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For: Nepomnyachiy S, Ben-Tal N, Kolodny R. CyToStruct: Augmenting the Network Visualization of Cytoscape with the Power of Molecular Viewers. Structure 2015;23:941-948. [PMID: 25865247 DOI: 10.1016/j.str.2015.02.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 02/20/2015] [Accepted: 02/24/2015] [Indexed: 12/18/2022]
Number Cited by Other Article(s)
1
Kilinc M, Jia K, Jernigan RL. JSONWP: a static website generator for protein bioinformatics research. BIOINFORMATICS ADVANCES 2023;3:vbad154. [PMID: 37904893 PMCID: PMC10613403 DOI: 10.1093/bioadv/vbad154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/18/2023] [Accepted: 10/24/2023] [Indexed: 11/01/2023]
2
Afshinpour M, Smith LA, Chakravarty S. AQcalc: A web server that identifies weak molecular interactions in protein structures. Protein Sci 2023;32:e4762. [PMID: 37596782 PMCID: PMC10503417 DOI: 10.1002/pro.4762] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/25/2023] [Accepted: 08/15/2023] [Indexed: 08/20/2023]
3
Qiu K, Ben‐Tal N, Kolodny R. Similar protein segments shared between domains of different evolutionary lineages. Protein Sci 2022;31:e4407. [PMID: 36040261 PMCID: PMC9387206 DOI: 10.1002/pro.4407] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/01/2022] [Accepted: 07/25/2022] [Indexed: 11/21/2022]
4
Schaffer LV, Ideker T. Mapping the multiscale structure of biological systems. Cell Syst 2021;12:622-635. [PMID: 34139169 PMCID: PMC8245186 DOI: 10.1016/j.cels.2021.05.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/04/2021] [Accepted: 05/14/2021] [Indexed: 01/14/2023]
5
Kolodny R, Nepomnyachiy S, Tawfik DS, Ben-Tal N. Bridging Themes: Short Protein Segments Found in Different Architectures. Mol Biol Evol 2021;38:2191-2208. [PMID: 33502503 PMCID: PMC8136508 DOI: 10.1093/molbev/msab017] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
6
Lima DB, Zhu Y, Liu F. XlinkCyNET: A Cytoscape Application for Visualization of Protein Interaction Networks Based on Cross-Linking Mass Spectrometry Identifications. J Proteome Res 2021;20:1943-1950. [PMID: 33689356 DOI: 10.1021/acs.jproteome.0c00957] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
7
Chakrabarty B, Naganathan V, Garg K, Agarwal Y, Parekh N. NAPS update: network analysis of molecular dynamics data and protein-nucleic acid complexes. Nucleic Acids Res 2020;47:W462-W470. [PMID: 31106363 PMCID: PMC6602509 DOI: 10.1093/nar/gkz399] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/30/2019] [Accepted: 05/07/2019] [Indexed: 02/04/2023]  Open
8
Franklin MW, Nepomnyachyi S, Feehan R, Ben-Tal N, Kolodny R, Slusky JS. Evolutionary pathways of repeat protein topology in bacterial outer membrane proteins. eLife 2018;7:40308. [PMID: 30489257 PMCID: PMC6340704 DOI: 10.7554/elife.40308] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/28/2018] [Indexed: 11/13/2022]  Open
9
Razban RM, Gilson AI, Durfee N, Strobelt H, Dinkla K, Choi JM, Pfister H, Shakhnovich EI. ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes. Bioinformatics 2018;34:3557-3565. [PMID: 29741573 PMCID: PMC6184454 DOI: 10.1093/bioinformatics/bty370] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 03/27/2018] [Accepted: 05/03/2018] [Indexed: 01/27/2023]  Open
10
Navigating Among Known Structures in Protein Space. Methods Mol Biol 2018. [PMID: 30298400 DOI: 10.1007/978-1-4939-8736-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
11
Franklin MW, Nepomnyachiy S, Feehan R, Ben-Tal N, Kolodny R, Slusky JSG. Efflux Pumps Represent Possible Evolutionary Convergence onto the β-Barrel Fold. Structure 2018;26:1266-1274.e2. [PMID: 30057025 PMCID: PMC6125174 DOI: 10.1016/j.str.2018.06.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 05/17/2018] [Accepted: 06/20/2018] [Indexed: 11/22/2022]
12
Salamanca Viloria J, Allega MF, Lambrughi M, Papaleo E. An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass. Sci Rep 2017;7:2838. [PMID: 28588190 PMCID: PMC5460117 DOI: 10.1038/s41598-017-01498-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 03/28/2017] [Indexed: 02/05/2023]  Open
13
Chakrabarty B, Parekh N. NAPS: Network Analysis of Protein Structures. Nucleic Acids Res 2016;44:W375-82. [PMID: 27151201 PMCID: PMC4987928 DOI: 10.1093/nar/gkw383] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 04/25/2016] [Indexed: 12/29/2022]  Open
14
Keskin O, Tuncbag N, Gursoy A. Predicting Protein–Protein Interactions from the Molecular to the Proteome Level. Chem Rev 2016;116:4884-909. [DOI: 10.1021/acs.chemrev.5b00683] [Citation(s) in RCA: 207] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
15
ConTemplate Suggests Possible Alternative Conformations for a Query Protein of Known Structure. Structure 2015;23:2162-70. [DOI: 10.1016/j.str.2015.08.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 07/31/2015] [Accepted: 08/24/2015] [Indexed: 10/22/2022]
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