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For: Chou KC, Shen HB. MemType-2L: A Web server for predicting membrane proteins and their types by incorporating evolution information through Pse-PSSM. Biochem Biophys Res Commun 2007;360:339-45. [PMID: 17586467 DOI: 10.1016/j.bbrc.2007.06.027] [Citation(s) in RCA: 307] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Accepted: 06/06/2007] [Indexed: 10/23/2022]
Number Cited by Other Article(s)
1
Rahman MA, Dalwani S, Venkatesan R. Structural enzymological studies of the long chain fatty acyl-CoA synthetase FadD5 from the mce1 operon of Mycobacterium tuberculosis. Biochem Biophys Res Commun 2025;769:151960. [PMID: 40347623 DOI: 10.1016/j.bbrc.2025.151960] [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: 03/07/2025] [Revised: 04/25/2025] [Accepted: 05/05/2025] [Indexed: 05/14/2025]
2
Leung K, Schaefer K, Lin Z, Yao Z, Wells JA. Engineered Proteins and Chemical Tools to Probe the Cell Surface Proteome. Chem Rev 2025;125:4069-4110. [PMID: 40178992 PMCID: PMC12022999 DOI: 10.1021/acs.chemrev.4c00554] [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: 07/25/2024] [Revised: 02/05/2025] [Accepted: 03/07/2025] [Indexed: 04/05/2025]
3
Xie W, Kong Y, Ren C, Wen Y, Ying M, Xing H. Chemistries on the inner leaflet of the cell membrane. Chem Commun (Camb) 2025;61:2387-2402. [PMID: 39810742 DOI: 10.1039/d4cc05186f] [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: 01/16/2025]
4
Xiong D, U K, Sun J, Cribbs AP. PLMC: Language Model of Protein Sequences Enhances Protein Crystallization Prediction. Interdiscip Sci 2024;16:802-813. [PMID: 39155325 DOI: 10.1007/s12539-024-00639-6] [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: 01/02/2024] [Revised: 05/13/2024] [Accepted: 05/21/2024] [Indexed: 08/20/2024]
5
Qi D, Song C, Liu T. PreDBP-PLMs: Prediction of DNA-binding proteins based on pre-trained protein language models and convolutional neural networks. Anal Biochem 2024;694:115603. [PMID: 38986796 DOI: 10.1016/j.ab.2024.115603] [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: 04/25/2024] [Revised: 06/15/2024] [Accepted: 07/06/2024] [Indexed: 07/12/2024]
6
Ruan X, Xia S, Li S, Su Z, Yang J. Hybrid framework for membrane protein type prediction based on the PSSM. Sci Rep 2024;14:17156. [PMID: 39060345 PMCID: PMC11282086 DOI: 10.1038/s41598-024-68163-7] [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: 01/14/2024] [Accepted: 07/22/2024] [Indexed: 07/28/2024]  Open
7
Ødum MT, Teufel F, Thumuluri V, Almagro Armenteros JJ, Johansen AR, Winther O, Nielsen H. DeepLoc 2.1: multi-label membrane protein type prediction using protein language models. Nucleic Acids Res 2024;52:W215-W220. [PMID: 38587188 PMCID: PMC11223819 DOI: 10.1093/nar/gkae237] [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: 01/31/2024] [Revised: 03/06/2024] [Accepted: 03/21/2024] [Indexed: 04/09/2024]  Open
8
Zheng D, Zhou S, Chen L, Pang G, Yang J. A deep learning method to predict bacterial ADP-ribosyltransferase toxins. Bioinformatics 2024;40:btae378. [PMID: 38885365 PMCID: PMC11219481 DOI: 10.1093/bioinformatics/btae378] [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: 04/27/2024] [Revised: 06/03/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024]  Open
9
Zhang X, Liu M, Li Z, Zhuo L, Fu X, Zou Q. Fusion of multi-source relationships and topology to infer lncRNA-protein interactions. MOLECULAR THERAPY. NUCLEIC ACIDS 2024;35:102187. [PMID: 38706631 PMCID: PMC11066462 DOI: 10.1016/j.omtn.2024.102187] [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: 12/18/2023] [Accepted: 04/03/2024] [Indexed: 05/07/2024]
10
Shen C, Mao D, Tang J, Liao Z, Chen S. Prediction of LncRNA-Protein Interactions Based on Kernel Combinations and Graph Convolutional Networks. IEEE J Biomed Health Inform 2024;28:1937-1948. [PMID: 37327093 DOI: 10.1109/jbhi.2023.3286917] [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: 06/18/2023]
11
Sun A, Li H, Dong G, Zhao Y, Zhang D. DBPboost:A method of classification of DNA-binding proteins based on improved differential evolution algorithm and feature extraction. Methods 2024;223:56-64. [PMID: 38237792 DOI: 10.1016/j.ymeth.2024.01.005] [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: 09/04/2023] [Revised: 12/29/2023] [Accepted: 01/13/2024] [Indexed: 02/01/2024]  Open
12
Ou YY, Ho QT, Chang HT. Recent advances in features generation for membrane protein sequences: From multiple sequence alignment to pre-trained language models. Proteomics 2023;23:e2200494. [PMID: 37863817 DOI: 10.1002/pmic.202200494] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/22/2023]
13
Shen J, Xia Y, Lu Y, Lu W, Qian M, Wu H, Fu Q, Chen J. Identification of membrane protein types via deep residual hypergraph neural network. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023;20:20188-20212. [PMID: 38052642 DOI: 10.3934/mbe.2023894] [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: 12/07/2023]
14
Liu Y, Guan S, Jiang T, Fu Q, Ma J, Cui Z, Ding Y, Wu H. DNA protein binding recognition based on lifelong learning. Comput Biol Med 2023;164:107094. [PMID: 37459792 DOI: 10.1016/j.compbiomed.2023.107094] [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: 04/01/2023] [Revised: 05/09/2023] [Accepted: 05/27/2023] [Indexed: 09/09/2023]
15
Fan R, Ding Y, Zou Q, Yuan L. Multi-view local hyperplane nearest neighbor model based on independence criterion for identifying vesicular transport proteins. Int J Biol Macromol 2023;247:125774. [PMID: 37437677 DOI: 10.1016/j.ijbiomac.2023.125774] [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: 05/11/2023] [Revised: 06/30/2023] [Accepted: 07/07/2023] [Indexed: 07/14/2023]
16
Grass GD, Ercan D, Obermayer AN, Shaw T, Stewart PA, Chahoud J, Dhillon J, Lopez A, Johnstone PAS, Rogatto SR, Spiess PE, Eschrich SA. An Assessment of the Penile Squamous Cell Carcinoma Surfaceome for Biomarker and Therapeutic Target Discovery. Cancers (Basel) 2023;15:3636. [PMID: 37509297 PMCID: PMC10377392 DOI: 10.3390/cancers15143636] [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: 06/01/2023] [Revised: 07/01/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023]  Open
17
Qian Y, Shang T, Guo F, Wang C, Cui Z, Ding Y, Wu H. Identification of DNA-binding protein based multiple kernel model. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023;20:13149-13170. [PMID: 37501482 DOI: 10.3934/mbe.2023586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
18
Ming Y, Liu H, Cui Y, Guo S, Ding Y, Liu R. Identification of DNA-binding proteins by Kernel Sparse Representation via L2,1-matrix norm. Comput Biol Med 2023;159:106849. [PMID: 37060772 DOI: 10.1016/j.compbiomed.2023.106849] [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: 12/14/2022] [Revised: 02/26/2023] [Accepted: 03/30/2023] [Indexed: 04/17/2023]
19
Overduin M, Kervin TA, Klarenbach Z, Adra TRC, Bhat RK. Comprehensive classification of proteins based on structures that engage lipids by COMPOSEL. Biophys Chem 2023;295:106971. [PMID: 36801589 DOI: 10.1016/j.bpc.2023.106971] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 02/05/2023] [Indexed: 02/11/2023]
20
Guan S, Qian Y, Jiang T, Jiang M, Ding Y, Wu H. MV-H-RKM: A Multiple View-Based Hypergraph Regularized Restricted Kernel Machine for Predicting DNA-Binding Proteins. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:1246-1256. [PMID: 35731758 DOI: 10.1109/tcbb.2022.3183191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
21
Qian Y, Ding Y, Zou Q, Guo F. Multi-View Kernel Sparse Representation for Identification of Membrane Protein Types. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:1234-1245. [PMID: 35857734 DOI: 10.1109/tcbb.2022.3191325] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
22
Sun J, Kulandaisamy A, Liu J, Hu K, Gromiha MM, Zhang Y. Machine learning in computational modelling of membrane protein sequences and structures: From methodologies to applications. Comput Struct Biotechnol J 2023;21:1205-1226. [PMID: 36817959 PMCID: PMC9932300 DOI: 10.1016/j.csbj.2023.01.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/16/2023] [Accepted: 01/25/2023] [Indexed: 01/29/2023]  Open
23
Vora DS, Kalakoti Y, Sundar D. Computational Methods and Deep Learning for Elucidating Protein Interaction Networks. Methods Mol Biol 2023;2553:285-323. [PMID: 36227550 DOI: 10.1007/978-1-0716-2617-7_15] [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: 06/16/2023]
24
Random Fourier features-based sparse representation classifier for identifying DNA-binding proteins. Comput Biol Med 2022;151:106268. [PMID: 36370585 DOI: 10.1016/j.compbiomed.2022.106268] [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] [Received: 08/24/2022] [Revised: 09/28/2022] [Accepted: 10/30/2022] [Indexed: 11/11/2022]
25
Jasni N, Saidin S, Kin WW, Arifin N, Othman N. Entamoeba histolytica: Membrane and Non-Membrane Protein Structure, Function, Immune Response Interaction, and Vaccine Development. MEMBRANES 2022;12:1079. [PMID: 36363634 PMCID: PMC9695907 DOI: 10.3390/membranes12111079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/26/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
26
Xiang R, Fernandez-Lopez L, Robles-Martín A, Ferrer M, Guallar V. EP-Pred: A Machine Learning Tool for Bioprospecting Promiscuous Ester Hydrolases. Biomolecules 2022;12:1529. [PMID: 36291739 PMCID: PMC9599548 DOI: 10.3390/biom12101529] [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: 09/02/2022] [Revised: 10/11/2022] [Accepted: 10/18/2022] [Indexed: 11/25/2022]  Open
27
Zhang T, Jia Y, Li H, Xu D, Zhou J, Wang G. CRISPRCasStack: a stacking strategy-based ensemble learning framework for accurate identification of Cas proteins. Brief Bioinform 2022;23:6674167. [PMID: 35998924 DOI: 10.1093/bib/bbac335] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/13/2022] [Accepted: 07/23/2022] [Indexed: 11/12/2022]  Open
28
Chen Y, Li S, Guo J. A method for identifying moonlighting proteins based on linear discriminant analysis and bagging-SVM. Front Genet 2022;13:963349. [PMID: 36046247 PMCID: PMC9420859 DOI: 10.3389/fgene.2022.963349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022]  Open
29
Fan R, Suo B, Ding Y. Identification of Vesicle Transport Proteins via Hypergraph Regularized K-Local Hyperplane Distance Nearest Neighbour Model. Front Genet 2022;13:960388. [PMID: 35910197 PMCID: PMC9326258 DOI: 10.3389/fgene.2022.960388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 06/22/2022] [Indexed: 12/04/2022]  Open
30
Chen Y, Li Z, Li Z. Prediction of Plant Resistance Proteins Based on Pairwise Energy Content and Stacking Framework. FRONTIERS IN PLANT SCIENCE 2022;13:912599. [PMID: 35712582 PMCID: PMC9194944 DOI: 10.3389/fpls.2022.912599] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
31
Lu W, Shen J, Zhang Y, Wu H, Qian Y, Chen X, Fu Q. Identifying Membrane Protein Types Based on Lifelong Learning With Dynamically Scalable Networks. Front Genet 2022;12:834488. [PMID: 35371189 PMCID: PMC8964460 DOI: 10.3389/fgene.2021.834488] [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: 12/13/2021] [Accepted: 12/21/2021] [Indexed: 11/13/2022]  Open
32
SE-BLTCNN: A Channel Attention Adapted Deep Learning Model Based on PSSM for Membrane Protein Classification. Comput Biol Chem 2022;98:107680. [DOI: 10.1016/j.compbiolchem.2022.107680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/07/2022] [Accepted: 04/04/2022] [Indexed: 11/17/2022]
33
Mohammadi A, Zahiri J, Mohammadi S, Khodarahmi M, Arab SS. PSSMCOOL: A Comprehensive R Package for Generating Evolutionary-based Descriptors of Protein Sequences from PSSM Profiles. BIOLOGY METHODS AND PROTOCOLS 2022;7:bpac008. [PMID: 35388370 PMCID: PMC8977839 DOI: 10.1093/biomethods/bpac008] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 01/21/2022] [Indexed: 11/14/2022]
34
Wang X, Li F, Xu J, Rong J, Webb GI, Ge Z, Li J, Song J. ASPIRER: a new computational approach for identifying non-classical secreted proteins based on deep learning. Brief Bioinform 2022;23:bbac031. [PMID: 35176756 PMCID: PMC8921646 DOI: 10.1093/bib/bbac031] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 01/10/2022] [Accepted: 01/22/2022] [Indexed: 12/15/2022]  Open
35
Tahir M, Khan F, Hayat M, Alshehri MD. An effective machine learning-based model for the prediction of protein–protein interaction sites in health systems. Neural Comput Appl 2022. [DOI: 10.1007/s00521-022-07024-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
36
Tu Y, Lei H, Shen HB, Yang Y. SIFLoc: a self-supervised pre-training method for enhancing the recognition of protein subcellular localization in immunofluorescence microscopic images. Brief Bioinform 2022;23:6527276. [DOI: 10.1093/bib/bbab605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/15/2021] [Accepted: 12/27/2021] [Indexed: 12/19/2022]  Open
37
Zhang Z, Gong Y, Gao B, Li H, Gao W, Zhao Y, Dong B. SNAREs-SAP: SNARE Proteins Identification With PSSM Profiles. Front Genet 2022;12:809001. [PMID: 34987554 PMCID: PMC8721734 DOI: 10.3389/fgene.2021.809001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 11/15/2021] [Indexed: 12/20/2022]  Open
38
Zou Y, Ding Y, Peng L, Zou Q. FTWSVM-SR: DNA-Binding Proteins Identification via Fuzzy Twin Support Vector Machines on Self-Representation. Interdiscip Sci 2021;14:372-384. [PMID: 34743286 DOI: 10.1007/s12539-021-00489-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 10/11/2021] [Accepted: 10/24/2021] [Indexed: 12/01/2022]
39
Alzahrani E, Alghamdi W, Ullah MZ, Khan YD. Identification of stress response proteins through fusion of machine learning models and statistical paradigms. Sci Rep 2021;11:21767. [PMID: 34741132 PMCID: PMC8571424 DOI: 10.1038/s41598-021-99083-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/13/2021] [Indexed: 11/08/2022]  Open
40
Agrawal S, Sisodia DS, Nagwani NK. Augmented sequence features and subcellular localization for functional characterization of unknown protein sequences. Med Biol Eng Comput 2021;59:2297-2310. [PMID: 34545514 DOI: 10.1007/s11517-021-02436-5] [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: 11/08/2020] [Accepted: 08/29/2021] [Indexed: 11/24/2022]
41
Ding Y, Tang J, Guo F. Protein Crystallization Identification via Fuzzy Model on Linear Neighborhood Representation. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021;18:1986-1995. [PMID: 31751248 DOI: 10.1109/tcbb.2019.2954826] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
42
Zhang Y, Ni J, Gao Y. RF-SVM: Identification of DNA-binding proteins based on comprehensive feature representation methods and support vector machine. Proteins 2021;90:395-404. [PMID: 34455627 DOI: 10.1002/prot.26229] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 08/10/2021] [Accepted: 08/24/2021] [Indexed: 01/07/2023]
43
Wang M, Yue L, Yang X, Wang X, Han Y, Yu B. Fertility-LightGBM: A fertility-related protein prediction model by multi-information fusion and light gradient boosting machine. Biomed Signal Process Control 2021. [DOI: 10.1016/j.bspc.2021.102630] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Wang S, Deng L, Xia X, Cao Z, Fei Y. Predicting antifreeze proteins with weighted generalized dipeptide composition and multi-regression feature selection ensemble. BMC Bioinformatics 2021;22:340. [PMID: 34162327 PMCID: PMC8220696 DOI: 10.1186/s12859-021-04251-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/09/2021] [Indexed: 12/15/2022]  Open
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Qian Y, Jiang L, Ding Y, Tang J, Guo F. A sequence-based multiple kernel model for identifying DNA-binding proteins. BMC Bioinformatics 2021;22:291. [PMID: 34058979 PMCID: PMC8167993 DOI: 10.1186/s12859-020-03875-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 11/13/2020] [Indexed: 11/18/2022]  Open
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Zhu YH, Hu J, Ge F, Li F, Song J, Zhang Y, Yu DJ. Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features. Brief Bioinform 2021;22:bbaa076. [PMID: 32436937 DOI: 10.1093/bib/bbaa076] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/09/2020] [Accepted: 04/13/2020] [Indexed: 11/13/2022]  Open
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Nanni L, Brahnam S. Robust ensemble of handcrafted and learned approaches for DNA-binding proteins. APPLIED COMPUTING AND INFORMATICS 2021. [DOI: 10.1108/aci-03-2021-0051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Zou Y, Wu H, Guo X, Peng L, Ding Y, Tang J, Guo F. MK-FSVM-SVDD: A Multiple Kernel-based Fuzzy SVM Model for Predicting DNA-binding Proteins via Support Vector Data Description. Curr Bioinform 2021. [DOI: 10.2174/1574893615999200607173829] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Sharifian Gh M. Recent Experimental Developments in Studying Passive Membrane Transport of Drug Molecules. Mol Pharm 2021;18:2122-2141. [PMID: 33914545 DOI: 10.1021/acs.molpharmaceut.1c00009] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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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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