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For: Song J, Wang Y, Li F, Akutsu T, Rawlings ND, Webb GI, Chou KC. iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites. Brief Bioinform 2020;20:638-658. [PMID: 29897410 PMCID: PMC6556904 DOI: 10.1093/bib/bby028] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 03/02/2018] [Indexed: 01/03/2023]  Open
Number Cited by Other Article(s)
1
Das S, Das A, Das N, Nath T, Langthasa M, Pandey P, Kumar V, Choure K, Kumar S, Pandey P. Harnessing the potential of microbial keratinases for bioconversion of keratin waste. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024:10.1007/s11356-024-34233-6. [PMID: 38985428 DOI: 10.1007/s11356-024-34233-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 06/30/2024] [Indexed: 07/11/2024]
2
Murter BM, Robinson SC, Banerjee H, Lau L, Uche U, Szymczak-Workman AL, Kane LP. Downregulation of PIK3IP1/TrIP on T cells is controlled by TCR signal strength, PKC, and metalloprotease-mediated cleavage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.591680. [PMID: 38746242 PMCID: PMC11092459 DOI: 10.1101/2024.04.29.591680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
3
Shen L, Sun X, Chen Z, Guo Y, Shen Z, Song Y, Xin W, Ding H, Ma X, Xu W, Zhou W, Che J, Tan L, Chen L, Chen S, Dong X, Fang L, Zhu F. ADCdb: the database of antibody-drug conjugates. Nucleic Acids Res 2024;52:D1097-D1109. [PMID: 37831118 PMCID: PMC10768060 DOI: 10.1093/nar/gkad831] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/07/2023] [Accepted: 09/28/2023] [Indexed: 10/14/2023]  Open
4
Ma X, Liang Y, Zhang S. iAVPs-ResBi: Identifying antiviral peptides by using deep residual network and bidirectional gated recurrent unit. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023;20:21563-21587. [PMID: 38124610 DOI: 10.3934/mbe.2023954] [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: 12/23/2023]
5
Lu C, Lubin JH, Sarma VV, Stentz SZ, Wang G, Wang S, Khare SD. Prediction and design of protease enzyme specificity using a structure-aware graph convolutional network. Proc Natl Acad Sci U S A 2023;120:e2303590120. [PMID: 37729196 PMCID: PMC10523478 DOI: 10.1073/pnas.2303590120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 08/14/2023] [Indexed: 09/22/2023]  Open
6
Li F, Wang C, Guo X, Akutsu T, Webb GI, Coin LJM, Kurgan L, Song J. ProsperousPlus: a one-stop and comprehensive platform for accurate protease-specific substrate cleavage prediction and machine-learning model construction. Brief Bioinform 2023;24:bbad372. [PMID: 37874948 DOI: 10.1093/bib/bbad372] [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: 07/30/2023] [Revised: 08/30/2023] [Accepted: 09/29/2023] [Indexed: 10/26/2023]  Open
7
Ameen SS, Griem-Krey N, Dufour A, Hossain MI, Hoque A, Sturgeon S, Nandurkar H, Draxler DF, Medcalf RL, Kamaruddin MA, Lucet IS, Leeming MG, Liu D, Dhillon A, Lim JP, Basheer F, Zhu HJ, Bokhari L, Roulston CL, Paradkar PN, Kleifeld O, Clarkson AN, Wellendorph P, Ciccotosto GD, Williamson NA, Ang CS, Cheng HC. N-Terminomic Changes in Neurons During Excitotoxicity Reveal Proteolytic Events Associated With Synaptic Dysfunctions and Potential Targets for Neuroprotection. Mol Cell Proteomics 2023;22:100543. [PMID: 37030595 PMCID: PMC10199228 DOI: 10.1016/j.mcpro.2023.100543] [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: 07/07/2022] [Revised: 02/23/2023] [Accepted: 04/04/2023] [Indexed: 04/10/2023]  Open
8
Tušar L, Loboda J, Impens F, Sosnowski P, Van Quickelberghe E, Vidmar R, Demol H, Sedeyn K, Saelens X, Vizovišek M, Mihelič M, Fonović M, Horvat J, Kosec G, Turk B, Gevaert K, Turk D. Proteomic data and structure analysis combined reveal interplay of structural rigidity and flexibility on selectivity of cysteine cathepsins. Commun Biol 2023;6:450. [PMID: 37095140 PMCID: PMC10124925 DOI: 10.1038/s42003-023-04772-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 03/28/2023] [Indexed: 04/26/2023]  Open
9
Lu C, Lubin JH, Sarma VV, Stentz SZ, Wang G, Wang S, Khare SD. Prediction and Design of Protease Enzyme Specificity Using a Structure-Aware Graph Convolutional Network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.16.528728. [PMID: 36824945 PMCID: PMC9949123 DOI: 10.1101/2023.02.16.528728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
10
Ding Y, He W, Tang J, Zou Q, Guo F. Laplacian Regularized Sparse Representation Based Classifier for Identifying DNA N4-Methylcytosine Sites via L2,1/2-Matrix Norm. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:500-511. [PMID: 34882559 DOI: 10.1109/tcbb.2021.3133309] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
11
Stanovova MV, Gazizova GR, Gorbushin AM. Transcriptomic profiling of immune-associated molecules in the coelomocytes of lugworm Arenicola marina (Linnaeus, 1758). JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2023;340:34-55. [PMID: 35438249 DOI: 10.1002/jez.b.23135] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/04/2022] [Accepted: 03/11/2022] [Indexed: 12/16/2022]
12
Henehan GT, Ryan BJ, Kinsella GK. Approaches to Avoid Proteolysis During Protein Expression and Purification. Methods Mol Biol 2023;2699:77-95. [PMID: 37646995 DOI: 10.1007/978-1-0716-3362-5_6] [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] [Indexed: 09/01/2023]
13
Bono N, Saroglia G, Marcuzzo S, Giagnorio E, Lauria G, Rosini E, De Nardo L, Athanassiou A, Candiani G, Perotto G. Silk fibroin microgels as a platform for cell microencapsulation. JOURNAL OF MATERIALS SCIENCE. MATERIALS IN MEDICINE 2022;34:3. [PMID: 36586059 PMCID: PMC9805413 DOI: 10.1007/s10856-022-06706-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
14
Onah E, Uzor PF, Ugwoke IC, Eze JU, Ugwuanyi ST, Chukwudi IR, Ibezim A. Prediction of HIV-1 protease cleavage site from octapeptide sequence information using selected classifiers and hybrid descriptors. BMC Bioinformatics 2022;23:466. [DOI: 10.1186/s12859-022-05017-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 10/11/2022] [Indexed: 11/10/2022]  Open
15
Yan K, Lv H, Guo Y, Peng W, Liu B. sAMPpred-GAT: prediction of antimicrobial peptide by graph attention network and predicted peptide structure. Bioinformatics 2022;39:6808615. [PMID: 36342186 PMCID: PMC9805557 DOI: 10.1093/bioinformatics/btac715] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 10/24/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022]  Open
16
Hu L, Li Z, Tang Z, Zhao C, Zhou X, Hu P. Effectively predicting HIV-1 protease cleavage sites by using an ensemble learning approach. BMC Bioinformatics 2022;23:447. [PMID: 36303135 PMCID: PMC9608884 DOI: 10.1186/s12859-022-04999-y] [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: 04/26/2022] [Accepted: 10/13/2022] [Indexed: 11/10/2022]  Open
17
FRTpred: A novel approach for accurate prediction of protein folding rate and type. Comput Biol Med 2022;149:105911. [DOI: 10.1016/j.compbiomed.2022.105911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/08/2022] [Accepted: 07/23/2022] [Indexed: 11/20/2022]
18
Hu J, Wang J, Li J, Hu H, Wu B, Ren H, Wang J. AHLS-pred: a novel sequence-based predictor of acyl-homoserine-lactone synthases using machine learning algorithms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022;14:616-631. [PMID: 35403334 DOI: 10.1111/1758-2229.13068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 06/14/2023]
19
Bell PA, Scheuermann S, Renner F, Pan CL, Lu HY, Turvey SE, Bornancin F, Régnier CH, Overall CM. Integrating knowledge of protein sequence with protein function for the prediction and validation of new MALT1 substrates. Comput Struct Biotechnol J 2022;20:4717-4732. [PMID: 36147669 PMCID: PMC9463181 DOI: 10.1016/j.csbj.2022.08.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/07/2022] [Accepted: 08/08/2022] [Indexed: 11/30/2022]  Open
20
Asim MN, Ibrahim MA, Imran Malik M, Dengel A, Ahmed S. Circ-LocNet: A Computational Framework for Circular RNA Sub-Cellular Localization Prediction. Int J Mol Sci 2022;23:ijms23158221. [PMID: 35897818 PMCID: PMC9329987 DOI: 10.3390/ijms23158221] [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: 06/16/2022] [Revised: 07/15/2022] [Accepted: 07/20/2022] [Indexed: 02/04/2023]  Open
21
Soleimany AP, Martin-Alonso C, Anahtar M, Wang CS, Bhatia SN. Protease Activity Analysis: A Toolkit for Analyzing Enzyme Activity Data. ACS OMEGA 2022;7:24292-24301. [PMID: 35874224 PMCID: PMC9301967 DOI: 10.1021/acsomega.2c01559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
22
Rezende PM, Xavier JS, Ascher DB, Fernandes GR, Pires DEV. Evaluating hierarchical machine learning approaches to classify biological databases. Brief Bioinform 2022;23:6611916. [PMID: 35724625 PMCID: PMC9310517 DOI: 10.1093/bib/bbac216] [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: 12/21/2021] [Revised: 04/29/2022] [Accepted: 05/09/2022] [Indexed: 12/04/2022]  Open
23
Deep Learning-Based Advances In Protein Posttranslational Modification Site and Protein Cleavage Prediction. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022;2499:285-322. [PMID: 35696087 DOI: 10.1007/978-1-0716-2317-6_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
24
Matrikines as mediators of tissue remodelling. Adv Drug Deliv Rev 2022;185:114240. [PMID: 35378216 DOI: 10.1016/j.addr.2022.114240] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/21/2022] [Accepted: 03/26/2022] [Indexed: 11/21/2022]
25
Naseer S, Hussain W, Khan YD, Rasool N. iPhosS(Deep)-PseAAC: Identification of Phosphoserine Sites in Proteins Using Deep Learning on General Pseudo Amino Acid Compositions. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:1703-1714. [PMID: 33242308 DOI: 10.1109/tcbb.2020.3040747] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
26
Identification of D Modification Sites Using a Random Forest Model Based on Nucleotide Chemical Properties. Int J Mol Sci 2022;23:ijms23063044. [PMID: 35328461 PMCID: PMC8950657 DOI: 10.3390/ijms23063044] [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: 02/08/2022] [Revised: 02/25/2022] [Accepted: 03/09/2022] [Indexed: 12/03/2022]  Open
27
Gupta Y, Maciorowski D, Medernach B, Becker DP, Durvasula R, Libertin CR, Kempaiah P. Iron dysregulation in COVID-19 and reciprocal evolution of SARS-CoV-2: Natura nihil frustra facit. J Cell Biochem 2022;123:601-619. [PMID: 34997606 PMCID: PMC9015563 DOI: 10.1002/jcb.30207] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/16/2021] [Indexed: 12/12/2022]
28
Shahid M, Ilyas M, Hussain W, Khan YD. ORI-Deep: improving the accuracy for predicting origin of replication sites by using a blend of features and long short-term memory network. Brief Bioinform 2022;23:6511972. [PMID: 35048955 DOI: 10.1093/bib/bbac001] [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: 11/04/2021] [Revised: 12/30/2021] [Accepted: 01/02/2022] [Indexed: 11/14/2022]  Open
29
Dyer RP, Weiss GA. Making the cut with protease engineering. Cell Chem Biol 2021;29:177-190. [PMID: 34921772 PMCID: PMC9127713 DOI: 10.1016/j.chembiol.2021.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 07/30/2021] [Accepted: 11/29/2021] [Indexed: 12/30/2022]
30
Fu T, Li F, Zhang Y, Yin J, Qiu W, Li X, Liu X, Xin W, Wang C, Yu L, Gao J, Zheng Q, Zeng S, Zhu F. VARIDT 2.0: structural variability of drug transporter. Nucleic Acids Res 2021;50:D1417-D1431. [PMID: 34747471 PMCID: PMC8728241 DOI: 10.1093/nar/gkab1013] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/08/2021] [Accepted: 11/04/2021] [Indexed: 12/20/2022]  Open
31
Zhao YW, Zhang S, Ding H. Recent development of machine learning methods in sumoylation sites prediction. Curr Med Chem 2021;29:894-907. [PMID: 34525906 DOI: 10.2174/0929867328666210915112030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/24/2021] [Accepted: 08/07/2021] [Indexed: 11/22/2022]
32
Melo MCR, Maasch JRMA, de la Fuente-Nunez C. Accelerating antibiotic discovery through artificial intelligence. Commun Biol 2021;4:1050. [PMID: 34504303 PMCID: PMC8429579 DOI: 10.1038/s42003-021-02586-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 07/16/2021] [Indexed: 02/07/2023]  Open
33
Akmal MA, Hussain W, Rasool N, Khan YD, Khan SA, Chou KC. Using CHOU'S 5-Steps Rule to Predict O-Linked Serine Glycosylation Sites by Blending Position Relative Features and Statistical Moment. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021;18:2045-2056. [PMID: 31985438 DOI: 10.1109/tcbb.2020.2968441] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
34
Yan K, Wen J, Liu JX, Xu Y, Liu B. Protein Fold Recognition by Combining Support Vector Machines and Pairwise Sequence Similarity Scores. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021;18:2008-2016. [PMID: 31940548 DOI: 10.1109/tcbb.2020.2966450] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
35
Jia C, Zhang M, Fan C, Li F, Song J. Formator: Predicting Lysine Formylation Sites Based on the Most Distant Undersampling and Safe-Level Synthetic Minority Oversampling. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021;18:1937-1945. [PMID: 31804942 DOI: 10.1109/tcbb.2019.2957758] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
36
Perpetuo L, Klein J, Ferreira R, Guedes S, Amado F, Leite-Moreira A, Silva AMS, Thongboonkerd V, Vitorino R. How can artificial intelligence be used for peptidomics? Expert Rev Proteomics 2021;18:527-556. [PMID: 34343059 DOI: 10.1080/14789450.2021.1962303] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
37
He S, Kong L, Chen J. iDNA6mA-Rice-DL: A local web server for identifying DNA N6-methyladenine sites in rice genome by deep learning method. J Bioinform Comput Biol 2021;19:2150019. [PMID: 34291710 DOI: 10.1142/s0219720021500190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
38
Vandooren J, Pereira RVS, Ugarte-Berzal E, Rybakin V, Noppen S, Stas MR, Bernaerts E, Ganseman E, Metzemaekers M, Schols D, Proost P, Opdenakker G. Internal Disulfide Bonding and Glycosylation of Interleukin-7 Protect Against Proteolytic Inactivation by Neutrophil Metalloproteinases and Serine Proteases. Front Immunol 2021;12:701739. [PMID: 34276694 PMCID: PMC8278288 DOI: 10.3389/fimmu.2021.701739] [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: 04/28/2021] [Accepted: 06/14/2021] [Indexed: 11/13/2022]  Open
39
Lai X, Tang J, ElSayed MEH. Recent advances in proteolytic stability for peptide, protein, and antibody drug discovery. Expert Opin Drug Discov 2021;16:1467-1482. [PMID: 34187273 DOI: 10.1080/17460441.2021.1942837] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
40
Li Q. Structure, Application, and Biochemistry of Microbial Keratinases. Front Microbiol 2021;12:674345. [PMID: 34248885 PMCID: PMC8260994 DOI: 10.3389/fmicb.2021.674345] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/17/2021] [Indexed: 12/17/2022]  Open
41
Malebary SJ, Khan YD. Evaluating machine learning methodologies for identification of cancer driver genes. Sci Rep 2021;11:12281. [PMID: 34112883 PMCID: PMC8192921 DOI: 10.1038/s41598-021-91656-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 05/19/2021] [Indexed: 02/06/2023]  Open
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Naseer S, Hussain W, Khan YD, Rasool N. NPalmitoylDeep-PseAAC: A Predictor of N-Palmitoylation Sites in Proteins Using Deep Representations of Proteins and PseAAC via Modified 5-Steps Rule. Curr Bioinform 2021. [DOI: 10.2174/1574893615999200605142828] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Liu S, Tang H, Liu H, Wang J. Multi-label Learning for the Diagnosis of Cancer and Identification of Novel Biomarkers with High-throughput Omics. Curr Bioinform 2021. [DOI: 10.2174/1574893615999200623130416] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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iAmideV-Deep: Valine Amidation Site Prediction in Proteins Using Deep Learning and Pseudo Amino Acid Compositions. Symmetry (Basel) 2021. [DOI: 10.3390/sym13040560] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]  Open
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Li Z, Hu L, Tang Z, Zhao C. Predicting HIV-1 Protease Cleavage Sites With Positive-Unlabeled Learning. Front Genet 2021;12:658078. [PMID: 33868387 PMCID: PMC8044780 DOI: 10.3389/fgene.2021.658078] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/08/2021] [Indexed: 11/13/2022]  Open
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Ozols M, Eckersley A, Platt CI, Stewart-McGuinness C, Hibbert SA, Revote J, Li F, Griffiths CEM, Watson REB, Song J, Bell M, Sherratt MJ. Predicting Proteolysis in Complex Proteomes Using Deep Learning. Int J Mol Sci 2021;22:3071. [PMID: 33803033 PMCID: PMC8002881 DOI: 10.3390/ijms22063071] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/10/2021] [Accepted: 03/12/2021] [Indexed: 12/27/2022]  Open
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Mapping specificity, cleavage entropy, allosteric changes and substrates of blood proteases in a high-throughput screen. Nat Commun 2021;12:1693. [PMID: 33727531 PMCID: PMC7966775 DOI: 10.1038/s41467-021-21754-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 02/10/2021] [Indexed: 02/06/2023]  Open
48
Awais M, Hussain W, Khan YD, Rasool N, Khan SA, Chou KC. iPhosH-PseAAC: Identify Phosphohistidine Sites in Proteins by Blending Statistical Moments and Position Relative Features According to the Chou's 5-Step Rule and General Pseudo Amino Acid Composition. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021;18:596-610. [PMID: 31144645 DOI: 10.1109/tcbb.2019.2919025] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
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Dowell AC, Munford H, Goel A, Gordon NS, James ND, Cheng KK, Zeegers MP, Ward DG, Bryan RT. PD-L2 Is Constitutively Expressed in Normal and Malignant Urothelium. Front Oncol 2021;11:626748. [PMID: 33718196 PMCID: PMC7951139 DOI: 10.3389/fonc.2021.626748] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/15/2021] [Indexed: 11/14/2022]  Open
50
iDRP-PseAAC: Identification of DNA Replication Proteins Using General PseAAC and Position Dependent Features. Int J Pept Res Ther 2021;27:1315-1329. [PMID: 33584161 PMCID: PMC7869428 DOI: 10.1007/s10989-021-10170-7] [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] [Accepted: 01/18/2021] [Indexed: 10/25/2022]
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