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For: Ofran Y, Mysore V, Rost B. Prediction of DNA-binding residues from sequence. ACTA ACUST UNITED AC 2007;23:i347-53. [PMID: 17646316 DOI: 10.1093/bioinformatics/btm174] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Number Cited by Other Article(s)
1
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
2
Pradhan UK, Meher PK, Naha S, Sharma NK, Agarwal A, Gupta A, Parsad R. DBPMod: a supervised learning model for computational recognition of DNA-binding proteins in model organisms. Brief Funct Genomics 2024;23:363-372. [PMID: 37651627 DOI: 10.1093/bfgp/elad039] [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: 05/08/2023] [Revised: 08/09/2023] [Accepted: 08/15/2023] [Indexed: 09/02/2023]  Open
3
Jia P, Zhang F, Wu C, Li M. A comprehensive review of protein-centric predictors for biomolecular interactions: from proteins to nucleic acids and beyond. Brief Bioinform 2024;25:bbae162. [PMID: 38739759 PMCID: PMC11089422 DOI: 10.1093/bib/bbae162] [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: 01/01/2024] [Revised: 02/17/2024] [Accepted: 03/31/2024] [Indexed: 05/16/2024]  Open
4
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
5
Zhu YH, Liu Z, Liu Y, Ji Z, Yu DJ. ULDNA: integrating unsupervised multi-source language models with LSTM-attention network for high-accuracy protein-DNA binding site prediction. Brief Bioinform 2024;25:bbae040. [PMID: 38349057 PMCID: PMC10939370 DOI: 10.1093/bib/bbae040] [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: 09/10/2023] [Revised: 01/02/2024] [Accepted: 01/22/2024] [Indexed: 02/15/2024]  Open
6
Guan S, Zou Q, Wu H, Ding Y. Protein-DNA Binding Residues Prediction Using a Deep Learning Model With Hierarchical Feature Extraction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:2619-2628. [PMID: 35834447 DOI: 10.1109/tcbb.2022.3190933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
7
Luo S, Xiong D, Zhao X, Duan L. An Attempt of Seeking Favorable Binding Free Energy Prediction Schemes Considering the Entropic Effect on Fis-DNA Binding. J Phys Chem B 2023;127:1312-1324. [PMID: 36735878 DOI: 10.1021/acs.jpcb.2c07811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
8
Manavi F, Sharma A, Sharma R, Tsunoda T, Shatabda S, Dehzangi I. CNN-Pred: Prediction of single-stranded and double-stranded DNA-binding protein using convolutional neural networks. Gene X 2023;853:147045. [PMID: 36503892 DOI: 10.1016/j.gene.2022.147045] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/10/2022] [Accepted: 11/08/2022] [Indexed: 11/27/2022]  Open
9
Pradhan UK, Meher PK, Naha S, Pal S, Gupta A, Parsad R. PlDBPred: a novel computational model for discovery of DNA binding proteins in plants. Brief Bioinform 2023;24:6840070. [PMID: 36416116 DOI: 10.1093/bib/bbac483] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 11/24/2022]  Open
10
He X, Chen X, Wang Y. Mass Spectrometry for Assessing Protein-Nucleic Acid Interactions. Anal Chem 2023;95:115-127. [PMID: 36625126 PMCID: PMC9869667 DOI: 10.1021/acs.analchem.2c04353] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
11
Varghese DM, Nussinov R, Ahmad S. Predictive modeling of moonlighting DNA-binding proteins. NAR Genom Bioinform 2022;4:lqac091. [PMID: 36474806 PMCID: PMC9716651 DOI: 10.1093/nargab/lqac091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 10/25/2022] [Accepted: 11/11/2022] [Indexed: 09/10/2024]  Open
12
Hu J, Bai YS, Zheng LL, Jia NX, Yu DJ, Zhang GJ. Protein-DNA Binding Residue Prediction via Bagging Strategy and Sequence-Based Cube-Format Feature. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:3635-3645. [PMID: 34714748 DOI: 10.1109/tcbb.2021.3123828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
13
Patiyal S, Dhall A, Raghava GPS. A deep learning-based method for the prediction of DNA interacting residues in a protein. Brief Bioinform 2022;23:6658239. [PMID: 35943134 DOI: 10.1093/bib/bbac322] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/01/2022] [Accepted: 07/15/2022] [Indexed: 11/13/2022]  Open
14
Xu D, Yang C, Fan H, Qiu W, Huang B, Zhuo R, He Z, Li H, Han X. Genome-Wide Characterization, Evolutionary Analysis of ARF Gene Family, and the Role of SaARF4 in Cd Accumulation of Sedum alfredii Hance. PLANTS (BASEL, SWITZERLAND) 2022;11:1273. [PMID: 35567274 PMCID: PMC9103128 DOI: 10.3390/plants11091273] [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: 03/23/2022] [Revised: 04/28/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
15
Cui F, Zhang Z, Cao C, Zou Q, Chen D, Su X. Protein-DNA/RNA interactions: Machine intelligence tools and approaches in the era of artificial intelligence and big data. Proteomics 2022;22:e2100197. [PMID: 35112474 DOI: 10.1002/pmic.202100197] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/02/2022] [Accepted: 01/17/2022] [Indexed: 11/09/2022]
16
Marques-Pereira C, Pires M, Moreira IS. Discovery of Virus-Host interactions using bioinformatic tools. Methods Cell Biol 2022;169:169-198. [PMID: 35623701 DOI: 10.1016/bs.mcb.2022.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
17
Littmann M, Heinzinger M, Dallago C, Weissenow K, Rost B. Protein embeddings and deep learning predict binding residues for various ligand classes. Sci Rep 2021;11:23916. [PMID: 34903827 PMCID: PMC8668950 DOI: 10.1038/s41598-021-03431-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/02/2021] [Indexed: 01/27/2023]  Open
18
Zhang J, Ghadermarzi S, Katuwawala A, Kurgan L. DNAgenie: accurate prediction of DNA-type-specific binding residues in protein sequences. Brief Bioinform 2021;22:6355416. [PMID: 34415020 DOI: 10.1093/bib/bbab336] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/02/2021] [Accepted: 07/28/2021] [Indexed: 01/02/2023]  Open
19
Ferraz RAC, Lopes ALG, da Silva JAF, Moreira DFV, Ferreira MJN, de Almeida Coimbra SV. DNA-protein interaction studies: a historical and comparative analysis. PLANT METHODS 2021;17:82. [PMID: 34301293 PMCID: PMC8299673 DOI: 10.1186/s13007-021-00780-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 07/11/2021] [Indexed: 05/05/2023]
20
Suvorova IA, Gelfand MS. Comparative Analysis of the IclR-Family of Bacterial Transcription Factors and Their DNA-Binding Motifs: Structure, Positioning, Co-Evolution, Regulon Content. Front Microbiol 2021;12:675815. [PMID: 34177859 PMCID: PMC8222616 DOI: 10.3389/fmicb.2021.675815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/14/2021] [Indexed: 11/13/2022]  Open
21
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
22
Li G, Du X, Li X, Zou L, Zhang G, Wu Z. Prediction of DNA binding proteins using local features and long-term dependencies with primary sequences based on deep learning. PeerJ 2021;9:e11262. [PMID: 33986992 PMCID: PMC8101451 DOI: 10.7717/peerj.11262] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 03/22/2021] [Indexed: 12/12/2022]  Open
23
Annie Lee ES, Zhou P, Wong AKC. WeMine Aligned Pattern Clustering System for Biosequence Pattern Analysis. Bioinformatics 2021. [DOI: 10.36255/exonpublications.bioinformatics.2021.ch8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
24
Sharma R, Kumar S, Tsunoda T, Kumarevel T, Sharma A. Single-stranded and double-stranded DNA-binding protein prediction using HMM profiles. Anal Biochem 2020;612:113954. [PMID: 32946833 DOI: 10.1016/j.ab.2020.113954] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/26/2020] [Accepted: 09/10/2020] [Indexed: 10/23/2022]
25
Xia X. Beyond Trees: Regulons and Regulatory Motif Characterization. Genes (Basel) 2020;11:genes11090995. [PMID: 32854400 PMCID: PMC7564462 DOI: 10.3390/genes11090995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 08/13/2020] [Accepted: 08/24/2020] [Indexed: 12/14/2022]  Open
26
Amirkhani A, Kolahdoozi M, Wang C, Kurgan LA. Prediction of DNA-Binding Residues in Local Segments of Protein Sequences with Fuzzy Cognitive Maps. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020;17:1372-1382. [PMID: 30602422 DOI: 10.1109/tcbb.2018.2890261] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
27
Qiu J, Bernhofer M, Heinzinger M, Kemper S, Norambuena T, Melo F, Rost B. ProNA2020 predicts protein-DNA, protein-RNA, and protein-protein binding proteins and residues from sequence. J Mol Biol 2020;432:2428-2443. [PMID: 32142788 DOI: 10.1016/j.jmb.2020.02.026] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 02/17/2020] [Accepted: 02/23/2020] [Indexed: 11/29/2022]
28
Zhao J, Cao Y, Zhang L. Exploring the computational methods for protein-ligand binding site prediction. Comput Struct Biotechnol J 2020;18:417-426. [PMID: 32140203 PMCID: PMC7049599 DOI: 10.1016/j.csbj.2020.02.008] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/23/2020] [Accepted: 02/11/2020] [Indexed: 12/21/2022]  Open
29
Zhou J, Lu Q, Xu R, Gui L, Wang H. EL_LSTM: Prediction of DNA-Binding Residue from Protein Sequence by Combining Long Short-Term Memory and Ensemble Learning. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020;17:124-135. [PMID: 30040656 DOI: 10.1109/tcbb.2018.2858806] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
30
Zhao Z, Xu Y, Zhao Y. SXGBsite: Prediction of Protein-Ligand Binding Sites Using Sequence Information and Extreme Gradient Boosting. Genes (Basel) 2019;10:E965. [PMID: 31771119 PMCID: PMC6947422 DOI: 10.3390/genes10120965] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/19/2019] [Accepted: 11/19/2019] [Indexed: 12/13/2022]  Open
31
Blanco JD, Radusky L, Climente-González H, Serrano L. FoldX accurate structural protein-DNA binding prediction using PADA1 (Protein Assisted DNA Assembly 1). Nucleic Acids Res 2019;46:3852-3863. [PMID: 29608705 PMCID: PMC5934639 DOI: 10.1093/nar/gky228] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 03/20/2018] [Indexed: 12/20/2022]  Open
32
Zhu YH, Hu J, Song XN, Yu DJ. DNAPred: Accurate Identification of DNA-Binding Sites from Protein Sequence by Ensembled Hyperplane-Distance-Based Support Vector Machines. J Chem Inf Model 2019;59:3057-3071. [PMID: 30943723 DOI: 10.1021/acs.jcim.8b00749] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
33
Survey of Computational Approaches for Prediction of DNA-Binding Residues on Protein Surfaces. Methods Mol Biol 2018. [PMID: 29536446 DOI: 10.1007/978-1-4939-7717-8_13] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
34
Identification of DNA-protein Binding Sites through Multi-Scale Local Average Blocks on Sequence Information. Molecules 2017;22:molecules22122079. [PMID: 29182548 PMCID: PMC6149935 DOI: 10.3390/molecules22122079] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/22/2017] [Accepted: 11/24/2017] [Indexed: 12/25/2022]  Open
35
Ding Y, Tang J, Guo F. Identification of Protein-Ligand Binding Sites by Sequence Information and Ensemble Classifier. J Chem Inf Model 2017;57:3149-3161. [PMID: 29125297 DOI: 10.1021/acs.jcim.7b00307] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
36
Hu J, Li Y, Zhang M, Yang X, Shen HB, Yu DJ. Predicting Protein-DNA Binding Residues by Weightedly Combining Sequence-Based Features and Boosting Multiple SVMs. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2017;14:1389-1398. [PMID: 27740495 DOI: 10.1109/tcbb.2016.2616469] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
37
Molecular Skin Surface-Based Transformation Visualization between Biological Macromolecules. JOURNAL OF HEALTHCARE ENGINEERING 2017;2017:4818604. [PMID: 29065609 PMCID: PMC5415869 DOI: 10.1155/2017/4818604] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/10/2017] [Indexed: 01/08/2023]
38
Yan J, Kurgan L. DRNApred, fast sequence-based method that accurately predicts and discriminates DNA- and RNA-binding residues. Nucleic Acids Res 2017;45:e84. [PMID: 28132027 PMCID: PMC5449545 DOI: 10.1093/nar/gkx059] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 01/24/2017] [Indexed: 01/18/2023]  Open
39
Zhou J, Lu Q, Xu R, He Y, Wang H. EL_PSSM-RT: DNA-binding residue prediction by integrating ensemble learning with PSSM Relation Transformation. BMC Bioinformatics 2017;18:379. [PMID: 28851273 PMCID: PMC5576297 DOI: 10.1186/s12859-017-1792-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 08/15/2017] [Indexed: 11/23/2022]  Open
40
Lee ESA, Sze-To HYA, Wong MH, Leung KS, Lau TCK, Wong AKC. Discovering Protein-DNA Binding Cores by Aligned Pattern Clustering. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2017;14:254-263. [PMID: 26336137 DOI: 10.1109/tcbb.2015.2474376] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
41
Zhao YN, Piao YZ, Zhang CM, Jiang YM, Liu A, Cui SH, Zhi DF, Zhen YH, Zhang SB. Replacement of quaternary ammonium headgroups by tri-ornithine in cationic lipids for the improvement of gene delivery in vitro and in vivo. J Mater Chem B 2017;5:7963-7973. [DOI: 10.1039/c7tb01915g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
42
Dutta S, Madan S, Parikh H, Sundar D. An ensemble micro neural network approach for elucidating interactions between zinc finger proteins and their target DNA. BMC Genomics 2016;17:1033. [PMID: 28155662 PMCID: PMC5260015 DOI: 10.1186/s12864-016-3323-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
43
Li Z, Liu Z, Zhong W, Huang M, Wu N, Xie Y, Dai Z, Zou X. Large-scale identification of human protein function using topological features of interaction network. Sci Rep 2016;6:37179. [PMID: 27849060 PMCID: PMC5111120 DOI: 10.1038/srep37179] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 10/26/2016] [Indexed: 12/25/2022]  Open
44
Chai H, Zhang J, Yang G, Ma Z. An evolution-based DNA-binding residue predictor using a dynamic query-driven learning scheme. MOLECULAR BIOSYSTEMS 2016;12:3643-3650. [PMID: 27730230 DOI: 10.1039/c6mb00626d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
45
A Novel Sequence-Based Feature for the Identification of DNA-Binding Sites in Proteins Using Jensen–Shannon Divergence. ENTROPY 2016. [DOI: 10.3390/e18100379] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Korostelev YD, Zharov IA, Mironov AA, Rakhmaininova AB, Gelfand MS. Identification of Position-Specific Correlations between DNA-Binding Domains and Their Binding Sites. Application to the MerR Family of Transcription Factors. PLoS One 2016;11:e0162681. [PMID: 27690309 PMCID: PMC5045206 DOI: 10.1371/journal.pone.0162681] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 08/26/2016] [Indexed: 11/25/2022]  Open
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Yachdav G, Wilzbach S, Rauscher B, Sheridan R, Sillitoe I, Procter J, Lewis SE, Rost B, Goldberg T. MSAViewer: interactive JavaScript visualization of multiple sequence alignments. Bioinformatics 2016;32:3501-3503. [PMID: 27412096 PMCID: PMC5181560 DOI: 10.1093/bioinformatics/btw474] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 06/03/2016] [Accepted: 06/29/2016] [Indexed: 11/29/2022]  Open
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EL-Manzalawy Y, Abbas M, Malluhi Q, Honavar V. FastRNABindR: Fast and Accurate Prediction of Protein-RNA Interface Residues. PLoS One 2016;11:e0158445. [PMID: 27383535 PMCID: PMC4934694 DOI: 10.1371/journal.pone.0158445] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 06/16/2016] [Indexed: 11/24/2022]  Open
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Zhou J, Xu R, He Y, Lu Q, Wang H, Kong B. PDNAsite: Identification of DNA-binding Site from Protein Sequence by Incorporating Spatial and Sequence Context. Sci Rep 2016;6:27653. [PMID: 27282833 PMCID: PMC4901350 DOI: 10.1038/srep27653] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 05/18/2016] [Indexed: 02/01/2023]  Open
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Maximova T, Moffatt R, Ma B, Nussinov R, Shehu A. Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics. PLoS Comput Biol 2016;12:e1004619. [PMID: 27124275 PMCID: PMC4849799 DOI: 10.1371/journal.pcbi.1004619] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]  Open
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