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For: Nithin C, Mukherjee S, Bahadur RP. A non-redundant protein-RNA docking benchmark version 2.0. Proteins 2016;85:256-267. [PMID: 27862282 DOI: 10.1002/prot.25211] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 10/27/2016] [Accepted: 11/08/2016] [Indexed: 12/23/2022]
Number Cited by Other Article(s)
1
Zeng C, Zhuo C, Gao J, Liu H, Zhao Y. Advances and Challenges in Scoring Functions for RNA-Protein Complex Structure Prediction. Biomolecules 2024;14:1245. [PMID: 39456178 PMCID: PMC11506084 DOI: 10.3390/biom14101245] [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: 09/04/2024] [Revised: 09/24/2024] [Accepted: 09/30/2024] [Indexed: 10/28/2024]  Open
2
Sabei A, Hognon C, Martin J, Frezza E. Dynamics of Protein-RNA Interfaces Using All-Atom Molecular Dynamics Simulations. J Phys Chem B 2024;128:4865-4886. [PMID: 38740056 DOI: 10.1021/acs.jpcb.3c07698] [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: 05/16/2024]
3
Harini K, Sekijima M, Gromiha MM. PRA-Pred: Structure-based prediction of protein-RNA binding affinity. Int J Biol Macromol 2024;259:129490. [PMID: 38224813 DOI: 10.1016/j.ijbiomac.2024.129490] [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: 12/10/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 01/17/2024]
4
Agarwal A, Kant S, Bahadur RP. Efficient mapping of RNA-binding residues in RNA-binding proteins using local sequence features of binding site residues in protein-RNA complexes. Proteins 2023;91:1361-1379. [PMID: 37254800 DOI: 10.1002/prot.26528] [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: 09/07/2022] [Revised: 04/13/2023] [Accepted: 05/02/2023] [Indexed: 06/01/2023]
5
Sabei A, Caldas Baia TG, Saffar R, Martin J, Frezza E. Internal Normal Mode Analysis Applied to RNA Flexibility and Conformational Changes. J Chem Inf Model 2023;63:2554-2572. [PMID: 36972178 DOI: 10.1021/acs.jcim.2c01509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
6
Li H, Huang E, Zhang Y, Huang S, Xiao Y. HDOCK update for modeling protein-RNA/DNA complex structures. Protein Sci 2022;31:e4441. [PMID: 36305764 PMCID: PMC9615301 DOI: 10.1002/pro.4441] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 11/05/2022]
7
Rodríguez-Lumbreras LA, Jiménez-García B, Giménez-Santamarina S, Fernández-Recio J. pyDockDNA: A new web server for energy-based protein-DNA docking and scoring. Front Mol Biosci 2022;9:988996. [PMID: 36275623 PMCID: PMC9582769 DOI: 10.3389/fmolb.2022.988996] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022]  Open
8
Yang R, Liu H, Yang L, Zhou T, Li X, Zhao Y. RPpocket: An RNA–Protein Intuitive Database with RNA Pocket Topology Resources. Int J Mol Sci 2022;23:ijms23136903. [PMID: 35805909 PMCID: PMC9266927 DOI: 10.3390/ijms23136903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/13/2022] [Accepted: 06/20/2022] [Indexed: 02/04/2023]  Open
9
Evtugyn G, Porfireva A, Tsekenis G, Oravczova V, Hianik T. Electrochemical Aptasensors for Antibiotics Detection: Recent Achievements and Applications for Monitoring Food Safety. SENSORS (BASEL, SWITZERLAND) 2022;22:3684. [PMID: 35632093 PMCID: PMC9143886 DOI: 10.3390/s22103684] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/05/2022] [Accepted: 05/07/2022] [Indexed: 06/15/2023]
10
Mias‐Lucquin D, Chauvot de Beauchene I. Conformational variability in proteins bound to single-stranded DNA: A new benchmark for new docking perspectives. Proteins 2022;90:625-631. [PMID: 34617336 PMCID: PMC9292434 DOI: 10.1002/prot.26258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 09/15/2021] [Accepted: 09/27/2021] [Indexed: 12/19/2022]
11
Nithin C, Mukherjee S, Basak J, Bahadur RP. NCodR: A multi-class support vector machine classification to distinguish non-coding RNAs in Viridiplantae. QUANTITATIVE PLANT BIOLOGY 2022;3:e23. [PMID: 37077974 PMCID: PMC10095871 DOI: 10.1017/qpb.2022.18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 05/02/2023]
12
A comparative analysis of machine learning classifiers for predicting protein-binding nucleotides in RNA sequences. Comput Struct Biotechnol J 2022;20:3195-3207. [PMID: 35832617 PMCID: PMC9249596 DOI: 10.1016/j.csbj.2022.06.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 11/24/2022]  Open
13
Ramos TAR, Galindo NRO, Arias-Carrasco R, da Silva CF, Maracaja-Coutinho V, do Rêgo TG. RNAmining: A machine learning stand-alone and web server tool for RNA coding potential prediction. F1000Res 2021;10:323. [PMID: 34164114 PMCID: PMC8201426 DOI: 10.12688/f1000research.52350.2] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/02/2021] [Indexed: 12/22/2022]  Open
14
González-Alemán R, Chevrollier N, Simoes M, Montero-Cabrera L, Leclerc F. MCSS-Based Predictions of Binding Mode and Selectivity of Nucleotide Ligands. J Chem Theory Comput 2021;17:2599-2618. [PMID: 33764770 DOI: 10.1021/acs.jctc.0c01339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
15
Wang H, Zhao Y. RBinds: A user-friendly server for RNA binding site prediction. Comput Struct Biotechnol J 2020;18:3762-3765. [PMID: 34136090 PMCID: PMC8164131 DOI: 10.1016/j.csbj.2020.10.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/27/2020] [Accepted: 10/31/2020] [Indexed: 12/03/2022]  Open
16
Yasmeen F, Seo H, Javaid N, Kim MS, Choi S. Therapeutic Interventions into Innate Immune Diseases by Means of Aptamers. Pharmaceutics 2020;12:pharmaceutics12100955. [PMID: 33050544 PMCID: PMC7600108 DOI: 10.3390/pharmaceutics12100955] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/03/2020] [Accepted: 10/04/2020] [Indexed: 12/25/2022]  Open
17
Zheng J, Hong X, Xie J, Tong X, Liu S. P3DOCK: a protein-RNA docking webserver based on template-based and template-free docking. Bioinformatics 2020;36:96-103. [PMID: 31173056 DOI: 10.1093/bioinformatics/btz478] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 05/24/2019] [Accepted: 06/04/2019] [Indexed: 01/02/2023]  Open
18
He J, Tao H, Huang SY. Protein-ensemble-RNA docking by efficient consideration of protein flexibility through homology models. Bioinformatics 2020;35:4994-5002. [PMID: 31086984 DOI: 10.1093/bioinformatics/btz388] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 04/28/2019] [Accepted: 05/03/2019] [Indexed: 12/18/2022]  Open
19
Yan Y, Tao H, He J, Huang SY. The HDOCK server for integrated protein–protein docking. Nat Protoc 2020;15:1829-1852. [DOI: 10.1038/s41596-020-0312-x] [Citation(s) in RCA: 288] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 02/03/2020] [Indexed: 12/27/2022]
20
Nithin C, Mukherjee S, Bahadur RP. A structure-based model for the prediction of protein-RNA binding affinity. RNA (NEW YORK, N.Y.) 2019;25:1628-1645. [PMID: 31395671 PMCID: PMC6859855 DOI: 10.1261/rna.071779.119] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 08/05/2019] [Indexed: 05/28/2023]
21
Protein-assisted RNA fragment docking (RnaX) for modeling RNA-protein interactions using ModelX. Proc Natl Acad Sci U S A 2019;116:24568-24573. [PMID: 31732673 PMCID: PMC6900601 DOI: 10.1073/pnas.1910999116] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
22
Yan Y, Zhang D, Zhou P, Li B, Huang SY. HDOCK: a web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy. Nucleic Acids Res 2019;45:W365-W373. [PMID: 28521030 PMCID: PMC5793843 DOI: 10.1093/nar/gkx407] [Citation(s) in RCA: 651] [Impact Index Per Article: 130.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 04/29/2017] [Indexed: 12/16/2022]  Open
23
Yan Y, Huang SY. RRDB: a comprehensive and non-redundant benchmark for RNA-RNA docking and scoring. Bioinformatics 2018;34:453-458. [PMID: 29028888 DOI: 10.1093/bioinformatics/btx615] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 09/23/2017] [Indexed: 12/15/2022]  Open
24
Krüger A, Zimbres FM, Kronenberger T, Wrenger C. Molecular Modeling Applied to Nucleic Acid-Based Molecule Development. Biomolecules 2018;8:E83. [PMID: 30150587 PMCID: PMC6163985 DOI: 10.3390/biom8030083] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/12/2018] [Accepted: 08/16/2018] [Indexed: 12/15/2022]  Open
25
Nithin C, Ghosh P, Bujnicki JM. Bioinformatics Tools and Benchmarks for Computational Docking and 3D Structure Prediction of RNA-Protein Complexes. Genes (Basel) 2018;9:genes9090432. [PMID: 30149645 PMCID: PMC6162694 DOI: 10.3390/genes9090432] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/26/2018] [Accepted: 08/21/2018] [Indexed: 12/29/2022]  Open
26
An account of solvent accessibility in protein-RNA recognition. Sci Rep 2018;8:10546. [PMID: 30002431 PMCID: PMC6043566 DOI: 10.1038/s41598-018-28373-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/21/2018] [Indexed: 01/16/2023]  Open
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