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For: Kim N, Zheng Z, Elmetwaly S, Schlick T. RNA graph partitioning for the discovery of RNA modularity: a novel application of graph partition algorithm to biology. PLoS One 2014;9:e106074. [PMID: 25188578 DOI: 10.1371/journal.pone.0106074] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Accepted: 07/31/2014] [Indexed: 11/19/2022]  Open
Number Cited by Other Article(s)
1
RNA-As-Graphs Motif Atlas—Dual Graph Library of RNA Modules and Viral Frameshifting-Element Applications. Int J Mol Sci 2022;23:ijms23169249. [PMID: 36012512 PMCID: PMC9408923 DOI: 10.3390/ijms23169249] [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: 07/26/2022] [Revised: 08/13/2022] [Accepted: 08/14/2022] [Indexed: 11/25/2022]  Open
2
Zhu Q, Schlick T. A Fiedler Vector Scoring Approach for Novel RNA Motif Selection. J Phys Chem B 2021;125:1144-1155. [PMID: 33471540 PMCID: PMC7872303 DOI: 10.1021/acs.jpcb.0c10685] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
3
Jain S, Zhu Q, Paz ASP, Schlick T. Identification of novel RNA design candidates by clustering the extended RNA-As-Graphs library. Biochim Biophys Acta Gen Subj 2020;1864:129534. [PMID: 31954797 DOI: 10.1016/j.bbagen.2020.129534] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 01/10/2020] [Accepted: 01/14/2020] [Indexed: 12/31/2022]
4
Inverse folding with RNA-As-Graphs produces a large pool of candidate sequences with target topologies. J Struct Biol 2019;209:107438. [PMID: 31874236 DOI: 10.1016/j.jsb.2019.107438] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 12/18/2019] [Accepted: 12/19/2019] [Indexed: 02/07/2023]
5
Jain S, Laederach A, Ramos SBV, Schlick T. A pipeline for computational design of novel RNA-like topologies. Nucleic Acids Res 2019;46:7040-7051. [PMID: 30137633 PMCID: PMC6101589 DOI: 10.1093/nar/gky524] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 05/24/2018] [Indexed: 12/11/2022]  Open
6
Bhattacharya S, Jhunjhunwala A, Halder A, Bhattacharyya D, Mitra A. Going beyond base-pairs: topology-based characterization of base-multiplets in RNA. RNA (NEW YORK, N.Y.) 2019;25:573-589. [PMID: 30792229 PMCID: PMC6467009 DOI: 10.1261/rna.068551.118] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 02/18/2019] [Indexed: 05/17/2023]
7
Jain S, Saju S, Petingi L, Schlick T. An extended dual graph library and partitioning algorithm applicable to pseudoknotted RNA structures. Methods 2019;162-163:74-84. [PMID: 30928508 DOI: 10.1016/j.ymeth.2019.03.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/28/2019] [Accepted: 03/22/2019] [Indexed: 12/18/2022]  Open
8
Jain S, Bayrak CS, Petingi L, Schlick T. Dual Graph Partitioning Highlights a Small Group of Pseudoknot-Containing RNA Submotifs. Genes (Basel) 2018;9:E371. [PMID: 30044451 PMCID: PMC6115904 DOI: 10.3390/genes9080371] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 06/26/2018] [Accepted: 06/26/2018] [Indexed: 12/31/2022]  Open
9
Schlick T. Adventures with RNA graphs. Methods 2018;143:16-33. [PMID: 29621619 PMCID: PMC6051918 DOI: 10.1016/j.ymeth.2018.03.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/07/2018] [Accepted: 03/26/2018] [Indexed: 12/20/2022]  Open
10
Jain S, Schlick T. F-RAG: Generating Atomic Coordinates from RNA Graphs by Fragment Assembly. J Mol Biol 2017;429:3587-3605. [PMID: 28988954 PMCID: PMC5693719 DOI: 10.1016/j.jmb.2017.09.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 09/12/2017] [Accepted: 09/22/2017] [Indexed: 10/18/2022]
11
Schlick T, Pyle AM. Opportunities and Challenges in RNA Structural Modeling and Design. Biophys J 2017;113:225-234. [PMID: 28162235 PMCID: PMC5529161 DOI: 10.1016/j.bpj.2016.12.037] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/08/2016] [Accepted: 12/19/2016] [Indexed: 01/27/2023]  Open
12
Petingi L, Schlick T. Partitioning and Classification of RNA Secondary Structures into Pseudonotted and Pseudoknot-free Regions Using a Graph-Theoretical Approach. IAENG INTERNATIONAL JOURNAL OF COMPUTER SCIENCE 2017;44:241-246. [PMID: 30474081 PMCID: PMC6250053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
13
Baba N, Elmetwaly S, Kim N, Schlick T. Predicting Large RNA-Like Topologies by a Knowledge-Based Clustering Approach. J Mol Biol 2015;428:811-821. [PMID: 26478223 DOI: 10.1016/j.jmb.2015.10.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 10/06/2015] [Indexed: 11/19/2022]
14
Kim N, Zahran M, Schlick T. Computational Prediction of Riboswitch Tertiary Structures Including Pseudoknots by RAGTOP. Methods Enzymol 2015;553:115-35. [DOI: 10.1016/bs.mie.2014.10.054] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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