D1): D1087-D1093.

[16] UniProt: the universal protein knowledgebase in 2023. Nucleic acids research 2023; 51(D1): D523-D531.

[17] Gull S, Shamim N, Minhas F. AMAP: Hierarchical multi-label prediction of biologically active and antimicrobial peptides. Computers

in biology and medicine 2019; 107: 172-181.

[18] Chung CR, Kuo TR, Wu LC, Lee TY, Horng JT. Characterization and identification of antimicrobial peptides with different functional

activities. Briefings in bioinformatics 2020; 21(3): 1098-1114.

[19] Xiao X, Shao YT, Cheng X, Stamatovic B. iAMP-CA2L: a new CNN-BiLSTM-SVM classifier based on cellular automata image for

identifying antimicrobial peptides and their functional types. Briefings in bioinformatics 2021; 22(6): bbab209.

DOI: http://dx.doi.org/10.70711/aitr.v2i6.5734

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Scineer Publishing is a publisher of open access journals. Covering various disciplines and promoting interdisciplinary development, Scineer Publishing adheres to a principle of respecting academics, and publishes insightful and rigorous academic research contents.

12 Eu Tong Sen Street, #07-168, Singapore 059819

E-mail: scineerpub@126.com

Copyright © 2023 Scineer Publishing Pte. Ltd.