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For: Xu J, Li F, Li C, Guo X, Landersdorfer C, Shen HH, Peleg AY, Li J, Imoto S, Yao J, Akutsu T, Song J. iAMPCN: a deep-learning approach for identifying antimicrobial peptides and their functional activities. Brief Bioinform 2023;24:bbad240. [PMID: 37369638 PMCID: PMC10359087 DOI: 10.1093/bib/bbad240] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 05/30/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023]  Open
Number Cited by Other Article(s)
1
Shaon MSH, Karim T, Sultan MF, Ali MM, Ahmed K, Hasan MZ, Moustafa A, Bui FM, Al-Zahrani FA. AMP-RNNpro: a two-stage approach for identification of antimicrobials using probabilistic features. Sci Rep 2024;14:12892. [PMID: 38839785 PMCID: PMC11153637 DOI: 10.1038/s41598-024-63461-6] [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: 02/16/2024] [Accepted: 05/29/2024] [Indexed: 06/07/2024]  Open
2
Aslan A, Ari Yuka S. Therapeutic peptides for coronary artery diseases: in silico methods and current perspectives. Amino Acids 2024;56:37. [PMID: 38822212 PMCID: PMC11143054 DOI: 10.1007/s00726-024-03397-3] [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: 01/25/2024] [Accepted: 05/06/2024] [Indexed: 06/02/2024]
3
Rusic D, Kumric M, Seselja Perisin A, Leskur D, Bukic J, Modun D, Vilovic M, Vrdoljak J, Martinovic D, Grahovac M, Bozic J. Tackling the Antimicrobial Resistance "Pandemic" with Machine Learning Tools: A Summary of Available Evidence. Microorganisms 2024;12:842. [PMID: 38792673 PMCID: PMC11123121 DOI: 10.3390/microorganisms12050842] [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: 03/16/2024] [Revised: 04/16/2024] [Accepted: 04/19/2024] [Indexed: 05/26/2024]  Open
4
Gu ZF, Hao YD, Wang TY, Cai PL, Zhang Y, Deng KJ, Lin H, Lv H. Prediction of blood-brain barrier penetrating peptides based on data augmentation with Augur. BMC Biol 2024;22:86. [PMID: 38637801 PMCID: PMC11027412 DOI: 10.1186/s12915-024-01883-4] [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: 01/03/2024] [Accepted: 04/05/2024] [Indexed: 04/20/2024]  Open
5
Karim T, Shaon MSH, Sultan MF, Hasan MZ, Kafy AA. ANNprob-ACPs: A novel anticancer peptide identifier based on probabilistic feature fusion approach. Comput Biol Med 2024;169:107915. [PMID: 38171261 DOI: 10.1016/j.compbiomed.2023.107915] [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: 08/20/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/05/2024]
6
Wang R, Wang T, Zhuo L, Wei J, Fu X, Zou Q, Yao X. Diff-AMP: tailored designed antimicrobial peptide framework with all-in-one generation, identification, prediction and optimization. Brief Bioinform 2024;25:bbae078. [PMID: 38446739 PMCID: PMC10939340 DOI: 10.1093/bib/bbae078] [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: 11/23/2023] [Revised: 01/25/2024] [Accepted: 02/08/2024] [Indexed: 03/08/2024]  Open
7
Chung CR, Liou JT, Wu LC, Horng JT, Lee TY. Multi-label classification and features investigation of antimicrobial peptides with various functional classes. iScience 2023;26:108250. [PMID: 38025779 PMCID: PMC10679894 DOI: 10.1016/j.isci.2023.108250] [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: 03/04/2023] [Revised: 07/15/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023]  Open
8
Xing W, Zhang J, Li C, Huo Y, Dong G. iAMP-Attenpred: a novel antimicrobial peptide predictor based on BERT feature extraction method and CNN-BiLSTM-Attention combination model. Brief Bioinform 2023;25:bbad443. [PMID: 38055840 PMCID: PMC10699745 DOI: 10.1093/bib/bbad443] [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: 09/08/2023] [Revised: 10/31/2023] [Accepted: 11/11/2023] [Indexed: 12/08/2023]  Open
9
Pham NT, Rakkiyapan R, Park J, Malik A, Manavalan B. H2Opred: a robust and efficient hybrid deep learning model for predicting 2'-O-methylation sites in human RNA. Brief Bioinform 2023;25:bbad476. [PMID: 38180830 PMCID: PMC10768780 DOI: 10.1093/bib/bbad476] [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: 09/30/2023] [Revised: 11/22/2023] [Accepted: 11/28/2023] [Indexed: 01/07/2024]  Open
10
Yao L, Zhang Y, Li W, Chung C, Guan J, Zhang W, Chiang Y, Lee T. DeepAFP: An effective computational framework for identifying antifungal peptides based on deep learning. Protein Sci 2023;32:e4758. [PMID: 37595093 PMCID: PMC10503419 DOI: 10.1002/pro.4758] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/02/2023] [Accepted: 08/10/2023] [Indexed: 08/20/2023]
11
Mou M, Pan Z, Zhou Z, Zheng L, Zhang H, Shi S, Li F, Sun X, Zhu F. A Transformer-Based Ensemble Framework for the Prediction of Protein-Protein Interaction Sites. RESEARCH (WASHINGTON, D.C.) 2023;6:0240. [PMID: 37771850 PMCID: PMC10528219 DOI: 10.34133/research.0240] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 09/08/2023] [Indexed: 09/30/2023]
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