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For: Manavalan B, Chandra Patra M. MLCPP 2.0: An updated cell-penetrating peptides and their uptake efficiency predictor. J Mol Biol 2022. [DOI: 10.1016/j.jmb.2022.167604] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 04/03/2022] [Accepted: 04/19/2022] [Indexed: 12/12/2022]
Number Cited by Other Article(s)
1
Hemmati S. Expanding the cryoprotectant toolbox in biomedicine by multifunctional antifreeze peptides. Biotechnol Adv 2025;81:108545. [PMID: 40023203 DOI: 10.1016/j.biotechadv.2025.108545] [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: 10/10/2024] [Revised: 01/07/2025] [Accepted: 02/23/2025] [Indexed: 03/04/2025]
2
Chen Q, Zhang Y, Gao J, Zhang J. CPPCGM: A Highly Efficient Sequence-Based Tool for Simultaneously Identifying and Generating Cell-Penetrating Peptides. J Chem Inf Model 2025;65:3357-3369. [PMID: 40105337 DOI: 10.1021/acs.jcim.5c00199] [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: 03/20/2025]
3
Sutcliffe R, Doherty CPA, Morgan HP, Dunne NJ, McCarthy HO. Strategies for the design of biomimetic cell-penetrating peptides using AI-driven in silico tools for drug delivery. BIOMATERIALS ADVANCES 2025;169:214153. [PMID: 39705787 DOI: 10.1016/j.bioadv.2024.214153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2024] [Revised: 12/08/2024] [Accepted: 12/14/2024] [Indexed: 12/23/2024]
4
Asim MN, Asif T, Mehmood F, Dengel A. Peptide classification landscape: An in-depth systematic literature review on peptide types, databases, datasets, predictors architectures and performance. Comput Biol Med 2025;188:109821. [PMID: 39987697 DOI: 10.1016/j.compbiomed.2025.109821] [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: 09/28/2024] [Revised: 02/03/2025] [Accepted: 02/05/2025] [Indexed: 02/25/2025]
5
Torres-Sánchez E, Martínez-Villaluenga C, Paterson S, Hernández-Ledesma B, Gutiérrez LF. Antidiabetic and Immunomodulatory Properties of Peptide Fractions from Sacha Inchi Oil Press-Cake. Foods 2025;14:1231. [PMID: 40238480 PMCID: PMC11988709 DOI: 10.3390/foods14071231] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2025] [Revised: 03/27/2025] [Accepted: 03/29/2025] [Indexed: 04/18/2025]  Open
6
Su Q, Phan LT, Pham NT, Wei L, Manavalan B. MST-m6A: A Novel Multi-Scale Transformer-based Framework for Accurate Prediction of m6A Modification Sites Across Diverse Cellular Contexts. J Mol Biol 2025;437:168856. [PMID: 39510345 DOI: 10.1016/j.jmb.2024.168856] [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: 07/16/2024] [Revised: 10/23/2024] [Accepted: 11/02/2024] [Indexed: 11/15/2024]
7
Zhang HQ, Arif M, Thafar MA, Albaradei S, Cai P, Zhang Y, Tang H, Lin H. PMPred-AE: a computational model for the detection and interpretation of pathological myopia based on artificial intelligence. Front Med (Lausanne) 2025;12:1529335. [PMID: 40182849 PMCID: PMC11965940 DOI: 10.3389/fmed.2025.1529335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2024] [Accepted: 02/27/2025] [Indexed: 04/05/2025]  Open
8
Biswas A, Periyasamy K, Maloverjan M, Porosk L, Arya G, Mehta S, Andla H, Raid R, Kisand V, Rätsep M, Wengel J, Rebane A, Pooga M. Engineered PepFect14 analog for efficient cellular delivery of oligonucleotides. Biomed Pharmacother 2025;184:117872. [PMID: 39891949 DOI: 10.1016/j.biopha.2025.117872] [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: 09/05/2024] [Revised: 01/21/2025] [Accepted: 01/27/2025] [Indexed: 02/03/2025]  Open
9
Lalor R, Tanaka A, Shiels J, Dixit A, Hoadley S, Dufourd E, Hamon S, To J, Taggart CC, Weldon S, O'Brien B, Greer J, Dalton JP, Donnelly S. An immunoregulatory amphipathic peptide derived from Fasciola hepatica helminth defense molecule (FhHDM-1.C2) exhibits potent biotherapeutic activity in a murine model of multiple sclerosis. FASEB J 2025;39:e70380. [PMID: 39950309 PMCID: PMC11826375 DOI: 10.1096/fj.202400793rr] [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: 04/08/2024] [Revised: 01/22/2025] [Accepted: 01/29/2025] [Indexed: 02/16/2025]
10
Kumar N, Du Z, Li Y. pLM4CPPs: Protein Language Model-Based Predictor for Cell Penetrating Peptides. J Chem Inf Model 2025;65:1128-1139. [PMID: 39878455 DOI: 10.1021/acs.jcim.4c01338] [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: 01/31/2025]
11
Wu CY, Xu ZX, Li N, Qi DY, Wu HY, Ding H, Jin YT. Predicting cyclins based on key features and machine learning methods. Methods 2025;234:112-119. [PMID: 39694304 DOI: 10.1016/j.ymeth.2024.12.009] [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: 08/03/2024] [Revised: 12/12/2024] [Accepted: 12/15/2024] [Indexed: 12/20/2024]  Open
12
Basith S, Manavalan B, Lee G. AntiT2DMP-Pred: Leveraging feature fusion and optimization for superior machine learning prediction of type 2 diabetes mellitus. Methods 2025;234:264-274. [PMID: 39798942 DOI: 10.1016/j.ymeth.2025.01.003] [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: 10/31/2024] [Revised: 12/26/2024] [Accepted: 01/04/2025] [Indexed: 01/15/2025]  Open
13
Imre A, Balogh B, Mándity I. GraphCPP: The new state-of-the-art method for cell-penetrating peptide prediction via graph neural networks. Br J Pharmacol 2025;182:495-509. [PMID: 39568115 DOI: 10.1111/bph.17388] [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: 12/01/2023] [Revised: 08/07/2024] [Accepted: 10/07/2024] [Indexed: 11/22/2024]  Open
14
Ramasundaram M, Sohn H, Madhavan T. A bird's-eye view of the biological mechanism and machine learning prediction approaches for cell-penetrating peptides. Front Artif Intell 2025;7:1497307. [PMID: 39839972 PMCID: PMC11747587 DOI: 10.3389/frai.2024.1497307] [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: 09/16/2024] [Accepted: 12/13/2024] [Indexed: 01/23/2025]  Open
15
Moreno-Vargas LM, Prada-Gracia D. Exploring the Chemical Features and Biomedical Relevance of Cell-Penetrating Peptides. Int J Mol Sci 2024;26:59. [PMID: 39795918 PMCID: PMC11720145 DOI: 10.3390/ijms26010059] [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: 10/23/2024] [Revised: 11/27/2024] [Accepted: 11/28/2024] [Indexed: 01/13/2025]  Open
16
Zhu L, Chen Z, Yang S. EnDM-CPP: A Multi-view Explainable Framework Based on Deep Learning and Machine Learning for Identifying Cell-Penetrating Peptides with Transformers and Analyzing Sequence Information. Interdiscip Sci 2024:10.1007/s12539-024-00673-4. [PMID: 39714579 DOI: 10.1007/s12539-024-00673-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 10/28/2024] [Accepted: 11/01/2024] [Indexed: 12/24/2024]
17
Torres-Sánchez E, Lorca-Alonso I, González-de la Fuente S, Hernández-Ledesma B, Gutiérrez LF. Antioxidant Peptides from Sacha Inchi Meal: An In Vitro, Ex Vivo, and In Silico Approach. Foods 2024;13:3924. [PMID: 39682997 DOI: 10.3390/foods13233924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2024] [Revised: 11/25/2024] [Accepted: 12/03/2024] [Indexed: 12/18/2024]  Open
18
Chen XC, Kong XW, Chen P, Li ZQ, Huang N, Zhao Z, Yang J, Zhao GX, Mo Q, Lu YT, Huang XM, Feng GK, Zeng MS. Design and characterization of defined alpha-helix mini-proteins with intrinsic cell permeability. Comput Biol Chem 2024;113:108271. [PMID: 39504601 DOI: 10.1016/j.compbiolchem.2024.108271] [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: 04/12/2024] [Revised: 09/23/2024] [Accepted: 10/25/2024] [Indexed: 11/08/2024]
19
Basith S, Sangaraju VK, Manavalan B, Lee G. mHPpred: Accurate identification of peptide hormones using multi-view feature learning. Comput Biol Med 2024;183:109297. [PMID: 39442438 DOI: 10.1016/j.compbiomed.2024.109297] [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: 08/20/2024] [Revised: 10/04/2024] [Accepted: 10/15/2024] [Indexed: 10/25/2024]
20
Su RL, Cao XW, Zhao J, Wang FJ. A high hydrophobic moment arginine-rich peptide screened by a machine learning algorithm enhanced ADC antitumor activity. J Pept Sci 2024;30:e3628. [PMID: 38950972 DOI: 10.1002/psc.3628] [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: 03/10/2024] [Revised: 04/15/2024] [Accepted: 06/05/2024] [Indexed: 07/03/2024]
21
Maleš M, Juretić D, Zoranić L. Role of Peptide Associations in Enhancing the Antimicrobial Activity of Adepantins: Comparative Molecular Dynamics Simulations and Design Assessments. Int J Mol Sci 2024;25:12009. [PMID: 39596078 PMCID: PMC11593906 DOI: 10.3390/ijms252212009] [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: 09/22/2024] [Revised: 10/29/2024] [Accepted: 11/04/2024] [Indexed: 11/28/2024]  Open
22
Rončević T, Gerdol M, Pacor S, Cvitanović A, Begić A, Weber I, Krce L, Caporale A, Mardirossian M, Tossi A, Zoranić L. Antimicrobial Peptide with a Bent Helix Motif Identified in Parasitic Flatworm Mesocestoides corti. Int J Mol Sci 2024;25:11690. [PMID: 39519242 PMCID: PMC11546468 DOI: 10.3390/ijms252111690] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2024] [Revised: 10/25/2024] [Accepted: 10/27/2024] [Indexed: 11/16/2024]  Open
23
Ma H, Zhou X, Zhang Z, Weng Z, Li G, Zhou Y, Yao Y. AI-Driven Design of Cell-Penetrating Peptides for Therapeutic Biotechnology. Int J Pept Res Ther 2024;30:69. [DOI: 10.1007/s10989-024-10654-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/22/2024] [Indexed: 01/05/2025]
24
Patel P, Benzle K, Pei D, Wang GL. Cell-penetrating peptides for sustainable agriculture. TRENDS IN PLANT SCIENCE 2024;29:1131-1144. [PMID: 38902122 PMCID: PMC11449662 DOI: 10.1016/j.tplants.2024.05.011] [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: 02/19/2024] [Revised: 05/24/2024] [Accepted: 05/30/2024] [Indexed: 06/22/2024]
25
Ahmed Z, Shahzadi K, Temesgen SA, Ahmad B, Chen X, Ning L, Zulfiqar H, Lin H, Jin YT. A protein pre-trained model-based approach for the identification of the liquid-liquid phase separation (LLPS) proteins. Int J Biol Macromol 2024;277:134146. [PMID: 39067723 DOI: 10.1016/j.ijbiomac.2024.134146] [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: 05/02/2024] [Revised: 07/06/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024]
26
Jin YT, Tan Y, Gan ZH, Hao YD, Wang TY, Lin H, Tang B. Identification of DNase I hypersensitive sites in the human genome by multiple sequence descriptors. Methods 2024;229:125-132. [PMID: 38964595 DOI: 10.1016/j.ymeth.2024.06.012] [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: 05/02/2024] [Revised: 06/01/2024] [Accepted: 06/27/2024] [Indexed: 07/06/2024]  Open
27
Lopuszynski J, Wang J, Zahid M. Beyond Transduction: Anti-Inflammatory Effects of Cell Penetrating Peptides. Molecules 2024;29:4088. [PMID: 39274936 PMCID: PMC11397606 DOI: 10.3390/molecules29174088] [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: 07/31/2024] [Revised: 08/24/2024] [Accepted: 08/27/2024] [Indexed: 09/16/2024]  Open
28
Skog A, Paracini N, Gerelli Y, Skepö M. Translocation of Antimicrobial Peptides across Model Membranes: The Role of Peptide Chain Length. Mol Pharm 2024;21:4082-4097. [PMID: 38993084 PMCID: PMC11304388 DOI: 10.1021/acs.molpharmaceut.4c00450] [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: 04/25/2024] [Revised: 06/28/2024] [Accepted: 06/28/2024] [Indexed: 07/13/2024]
29
Zhang F, Li J, Wen Z, Fang C. FusPB-ESM2: Fusion model of ProtBERT and ESM-2 for cell-penetrating peptide prediction. Comput Biol Chem 2024;111:108098. [PMID: 38820799 DOI: 10.1016/j.compbiolchem.2024.108098] [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: 02/02/2024] [Revised: 04/18/2024] [Accepted: 05/16/2024] [Indexed: 06/02/2024]
30
Kuang K, Chen X, Wang M, Han W, Qiu X, Jin T, Xu R, Yuan B, Qian M, Li C, Xiang R, Li F, Zhang S, Yang Z, Du J, Li D, Zhang C, Wang Q, Jia T. Design and Discovery of New Collagen V-Derived FGF2-Blocking Natural Peptides Inhibiting Lung Squamous Cell Carcinoma In Vitro and In Vivo. J Med Chem 2024. [PMID: 39045829 DOI: 10.1021/acs.jmedchem.4c00654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
31
Basith S, Pham NT, Manavalan B, Lee G. SEP-AlgPro: An efficient allergen prediction tool utilizing traditional machine learning and deep learning techniques with protein language model features. Int J Biol Macromol 2024;273:133085. [PMID: 38871100 DOI: 10.1016/j.ijbiomac.2024.133085] [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: 11/24/2023] [Revised: 05/20/2024] [Accepted: 06/09/2024] [Indexed: 06/15/2024]
32
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
33
Eweje F, Walsh ML, Ahmad K, Ibrahim V, Alrefai A, Chen J, Chaikof EL. Protein-based nanoparticles for therapeutic nucleic acid delivery. Biomaterials 2024;305:122464. [PMID: 38181574 PMCID: PMC10872380 DOI: 10.1016/j.biomaterials.2023.122464] [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: 09/23/2023] [Revised: 12/25/2023] [Accepted: 12/31/2023] [Indexed: 01/07/2024]
34
Zhang HQ, Liu SH, Li R, Yu JW, Ye DX, Yuan SS, Lin H, Huang CB, Tang H. MIBPred: Ensemble Learning-Based Metal Ion-Binding Protein Classifier. ACS OMEGA 2024;9:8439-8447. [PMID: 38405489 PMCID: PMC10882704 DOI: 10.1021/acsomega.3c09587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 02/27/2024]
35
Preto AJ, Caniceiro AB, Duarte F, Fernandes H, Ferreira L, Mourão J, Moreira IS. POSEIDON: Peptidic Objects SEquence-based Interaction with cellular DOmaiNs: a new database and predictor. J Cheminform 2024;16:18. [PMID: 38365724 PMCID: PMC10874016 DOI: 10.1186/s13321-024-00810-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 02/07/2024] [Indexed: 02/18/2024]  Open
36
Shi K, Xiong Y, Wang Y, Deng Y, Wang W, Jing B, Gao X. PractiCPP: a deep learning approach tailored for extremely imbalanced datasets in cell-penetrating peptide prediction. Bioinformatics 2024;40:btae058. [PMID: 38305405 PMCID: PMC11212486 DOI: 10.1093/bioinformatics/btae058] [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: 11/29/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/03/2024]  Open
37
Shin HJ, Lee BK, Kang HA. Transdermal Properties of Cell-Penetrating Peptides: Applications and Skin Penetration Mechanisms. ACS APPLIED BIO MATERIALS 2024;7:1-16. [PMID: 38079575 DOI: 10.1021/acsabm.3c00659] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
38
Pham NT, Phan LT, Seo J, Kim Y, Song M, Lee S, Jeon YJ, Manavalan B. Advancing the accuracy of SARS-CoV-2 phosphorylation site detection via meta-learning approach. Brief Bioinform 2023;25:bbad433. [PMID: 38058187 PMCID: PMC10753650 DOI: 10.1093/bib/bbad433] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 10/30/2023] [Accepted: 11/05/2023] [Indexed: 12/08/2023]  Open
39
Zou X, Ren L, Cai P, Zhang Y, Ding H, Deng K, Yu X, Lin H, Huang C. Accurately identifying hemagglutinin using sequence information and machine learning methods. Front Med (Lausanne) 2023;10:1281880. [PMID: 38020152 PMCID: PMC10644030 DOI: 10.3389/fmed.2023.1281880] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023]  Open
40
Yan Y, Shi Z, Wei H. ROSes-FINDER: a multi-task deep learning framework for accurate prediction of microorganism reactive oxygen species scavenging enzymes. Front Microbiol 2023;14:1245805. [PMID: 37744924 PMCID: PMC10513406 DOI: 10.3389/fmicb.2023.1245805] [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: 06/23/2023] [Accepted: 08/21/2023] [Indexed: 09/26/2023]  Open
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Cui Z, Wang SG, He Y, Chen ZH, Zhang QH. DeepTPpred: A Deep Learning Approach With Matrix Factorization for Predicting Therapeutic Peptides by Integrating Length Information. IEEE J Biomed Health Inform 2023;27:4611-4622. [PMID: 37368803 DOI: 10.1109/jbhi.2023.3290014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
42
Momanyi BM, Zulfiqar H, Grace-Mercure BK, Ahmed Z, Ding H, Gao H, Liu F. CFNCM: Collaborative filtering neighborhood-based model for predicting miRNA-disease associations. Comput Biol Med 2023;163:107165. [PMID: 37315383 DOI: 10.1016/j.compbiomed.2023.107165] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/31/2023] [Accepted: 06/08/2023] [Indexed: 06/16/2023]
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Gori A, Lodigiani G, Colombarolli SG, Bergamaschi G, Vitali A. Cell Penetrating Peptides: Classification, Mechanisms, Methods of Study, and Applications. ChemMedChem 2023;18:e202300236. [PMID: 37389978 DOI: 10.1002/cmdc.202300236] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/28/2023] [Accepted: 06/28/2023] [Indexed: 07/02/2023]
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Saini S, Rathore A, Sharma S, Saini A. Exploratory data analysis of physicochemical parameters of natural antimicrobial and anticancer peptides: Unraveling the patterns and trends for the rational design of novel peptides. BIOIMPACTS : BI 2023;14:26438. [PMID: 38327633 PMCID: PMC10844588 DOI: 10.34172/bi.2023.26438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 11/04/2022] [Accepted: 12/04/2022] [Indexed: 02/09/2024]
45
Zhu W, Yuan SS, Li J, Huang CB, Lin H, Liao B. A First Computational Frame for Recognizing Heparin-Binding Protein. Diagnostics (Basel) 2023;13:2465. [PMID: 37510209 PMCID: PMC10377868 DOI: 10.3390/diagnostics13142465] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/13/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023]  Open
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da Silva Sanches PR, Sanchez-Velazquez R, Batista MN, Carneiro BM, Bittar C, De Lorenzo G, Rahal P, Patel AH, Cilli EM. Antiviral Evaluation of New Synthetic Bioconjugates Based on GA-Hecate: A New Class of Antivirals Targeting Different Steps of Zika Virus Replication. Molecules 2023;28:4884. [PMID: 37446546 PMCID: PMC10343505 DOI: 10.3390/molecules28134884] [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: 05/18/2023] [Revised: 06/05/2023] [Accepted: 06/15/2023] [Indexed: 07/15/2023]  Open
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Su W, Qian X, Yang K, Ding H, Huang C, Zhang Z. Recognition of outer membrane proteins using multiple feature fusion. Front Genet 2023;14:1211020. [PMID: 37351347 PMCID: PMC10284346 DOI: 10.3389/fgene.2023.1211020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 05/24/2023] [Indexed: 06/24/2023]  Open
48
Firoz A, Malik A, Ali HM, Akhter Y, Manavalan B, Kim CB. PRR-HyPred: A two-layer hybrid framework to predict pattern recognition receptors and their families by employing sequence encoded optimal features. Int J Biol Macromol 2023;234:123622. [PMID: 36773859 DOI: 10.1016/j.ijbiomac.2023.123622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023]
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Zulfiqar H, Ahmed Z, Kissanga Grace-Mercure B, Hassan F, Zhang ZY, Liu F. Computational prediction of promotors in Agrobacterium tumefaciens strain C58 by using the machine learning technique. Front Microbiol 2023;14:1170785. [PMID: 37125199 PMCID: PMC10133480 DOI: 10.3389/fmicb.2023.1170785] [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: 02/21/2023] [Accepted: 03/17/2023] [Indexed: 05/02/2023]  Open
50
Yang YH, Ma CY, Gao D, Liu XW, Yuan SS, Ding H. i2OM: Toward a better prediction of 2'-O-methylation in human RNA. Int J Biol Macromol 2023;239:124247. [PMID: 37003392 DOI: 10.1016/j.ijbiomac.2023.124247] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/06/2023] [Accepted: 03/22/2023] [Indexed: 04/03/2023]
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