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For: Aguilera-Mendoza L, Marrero-Ponce Y, Beltran JA, Tellez Ibarra R, Guillen-Ramirez HA, Brizuela CA. Graph-based data integration from bioactive peptide databases of pharmaceutical interest: toward an organized collection enabling visual network analysis. Bioinformatics 2020;35:4739-4747. [PMID: 30994884 DOI: 10.1093/bioinformatics/btz260] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 03/30/2019] [Accepted: 04/10/2019] [Indexed: 11/13/2022]  Open
Number Cited by Other Article(s)
1
Yin K, Li R, Zhang S, Sun Y, Huang L, Jiang M, Xu D, Xu W. Deep Learning Combined with Quantitative Structure‒Activity Relationship Accelerates De Novo Design of Antifungal Peptides. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025;12:e2412488. [PMID: 39921483 PMCID: PMC11967820 DOI: 10.1002/advs.202412488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2024] [Revised: 01/20/2025] [Indexed: 02/10/2025]
2
Wei Z, Shen Y, Tang X, Wen J, Song Y, Wei M, Cheng J, Zhu X. AVPpred-BWR: antiviral peptides prediction via biological words representation. Bioinformatics 2025;41:btaf126. [PMID: 40152250 PMCID: PMC11968319 DOI: 10.1093/bioinformatics/btaf126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2024] [Revised: 02/17/2025] [Accepted: 03/26/2025] [Indexed: 03/29/2025]  Open
3
Wang Y, Song M, Liu F, Liang Z, Hong R, Dong Y, Luan H, Fu X, Yuan W, Fang W, Li G, Lou H, Chang W. Artificial intelligence using a latent diffusion model enables the generation of diverse and potent antimicrobial peptides. SCIENCE ADVANCES 2025;11:eadp7171. [PMID: 39908380 PMCID: PMC11797553 DOI: 10.1126/sciadv.adp7171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 01/07/2025] [Indexed: 02/07/2025]
4
Barroso RA, Agüero-Chapin G, Sousa R, Marrero-Ponce Y, Antunes A. Unlocking Antimicrobial Peptides: In Silico Proteolysis and Artificial Intelligence-Driven Discovery from Cnidarian Omics. Molecules 2025;30:550. [PMID: 39942653 PMCID: PMC11820242 DOI: 10.3390/molecules30030550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2024] [Revised: 01/20/2025] [Accepted: 01/21/2025] [Indexed: 02/16/2025]  Open
5
Rodrigues T, Guardiola FA, Almeida D, Antunes A. Aquatic Invertebrate Antimicrobial Peptides in the Fight Against Aquaculture Pathogens. Microorganisms 2025;13:156. [PMID: 39858924 PMCID: PMC11767717 DOI: 10.3390/microorganisms13010156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2024] [Revised: 01/07/2025] [Accepted: 01/11/2025] [Indexed: 01/27/2025]  Open
6
Brizuela CA, Liu G, Stokes JM, de la Fuente‐Nunez C. AI Methods for Antimicrobial Peptides: Progress and Challenges. Microb Biotechnol 2025;18:e70072. [PMID: 39754551 PMCID: PMC11702388 DOI: 10.1111/1751-7915.70072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 11/18/2024] [Accepted: 12/16/2024] [Indexed: 01/06/2025]  Open
7
Castillo-Mendieta K, Agüero-Chapin G, Mora JR, Pérez N, Contreras-Torres E, Valdes-Martini JR, Martinez-Rios F, Marrero-Ponce Y. Unraveling the hemolytic toxicity tapestry of peptides using chemical space complex networks. Toxicol Sci 2024;202:236-249. [PMID: 39254655 DOI: 10.1093/toxsci/kfae115] [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] [Indexed: 09/11/2024]  Open
8
Agüero-Chapin G, Domínguez-Pérez D, Marrero-Ponce Y, Castillo-Mendieta K, Antunes A. Unveiling Encrypted Antimicrobial Peptides from Cephalopods' Salivary Glands: A Proteolysis-Driven Virtual Approach. ACS OMEGA 2024;9:43353-43367. [PMID: 39494035 PMCID: PMC11525497 DOI: 10.1021/acsomega.4c01959] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/26/2024] [Accepted: 04/30/2024] [Indexed: 11/05/2024]
9
Castillo-Mendieta K, Agüero-Chapin G, Marquez EA, Perez-Castillo Y, Barigye SJ, Vispo NS, García-Jacas CR, Marrero-Ponce Y. Peptide hemolytic activity analysis using visual data mining of similarity-based complex networks. NPJ Syst Biol Appl 2024;10:115. [PMID: 39367008 PMCID: PMC11452708 DOI: 10.1038/s41540-024-00429-2] [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: 06/29/2023] [Accepted: 08/22/2024] [Indexed: 10/06/2024]  Open
10
Mazein I, Rougny A, Mazein A, Henkel R, Gütebier L, Michaelis L, Ostaszewski M, Schneider R, Satagopam V, Jensen LJ, Waltemath D, Wodke JAH, Balaur I. Graph databases in systems biology: a systematic review. Brief Bioinform 2024;25:bbae561. [PMID: 39565895 PMCID: PMC11578065 DOI: 10.1093/bib/bbae561] [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: 04/18/2024] [Revised: 09/28/2024] [Accepted: 10/21/2024] [Indexed: 11/22/2024]  Open
11
Madhavi BGK, Wijethunga AM, Okagu OD, Sun X. Defatted Wheat Germ Protein-Derived Peptides Showed Multiple Biological Activities from the Stomach to Small Intestine: In Silico and In Vitro Approaches. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024;72:20527-20536. [PMID: 39231371 DOI: 10.1021/acs.jafc.4c06539] [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: 09/06/2024]
12
de Llano García D, Marrero-Ponce Y, Agüero-Chapin G, Ferri FJ, Antunes A, Martinez-Rios F, Rodríguez H. Innovative Alignment-Based Method for Antiviral Peptide Prediction. Antibiotics (Basel) 2024;13:768. [PMID: 39200068 PMCID: PMC11350826 DOI: 10.3390/antibiotics13080768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2024] [Revised: 08/08/2024] [Accepted: 08/09/2024] [Indexed: 09/01/2024]  Open
13
Santos-Júnior CD, Torres MDT, Duan Y, Rodríguez Del Río Á, Schmidt TSB, Chong H, Fullam A, Kuhn M, Zhu C, Houseman A, Somborski J, Vines A, Zhao XM, Bork P, Huerta-Cepas J, de la Fuente-Nunez C, Coelho LP. Discovery of antimicrobial peptides in the global microbiome with machine learning. Cell 2024;187:3761-3778.e16. [PMID: 38843834 PMCID: PMC11666328 DOI: 10.1016/j.cell.2024.05.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 04/11/2024] [Accepted: 05/06/2024] [Indexed: 06/25/2024]
14
Cordoves-Delgado G, García-Jacas CR. Predicting Antimicrobial Peptides Using ESMFold-Predicted Structures and ESM-2-Based Amino Acid Features with Graph Deep Learning. J Chem Inf Model 2024;64:4310-4321. [PMID: 38739853 DOI: 10.1021/acs.jcim.3c02061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
15
Castillo-Mendieta K, Agüero-Chapin G, Marquez E, Perez-Castillo Y, Barigye SJ, Pérez-Cárdenas M, Peréz-Giménez F, Marrero-Ponce Y. Multiquery Similarity Searching Models: An Alternative Approach for Predicting Hemolytic Activity from Peptide Sequence. Chem Res Toxicol 2024;37:580-589. [PMID: 38501392 DOI: 10.1021/acs.chemrestox.3c00408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
16
Martínez‐Mauricio KL, García‐Jacas CR, Cordoves‐Delgado G. Examining evolutionary scale modeling-derived different-dimensional embeddings in the antimicrobial peptide classification through a KNIME workflow. Protein Sci 2024;33:e4928. [PMID: 38501511 PMCID: PMC10949403 DOI: 10.1002/pro.4928] [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: 09/07/2023] [Revised: 01/28/2024] [Accepted: 01/30/2024] [Indexed: 03/20/2024]
17
Goshisht MK. Machine Learning and Deep Learning in Synthetic Biology: Key Architectures, Applications, and Challenges. ACS OMEGA 2024;9:9921-9945. [PMID: 38463314 PMCID: PMC10918679 DOI: 10.1021/acsomega.3c05913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 01/19/2024] [Accepted: 01/30/2024] [Indexed: 03/12/2024]
18
Li Z, Jin J, He W, Long W, Yu H, Gao X, Nakai K, Zou Q, Wei L. CoraL: interpretable contrastive meta-learning for the prediction of cancer-associated ncRNA-encoded small peptides. Brief Bioinform 2023;24:bbad352. [PMID: 37861173 DOI: 10.1093/bib/bbad352] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/29/2023] [Accepted: 09/17/2023] [Indexed: 10/21/2023]  Open
19
Santos-Júnior CD, Der Torossian Torres M, Duan Y, del Río ÁR, Schmidt TS, Chong H, Fullam A, Kuhn M, Zhu C, Houseman A, Somborski J, Vines A, Zhao XM, Bork P, Huerta-Cepas J, de la Fuente-Nunez C, Coelho LP. Computational exploration of the global microbiome for antibiotic discovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.31.555663. [PMID: 37693522 PMCID: PMC10491242 DOI: 10.1101/2023.08.31.555663] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
20
Singh V, Singh SK. A separable temporal convolutional networks based deep learning technique for discovering antiviral medicines. Sci Rep 2023;13:13722. [PMID: 37608092 PMCID: PMC10444765 DOI: 10.1038/s41598-023-40922-y] [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: 04/09/2023] [Accepted: 08/18/2023] [Indexed: 08/24/2023]  Open
21
Aguilera-Mendoza L, Ayala-Ruano S, Martinez-Rios F, Chavez E, García-Jacas CR, Brizuela CA, Marrero-Ponce Y. StarPep Toolbox: an open-source software to assist chemical space analysis of bioactive peptides and their functions using complex networks. Bioinformatics 2023;39:btad506. [PMID: 37603724 PMCID: PMC10469104 DOI: 10.1093/bioinformatics/btad506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 07/24/2023] [Accepted: 08/18/2023] [Indexed: 08/23/2023]  Open
22
Agüero-Chapin G, Antunes A, Mora JR, Pérez N, Contreras-Torres E, Valdes-Martini JR, Martinez-Rios F, Zambrano CH, Marrero-Ponce Y. Complex Networks Analyses of Antibiofilm Peptides: An Emerging Tool for Next-Generation Antimicrobials' Discovery. Antibiotics (Basel) 2023;12:antibiotics12040747. [PMID: 37107109 PMCID: PMC10135022 DOI: 10.3390/antibiotics12040747] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/04/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023]  Open
23
Tonolo F, Grinzato A, Bindoli A, Rigobello MP. From In Silico to a Cellular Model: Molecular Docking Approach to Evaluate Antioxidant Bioactive Peptides. Antioxidants (Basel) 2023;12:antiox12030665. [PMID: 36978913 PMCID: PMC10045749 DOI: 10.3390/antiox12030665] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/10/2023]  Open
24
Li Z, Gao E, Zhou J, Han W, Xu X, Gao X. Applications of deep learning in understanding gene regulation. CELL REPORTS METHODS 2023;3:100384. [PMID: 36814848 PMCID: PMC9939384 DOI: 10.1016/j.crmeth.2022.100384] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
25
Carballo GM, Vázquez KG, García-González LA, Rio GD, Brizuela CA. Embedded-AMP: A Multi-Thread Computational Method for the Systematic Identification of Antimicrobial Peptides Embedded in Proteome Sequences. Antibiotics (Basel) 2023;12:antibiotics12010139. [PMID: 36671338 PMCID: PMC9854971 DOI: 10.3390/antibiotics12010139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 01/12/2023]  Open
26
Ayala-Ruano S, Marrero-Ponce Y, Aguilera-Mendoza L, Pérez N, Agüero-Chapin G, Antunes A, Aguilar AC. Network Science and Group Fusion Similarity-Based Searching to Explore the Chemical Space of Antiparasitic Peptides. ACS OMEGA 2022;7:46012-46036. [PMID: 36570318 PMCID: PMC9773354 DOI: 10.1021/acsomega.2c03398] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 11/21/2022] [Indexed: 05/13/2023]
27
ABP-Finder: A Tool to Identify Antibacterial Peptides and the Gram-Staining Type of Targeted Bacteria. Antibiotics (Basel) 2022;11:antibiotics11121708. [PMID: 36551365 PMCID: PMC9774453 DOI: 10.3390/antibiotics11121708] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 11/29/2022]  Open
28
García-Jacas CR, García-González LA, Martinez-Rios F, Tapia-Contreras IP, Brizuela CA. Handcrafted versus non-handcrafted (self-supervised) features for the classification of antimicrobial peptides: complementary or redundant? Brief Bioinform 2022;23:6754757. [PMID: 36215083 DOI: 10.1093/bib/bbac428] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/28/2022] [Accepted: 09/02/2022] [Indexed: 12/14/2022]  Open
29
Antimicrobial peptides with cell-penetrating activity as prophylactic and treatment drugs. Biosci Rep 2022;42:231731. [PMID: 36052730 PMCID: PMC9508529 DOI: 10.1042/bsr20221789] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 01/18/2023]  Open
30
Agüero-Chapin G, Galpert-Cañizares D, Domínguez-Pérez D, Marrero-Ponce Y, Pérez-Machado G, Teijeira M, Antunes A. Emerging Computational Approaches for Antimicrobial Peptide Discovery. Antibiotics (Basel) 2022;11:antibiotics11070936. [PMID: 35884190 PMCID: PMC9311958 DOI: 10.3390/antibiotics11070936] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/01/2022] [Accepted: 07/08/2022] [Indexed: 02/05/2023]  Open
31
A Novel Network Science and Similarity-Searching-Based Approach for Discovering Potential Tumor-Homing Peptides from Antimicrobials. Antibiotics (Basel) 2022;11:antibiotics11030401. [PMID: 35326864 PMCID: PMC8944733 DOI: 10.3390/antibiotics11030401] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/13/2022] [Accepted: 03/15/2022] [Indexed: 02/01/2023]  Open
32
Singh V, Shrivastava S, Kumar Singh S, Kumar A, Saxena S. Accelerating the discovery of antifungal peptides using deep temporal convolutional networks. Brief Bioinform 2022;23:6526725. [DOI: 10.1093/bib/bbac008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/27/2021] [Accepted: 01/06/2022] [Indexed: 02/02/2023]  Open
33
Vidal-Limon A, Aguilar-Toalá JE, Liceaga AM. Integration of Molecular Docking Analysis and Molecular Dynamics Simulations for Studying Food Proteins and Bioactive Peptides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022;70:934-943. [PMID: 34990125 DOI: 10.1021/acs.jafc.1c06110] [Citation(s) in RCA: 175] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
34
Singh V, Shrivastava S, Kumar Singh S, Kumar A, Saxena S. StaBle-ABPpred: a stacked ensemble predictor based on biLSTM and attention mechanism for accelerated discovery of antibacterial peptides. Brief Bioinform 2021;23:6423526. [PMID: 34750606 DOI: 10.1093/bib/bbab439] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/06/2021] [Accepted: 09/24/2021] [Indexed: 01/29/2023]  Open
35
Sharma R, Shrivastava S, Kumar Singh S, Kumar A, Saxena S, Kumar Singh R. Deep-AFPpred: identifying novel antifungal peptides using pretrained embeddings from seq2vec with 1DCNN-BiLSTM. Brief Bioinform 2021;23:6404058. [PMID: 34670278 DOI: 10.1093/bib/bbab422] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/03/2021] [Accepted: 09/12/2021] [Indexed: 01/04/2023]  Open
36
Sharma R, Shrivastava S, Kumar Singh S, Kumar A, Saxena S, Kumar Singh R. AniAMPpred: artificial intelligence guided discovery of novel antimicrobial peptides in animal kingdom. Brief Bioinform 2021;22:6320952. [PMID: 34259329 DOI: 10.1093/bib/bbab242] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 06/02/2021] [Accepted: 06/21/2021] [Indexed: 12/12/2022]  Open
37
Pinacho-Castellanos SA, García-Jacas CR, Gilson MK, Brizuela CA. Alignment-Free Antimicrobial Peptide Predictors: Improving Performance by a Thorough Analysis of the Largest Available Data Set. J Chem Inf Model 2021;61:3141-3157. [PMID: 34081438 DOI: 10.1021/acs.jcim.1c00251] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
38
Zhang Y, Lin J, Zhao L, Zeng X, Liu X. A novel antibacterial peptide recognition algorithm based on BERT. Brief Bioinform 2021;22:6284370. [PMID: 34037687 DOI: 10.1093/bib/bbab200] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 04/19/2021] [Accepted: 05/03/2021] [Indexed: 12/31/2022]  Open
39
Hashemi ZS, Zarei M, Fath MK, Ganji M, Farahani MS, Afsharnouri F, Pourzardosht N, Khalesi B, Jahangiri A, Rahbar MR, Khalili S. In silico Approaches for the Design and Optimization of Interfering Peptides Against Protein-Protein Interactions. Front Mol Biosci 2021;8:669431. [PMID: 33996914 PMCID: PMC8113820 DOI: 10.3389/fmolb.2021.669431] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/06/2021] [Indexed: 01/01/2023]  Open
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Evolutionary algorithm-based generation of optimum peptide sequences with dengue virus inhibitory activity. Future Med Chem 2021;13:993-1000. [PMID: 33890502 DOI: 10.4155/fmc-2020-0372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
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Sharma R, Shrivastava S, Kumar Singh S, Kumar A, Saxena S, Kumar Singh R. Deep-ABPpred: identifying antibacterial peptides in protein sequences using bidirectional LSTM with word2vec. Brief Bioinform 2021;22:6204762. [PMID: 33784381 DOI: 10.1093/bib/bbab065] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/04/2021] [Indexed: 12/13/2022]  Open
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Shotgun Proteomics and Protein-Based Bioinformatics for the Characterization of Food-Derived Bioactive Peptides. Methods Mol Biol 2021. [PMID: 33687718 DOI: 10.1007/978-1-0716-1178-4_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
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Pirtskhalava M, Amstrong AA, Grigolava M, Chubinidze M, Alimbarashvili E, Vishnepolsky B, Gabrielian A, Rosenthal A, Hurt DE, Tartakovsky M. DBAASP v3: database of antimicrobial/cytotoxic activity and structure of peptides as a resource for development of new therapeutics. Nucleic Acids Res 2021;49:D288-D297. [PMID: 33151284 PMCID: PMC7778994 DOI: 10.1093/nar/gkaa991] [Citation(s) in RCA: 307] [Impact Index Per Article: 76.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/09/2020] [Accepted: 10/14/2020] [Indexed: 12/30/2022]  Open
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Aguilera-Mendoza L, Marrero-Ponce Y, García-Jacas CR, Chavez E, Beltran JA, Guillen-Ramirez HA, Brizuela CA. Automatic construction of molecular similarity networks for visual graph mining in chemical space of bioactive peptides: an unsupervised learning approach. Sci Rep 2020;10:18074. [PMID: 33093586 PMCID: PMC7583304 DOI: 10.1038/s41598-020-75029-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 09/23/2020] [Indexed: 12/15/2022]  Open
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Barigye SJ, Gómez-Ganau S, Serrano-Candelas E, Gozalbes R. PeptiDesCalculator: Software for computation of peptide descriptors. Definition, implementation and case studies for 9 bioactivity endpoints. Proteins 2020;89:174-184. [PMID: 32881068 DOI: 10.1002/prot.26003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 08/05/2020] [Accepted: 08/27/2020] [Indexed: 11/09/2022]
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Nava Lara RA, Beltrán JA, Brizuela CA, Del Rio G. Relevant Features of Polypharmacologic Human-Target Antimicrobials Discovered by Machine-Learning Techniques. Pharmaceuticals (Basel) 2020;13:ph13090204. [PMID: 32825532 PMCID: PMC7559829 DOI: 10.3390/ph13090204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/07/2020] [Accepted: 08/07/2020] [Indexed: 11/16/2022]  Open
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Carrera M, Ezquerra-Brauer JM, Aubourg SP. Characterization of the Jumbo Squid (Dosidicus gigas) Skin By-Product by Shotgun Proteomics and Protein-Based Bioinformatics. Mar Drugs 2019;18:md18010031. [PMID: 31905758 PMCID: PMC7024357 DOI: 10.3390/md18010031] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/19/2019] [Accepted: 12/26/2019] [Indexed: 12/16/2022]  Open
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