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For: Deng L, Pan J, Xu X, Yang W, Liu C, Liu H. PDRLGB: precise DNA-binding residue prediction using a light gradient boosting machine. BMC Bioinformatics 2018;19:522. [PMID: 30598073 PMCID: PMC6311926 DOI: 10.1186/s12859-018-2527-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
Number Cited by Other Article(s)
1
Cai J, Zhao J, Bin Y, Xia J, Zheng C. iAmyP: A Multi-view Learning for Amyloidogenic Hexapeptides Identification Based on Sequence Least Squares Programming. Interdiscip Sci 2025;17:277-292. [PMID: 39546159 DOI: 10.1007/s12539-024-00666-3] [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] [Revised: 10/07/2024] [Accepted: 10/09/2024] [Indexed: 11/17/2024]
2
Tahmid MT, Hasan AKMM, Bayzid MS. TransBind allows precise detection of DNA-binding proteins and residues using language models and deep learning. Commun Biol 2025;8:568. [PMID: 40185915 PMCID: PMC11971327 DOI: 10.1038/s42003-025-07534-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/13/2025] [Indexed: 04/07/2025]  Open
3
Chen R, You Y, Liu Y, Sun X, Ma T, Lao X, Zheng H. Deep-Learning-Based Approaches for Rational Design of Stapled Peptides With High Antimicrobial Activity and Stability. Microb Biotechnol 2025;18:e70121. [PMID: 40042163 PMCID: PMC11881016 DOI: 10.1111/1751-7915.70121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2024] [Revised: 02/09/2025] [Accepted: 02/15/2025] [Indexed: 05/12/2025]  Open
4
Basu S, Yu J, Kihara D, Kurgan L. Twenty years of advances in prediction of nucleic acid-binding residues in protein sequences. Brief Bioinform 2024;26:bbaf016. [PMID: 39833102 PMCID: PMC11745544 DOI: 10.1093/bib/bbaf016] [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: 10/03/2024] [Revised: 12/24/2024] [Accepted: 01/06/2025] [Indexed: 01/22/2025]  Open
5
Kawai M, Fukuda A, Otomo R, Obata S, Minaga K, Asada M, Umemura A, Uenoyama Y, Hieda N, Morita T, Minami R, Marui S, Yamauchi Y, Nakai Y, Takada Y, Ikuta K, Yoshioka T, Mizukoshi K, Iwane K, Yamakawa G, Namikawa M, Sono M, Nagao M, Maruno T, Nakanishi Y, Hirai M, Kanda N, Shio S, Itani T, Fujii S, Kimura T, Matsumura K, Ohana M, Yazumi S, Kawanami C, Yamashita Y, Marusawa H, Watanabe T, Ito Y, Kudo M, Seno H. Early detection of pancreatic cancer by comprehensive serum miRNA sequencing with automated machine learning. Br J Cancer 2024;131:1158-1168. [PMID: 39198617 PMCID: PMC11442445 DOI: 10.1038/s41416-024-02794-5] [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: 10/26/2023] [Revised: 06/26/2024] [Accepted: 07/03/2024] [Indexed: 09/01/2024]  Open
6
Liu K, Geng S, Shen P, Zhao L, Zhou P, Liu W. Development and application of a machine learning-based predictive model for obstructive sleep apnea screening. Front Big Data 2024;7:1353469. [PMID: 38817683 PMCID: PMC11137315 DOI: 10.3389/fdata.2024.1353469] [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: 12/12/2023] [Accepted: 04/29/2024] [Indexed: 06/01/2024]  Open
7
Tao L, Zhou T, Wu Z, Hu F, Yang S, Kong X, Li C. ESPDHot: An Effective Machine Learning-Based Approach for Predicting Protein-DNA Interaction Hotspots. J Chem Inf Model 2024;64:3548-3557. [PMID: 38587997 DOI: 10.1021/acs.jcim.3c02011] [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: 04/10/2024]
8
Kabir MWU, Alawad DM, Pokhrel P, Hoque MT. DRBpred: A sequence-based machine learning method to effectively predict DNA- and RNA-binding residues. Comput Biol Med 2024;170:108081. [PMID: 38295475 PMCID: PMC10922697 DOI: 10.1016/j.compbiomed.2024.108081] [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: 08/16/2023] [Revised: 01/12/2024] [Accepted: 01/27/2024] [Indexed: 02/02/2024]
9
Zhu L, Wang L, Yang Z, Xu P, Yang S. PPSNO: A Feature-Rich SNO Sites Predictor by Stacking Ensemble Strategy from Protein Sequence-Derived Information. Interdiscip Sci 2024;16:192-217. [PMID: 38206557 DOI: 10.1007/s12539-023-00595-7] [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: 07/01/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 01/12/2024]
10
Zhang J, Basu S, Kurgan L. HybridDBRpred: improved sequence-based prediction of DNA-binding amino acids using annotations from structured complexes and disordered proteins. Nucleic Acids Res 2024;52:e10. [PMID: 38048333 PMCID: PMC10810184 DOI: 10.1093/nar/gkad1131] [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: 03/29/2023] [Accepted: 11/10/2023] [Indexed: 12/06/2023]  Open
11
Pradhan UK, Meher PK, Naha S, Pal S, Gupta S, Gupta A, Parsad R. RBPLight: a computational tool for discovery of plant-specific RNA-binding proteins using light gradient boosting machine and ensemble of evolutionary features. Brief Funct Genomics 2023;22:401-410. [PMID: 37158175 DOI: 10.1093/bfgp/elad016] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 04/12/2023] [Accepted: 04/21/2023] [Indexed: 05/10/2023]  Open
12
Jain A, Begum T, Ahmad S. Analysis and Prediction of Pathogen Nucleic Acid Specificity for Toll-like Receptors in Vertebrates. J Mol Biol 2023;435:168208. [PMID: 37479078 DOI: 10.1016/j.jmb.2023.168208] [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: 02/27/2023] [Revised: 06/20/2023] [Accepted: 07/13/2023] [Indexed: 07/23/2023]
13
Rai BK, Apgar JR, Bennett EM. Low-data interpretable deep learning prediction of antibody viscosity using a biophysically meaningful representation. Sci Rep 2023;13:2917. [PMID: 36806303 PMCID: PMC9941094 DOI: 10.1038/s41598-023-28841-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 01/25/2023] [Indexed: 02/22/2023]  Open
14
Zhu Y, Liu Y, Chen Y, Li L. ResSUMO: A Deep Learning Architecture Based on Residual Structure for Prediction of Lysine SUMOylation Sites. Cells 2022;11:2646. [PMID: 36078053 PMCID: PMC9454673 DOI: 10.3390/cells11172646] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 12/26/2022]  Open
15
Li J, Zhu W, Zhou J, Yun W, Li X, Guan Q, Lv W, Cheng Y, Ni H, Xie Z, Li M, Zhang L, Xu Y, Zhang Q. A Presurgical Unfavorable Prediction Scale of Endovascular Treatment for Acute Ischemic Stroke. Front Aging Neurosci 2022;14:942285. [PMID: 35847671 PMCID: PMC9284674 DOI: 10.3389/fnagi.2022.942285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 06/02/2022] [Indexed: 11/13/2022]  Open
16
Arya A, Mary Varghese D, Kumar Verma A, Ahmad S. Inadequacy of evolutionary profiles vis-a-vis single sequences in predicting transient DNA-binding sites in proteins. J Mol Biol 2022;434:167640. [PMID: 35597551 DOI: 10.1016/j.jmb.2022.167640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/01/2022] [Accepted: 05/16/2022] [Indexed: 10/18/2022]
17
A Comprehensive Review of Computation-Based Metal-Binding Prediction Approaches at the Residue Level. BIOMED RESEARCH INTERNATIONAL 2022;2022:8965712. [PMID: 35402609 PMCID: PMC8989566 DOI: 10.1155/2022/8965712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 03/04/2022] [Indexed: 12/29/2022]
18
Arif M, Ahmed S, Ge F, Kabir M, Khan YD, Yu DJ, Thafar M. StackACPred: Prediction of anticancer peptides by integrating optimized multiple feature descriptors with stacked ensemble approach. CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS 2022;220:104458. [DOI: 10.1016/j.chemolab.2021.104458] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2024]
19
Herrera-Bravo J, Farías JG, Contreras FP, Herrera-Belén L, Norambuena JA, Beltrán JF. VirVACPRED: A Web Server for Prediction of Protective Viral Antigens. Int J Pept Res Ther 2021;28:35. [PMID: 34934411 PMCID: PMC8679566 DOI: 10.1007/s10989-021-10345-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2021] [Indexed: 11/25/2022]
20
Arslan E, Schulz J, Rai K. Machine Learning in Epigenomics: Insights into Cancer Biology and Medicine. Biochim Biophys Acta Rev Cancer 2021;1876:188588. [PMID: 34245839 PMCID: PMC8595561 DOI: 10.1016/j.bbcan.2021.188588] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/29/2021] [Accepted: 07/02/2021] [Indexed: 02/01/2023]
21
Rauer C, Sen N, Waman VP, Abbasian M, Orengo CA. Computational approaches to predict protein functional families and functional sites. Curr Opin Struct Biol 2021;70:108-122. [PMID: 34225010 DOI: 10.1016/j.sbi.2021.05.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/13/2021] [Accepted: 05/25/2021] [Indexed: 01/06/2023]
22
Hendrix SG, Chang KY, Ryu Z, Xie ZR. DeepDISE: DNA Binding Site Prediction Using a Deep Learning Method. Int J Mol Sci 2021;22:ijms22115510. [PMID: 34073705 PMCID: PMC8197219 DOI: 10.3390/ijms22115510] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/30/2021] [Accepted: 05/19/2021] [Indexed: 11/18/2022]  Open
23
Chen YZ, Wang ZZ, Wang Y, Ying G, Chen Z, Song J. nhKcr: a new bioinformatics tool for predicting crotonylation sites on human nonhistone proteins based on deep learning. Brief Bioinform 2021;22:6277413. [PMID: 34002774 DOI: 10.1093/bib/bbab146] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/18/2021] [Accepted: 03/25/2021] [Indexed: 12/20/2022]  Open
24
Prasasty VD, Hutagalung RA, Gunadi R, Sofia DY, Rosmalena R, Yazid F, Sinaga E. Prediction of human-Streptococcus pneumoniae protein-protein interactions using logistic regression. Comput Biol Chem 2021;92:107492. [PMID: 33964803 DOI: 10.1016/j.compbiolchem.2021.107492] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/21/2021] [Indexed: 02/07/2023]
25
Development of machine learning model for diagnostic disease prediction based on laboratory tests. Sci Rep 2021;11:7567. [PMID: 33828178 PMCID: PMC8026627 DOI: 10.1038/s41598-021-87171-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 03/19/2021] [Indexed: 01/16/2023]  Open
26
Zhang Y, Chen P, Gao Y, Ni J, Wang X. DBP-PSSM: Combination of Evolutionary Profiles with the XGBoost Algorithm to Improve the Identification of DNA-binding Proteins. Comb Chem High Throughput Screen 2020;25:3-12. [PMID: 33238837 DOI: 10.2174/1386207323999201124203531] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 10/16/2020] [Accepted: 10/29/2020] [Indexed: 11/22/2022]
27
Bianchi J, de Oliveira Ruellas AC, Gonçalves JR, Paniagua B, Prieto JC, Styner M, Li T, Zhu H, Sugai J, Giannobile W, Benavides E, Soki F, Yatabe M, Ashman L, Walker D, Soroushmehr R, Najarian K, Cevidanes LHS. Osteoarthritis of the Temporomandibular Joint can be diagnosed earlier using biomarkers and machine learning. Sci Rep 2020;10:8012. [PMID: 32415284 PMCID: PMC7228972 DOI: 10.1038/s41598-020-64942-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 04/21/2020] [Indexed: 12/26/2022]  Open
28
Li F, Chen J, Ge Z, Wen Y, Yue Y, Hayashida M, Baggag A, Bensmail H, Song J. Computational prediction and interpretation of both general and specific types of promoters in Escherichia coli by exploiting a stacked ensemble-learning framework. Brief Bioinform 2020;22:2126-2140. [PMID: 32363397 DOI: 10.1093/bib/bbaa049] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/25/2020] [Accepted: 03/11/2020] [Indexed: 12/12/2022]  Open
29
Qiu H, Luo L, Su Z, Zhou L, Wang L, Chen Y. Machine learning approaches to predict peak demand days of cardiovascular admissions considering environmental exposure. BMC Med Inform Decis Mak 2020;20:83. [PMID: 32357880 PMCID: PMC7195717 DOI: 10.1186/s12911-020-1101-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/23/2020] [Indexed: 02/05/2023]  Open
30
Hyland SL, Faltys M, Hüser M, Lyu X, Gumbsch T, Esteban C, Bock C, Horn M, Moor M, Rieck B, Zimmermann M, Bodenham D, Borgwardt K, Rätsch G, Merz TM. Early prediction of circulatory failure in the intensive care unit using machine learning. Nat Med 2020;26:364-373. [DOI: 10.1038/s41591-020-0789-4] [Citation(s) in RCA: 196] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 02/04/2020] [Indexed: 01/12/2023]
31
PreDBA: A heterogeneous ensemble approach for predicting protein-DNA binding affinity. Sci Rep 2020;10:1278. [PMID: 31992738 PMCID: PMC6987227 DOI: 10.1038/s41598-020-57778-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 01/06/2020] [Indexed: 11/17/2022]  Open
32
Real-time automatic surgical phase recognition in laparoscopic sigmoidectomy using the convolutional neural network-based deep learning approach. Surg Endosc 2019;34:4924-4931. [PMID: 31797047 DOI: 10.1007/s00464-019-07281-0] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 11/23/2019] [Indexed: 02/06/2023]
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