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For: Craveur P, Rebehmed J, de Brevern AG. PTM-SD: a database of structurally resolved and annotated posttranslational modifications in proteins. Database (Oxford) 2014;2014:bau041. [PMID: 24857970 PMCID: PMC4038255 DOI: 10.1093/database/bau041] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Number Cited by Other Article(s)
1
Balakrishnan A, Mishra SK, Georrge JJ. Insight into Protein Engineering: From In silico Modelling to In vitro Synthesis. Curr Pharm Des 2025;31:179-202. [PMID: 39354773 DOI: 10.2174/0113816128349577240927071706] [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: 08/15/2024] [Revised: 09/12/2024] [Accepted: 09/13/2024] [Indexed: 10/03/2024]
2
Kim DN, Yin T, Zhang T, Im AK, Cort JR, Rozum JC, Pollock D, Qian WJ, Feng S. Artificial Intelligence Transforming Post-Translational Modification Research. Bioengineering (Basel) 2024;12:26. [PMID: 39851300 PMCID: PMC11762806 DOI: 10.3390/bioengineering12010026] [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: 10/31/2024] [Revised: 12/16/2024] [Accepted: 12/29/2024] [Indexed: 01/26/2025]  Open
3
Zhang O, Naik SA, Liu ZH, Forman-Kay J, Head-Gordon T. A curated rotamer library for common post-translational modifications of proteins. Bioinformatics 2024;40:btae444. [PMID: 38995731 PMCID: PMC11254353 DOI: 10.1093/bioinformatics/btae444] [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: 04/26/2024] [Revised: 06/06/2024] [Accepted: 07/11/2024] [Indexed: 07/14/2024]  Open
4
Kellman BP, Mariethoz J, Zhang Y, Shaul S, Alteri M, Sandoval D, Jeffris M, Armingol E, Bao B, Lisacek F, Bojar D, Lewis NE. Decoding glycosylation potential from protein structure across human glycoproteins with a multi-view recurrent neural network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.15.594334. [PMID: 38798633 PMCID: PMC11118808 DOI: 10.1101/2024.05.15.594334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
5
Zhang O, Naik SA, Liu ZH, Forman-Kay J, Head-Gordon T. A Curated Rotamer Library for Common Post-Translational Modifications of Proteins. ARXIV 2024:arXiv:2405.03120v1. [PMID: 38764597 PMCID: PMC11100909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/21/2024]
6
Esmaili F, Pourmirzaei M, Ramazi S, Shojaeilangari S, Yavari E. A Review of Machine Learning and Algorithmic Methods for Protein Phosphorylation Site Prediction. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023;21:1266-1285. [PMID: 37863385 PMCID: PMC11082408 DOI: 10.1016/j.gpb.2023.03.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 01/16/2023] [Accepted: 03/23/2023] [Indexed: 10/22/2023]
7
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: 0.5] [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]
8
Sharapov SZ, Timoshchuk AN, Aulchenko YS. Genetic control of N-glycosylation of human blood plasma proteins. Vavilovskii Zhurnal Genet Selektsii 2023;27:224-239. [PMID: 37293449 PMCID: PMC10244589 DOI: 10.18699/vjgb-23-29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/20/2023] [Accepted: 01/23/2022] [Indexed: 06/10/2023]  Open
9
Kuschert S, Stroet M, Chin YKY, Conibear AC, Jia X, Lee T, Bartling CRO, Strømgaard K, Güntert P, Rosengren KJ, Mark AE, Mobli M. Facilitating the structural characterisation of non-canonical amino acids in biomolecular NMR. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2023;4:57-72. [PMID: 37904802 PMCID: PMC10583272 DOI: 10.5194/mr-4-57-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/07/2023] [Indexed: 11/01/2023]
10
Weigle AT, Feng J, Shukla D. Thirty years of molecular dynamics simulations on posttranslational modifications of proteins. Phys Chem Chem Phys 2022;24:26371-26397. [PMID: 36285789 PMCID: PMC9704509 DOI: 10.1039/d2cp02883b] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
11
England WE, Wang J, Chen S, Baldi P, Flynn RA, Spitale RC. An atlas of posttranslational modifications on RNA binding proteins. Nucleic Acids Res 2022;50:4329-4339. [PMID: 35438783 PMCID: PMC9071496 DOI: 10.1093/nar/gkac243] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/24/2022] [Accepted: 04/15/2022] [Indexed: 12/13/2022]  Open
12
Methodological advances in the design of peptide-based vaccines. Drug Discov Today 2022;27:1367-1380. [DOI: 10.1016/j.drudis.2022.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/02/2021] [Accepted: 03/07/2022] [Indexed: 12/11/2022]
13
Gan SKE, Phua SX, Yeo JY. Sagacious epitope selection for vaccines, and both antibody-based therapeutics and diagnostics: tips from virology and oncology. Antib Ther 2022;5:63-72. [PMID: 35372784 PMCID: PMC8972324 DOI: 10.1093/abt/tbac005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/24/2022] [Accepted: 02/12/2022] [Indexed: 11/12/2022]  Open
14
de Brevern AG, Rebehmed J. Current status of PTMs structural databases: applications, limitations and prospects. Amino Acids 2022;54:575-590. [PMID: 35020020 DOI: 10.1007/s00726-021-03119-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 12/20/2021] [Indexed: 12/11/2022]
15
Craveur P, Narwani TJ, Srinivasan N, Gelly JC, Rebehmed J, de Brevern AG. Shaking the β-Bulges. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:14-18. [PMID: 34115590 DOI: 10.1109/tcbb.2021.3088444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
16
Zhang H, He J, Hu G, Zhu F, Jiang H, Gao J, Zhou H, Lin H, Wang Y, Chen K, Meng F, Hao M, Zhao K, Luo C, Liang Z. Dynamics of Post-Translational Modification Inspires Drug Design in the Kinase Family. J Med Chem 2021;64:15111-15125. [PMID: 34668699 DOI: 10.1021/acs.jmedchem.1c01076] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
17
Bonne Køhler J, Jers C, Senissar M, Shi L, Derouiche A, Mijakovic I. Importance of protein Ser/Thr/Tyr phosphorylation for bacterial pathogenesis. FEBS Lett 2020;594:2339-2369. [PMID: 32337704 DOI: 10.1002/1873-3468.13797] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 12/13/2022]
18
Li F, Fan C, Marquez-Lago TT, Leier A, Revote J, Jia C, Zhu Y, Smith AI, Webb GI, Liu Q, Wei L, Li J, Song J. PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact. Brief Bioinform 2020;21:1069-1079. [PMID: 31161204 PMCID: PMC7299293 DOI: 10.1093/bib/bbz050] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/26/2019] [Accepted: 03/29/2019] [Indexed: 12/26/2022]  Open
19
Santhosh R, Bankoti N, Gurudarshan M, Jeyakanthan J, Sekar K. IMRPS: Inserted and Modified Residues in Protein Structures. A database. J Appl Crystallogr 2020. [DOI: 10.1107/s1600576720001880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]  Open
20
Accurate Representation of Protein-Ligand Structural Diversity in the Protein Data Bank (PDB). Int J Mol Sci 2020;21:ijms21062243. [PMID: 32213914 PMCID: PMC7139665 DOI: 10.3390/ijms21062243] [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] [Received: 01/28/2020] [Revised: 03/06/2020] [Accepted: 03/20/2020] [Indexed: 11/16/2022]  Open
21
Narwani TJ, Craveur P, Shinada NK, Floch A, Santuz H, Vattekatte AM, Srinivasan N, Rebehmed J, Gelly JC, Etchebest C, de Brevern AG. Discrete analyses of protein dynamics. J Biomol Struct Dyn 2019;38:2988-3002. [PMID: 31361191 DOI: 10.1080/07391102.2019.1650112] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
22
Sharapov SZ, Tsepilov YA, Klaric L, Mangino M, Thareja G, Shadrina AS, Simurina M, Dagostino C, Dmitrieva J, Vilaj M, Vuckovic F, Pavic T, Stambuk J, Trbojevic-Akmacic I, Kristic J, Simunovic J, Momcilovic A, Campbell H, Doherty M, Dunlop MG, Farrington SM, Pucic-Bakovic M, Gieger C, Allegri M, Louis E, Georges M, Suhre K, Spector T, Williams FMK, Lauc G, Aulchenko YS. Defining the genetic control of human blood plasma N-glycome using genome-wide association study. Hum Mol Genet 2019;28:2062-2077. [PMID: 31163085 PMCID: PMC6664388 DOI: 10.1093/hmg/ddz054] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 03/01/2019] [Accepted: 03/06/2019] [Indexed: 01/10/2023]  Open
23
Craveur P, Narwani TJ, Rebehmed J, de Brevern AG. Investigation of the impact of PTMs on the protein backbone conformation. Amino Acids 2019;51:1065-1079. [DOI: 10.1007/s00726-019-02747-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 05/18/2019] [Indexed: 12/17/2022]
24
Pascovici D, Wu JX, McKay MJ, Joseph C, Noor Z, Kamath K, Wu Y, Ranganathan S, Gupta V, Mirzaei M. Clinically Relevant Post-Translational Modification Analyses-Maturing Workflows and Bioinformatics Tools. Int J Mol Sci 2018;20:E16. [PMID: 30577541 PMCID: PMC6337699 DOI: 10.3390/ijms20010016] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/09/2018] [Accepted: 12/17/2018] [Indexed: 01/04/2023]  Open
25
Dehzangi A, López Y, Taherzadeh G, Sharma A, Tsunoda T. SumSec: Accurate Prediction of Sumoylation Sites Using Predicted Secondary Structure. Molecules 2018;23:E3260. [PMID: 30544729 PMCID: PMC6320791 DOI: 10.3390/molecules23123260] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 11/30/2018] [Accepted: 12/05/2018] [Indexed: 12/13/2022]  Open
26
Srivastava A, Nagai T, Srivastava A, Miyashita O, Tama F. Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics. Int J Mol Sci 2018;19:E3401. [PMID: 30380757 PMCID: PMC6274748 DOI: 10.3390/ijms19113401] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 10/20/2018] [Accepted: 10/27/2018] [Indexed: 12/13/2022]  Open
27
Ledesma L, Sandoval E, Cruz-Martínez U, Escalante AM, Mejía S, Moreno-Álvarez P, Ávila E, García E, Coello G, Torres-Quiroz F. YAAM: Yeast Amino Acid Modifications Database. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018;2018:4797096. [PMID: 29688347 PMCID: PMC7206644 DOI: 10.1093/database/bax099] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 12/06/2017] [Indexed: 01/29/2023]
28
Su MG, Weng JTY, Hsu JBK, Huang KY, Chi YH, Lee TY. Investigation and identification of functional post-translational modification sites associated with drug binding and protein-protein interactions. BMC SYSTEMS BIOLOGY 2017;11:132. [PMID: 29322920 PMCID: PMC5763307 DOI: 10.1186/s12918-017-0506-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
29
Abriata LA. Structural database resources for biological macromolecules. Brief Bioinform 2017;18:659-669. [PMID: 27273290 DOI: 10.1093/bib/bbw049] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Indexed: 12/30/2022]  Open
30
Laurie J, Chattopadhyay AK, Flower DR. Protein lipograms. J Theor Biol 2017;430:109-116. [PMID: 28716385 DOI: 10.1016/j.jtbi.2017.07.009] [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: 03/10/2017] [Revised: 06/30/2017] [Accepted: 07/12/2017] [Indexed: 11/20/2022]
31
Shen X, Klarić L, Sharapov S, Mangino M, Ning Z, Wu D, Trbojević-Akmačić I, Pučić-Baković M, Rudan I, Polašek O, Hayward C, Spector TD, Wilson JF, Lauc G, Aulchenko YS. Multivariate discovery and replication of five novel loci associated with Immunoglobulin G N-glycosylation. Nat Commun 2017;8:447. [PMID: 28878392 PMCID: PMC5587582 DOI: 10.1038/s41467-017-00453-3] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/29/2017] [Indexed: 01/20/2023]  Open
32
Tay AP, Pang CNI, Winter DL, Wilkins MR. PTMOracle: A Cytoscape App for Covisualizing and Coanalyzing Post-Translational Modifications in Protein Interaction Networks. J Proteome Res 2017;16:1988-2003. [PMID: 28349685 DOI: 10.1021/acs.jproteome.6b01052] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
33
Dewhurst HM, Torres MP. Systematic analysis of non-structural protein features for the prediction of PTM function potential by artificial neural networks. PLoS One 2017;12:e0172572. [PMID: 28225828 PMCID: PMC5321281 DOI: 10.1371/journal.pone.0172572] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 02/07/2017] [Indexed: 12/31/2022]  Open
34
Minguez P, Bork P. Bioinformatics Analysis of Functional Associations of PTMs. Methods Mol Biol 2017;1558:303-320. [PMID: 28150244 DOI: 10.1007/978-1-4939-6783-4_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
35
Korkuć P, Walther D. Towards understanding the crosstalk between protein post-translational modifications: Homo- and heterotypic PTM pair distances on protein surfaces are not random. Proteins 2016;85:78-92. [PMID: 27802577 DOI: 10.1002/prot.25200] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/29/2016] [Accepted: 10/20/2016] [Indexed: 12/18/2022]
36
Noël F, Malpertuy A, de Brevern AG. Global analysis of VHHs framework regions with a structural alphabet. Biochimie 2016;131:11-19. [PMID: 27613403 DOI: 10.1016/j.biochi.2016.09.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/05/2016] [Accepted: 09/05/2016] [Indexed: 02/08/2023]
37
Sirota FL, Maurer-Stroh S, Eisenhaber B, Eisenhaber F. Single-residue posttranslational modification sites at the N-terminus, C-terminus or in-between: To be or not to be exposed for enzyme access. Proteomics 2016;15:2525-46. [PMID: 26038108 PMCID: PMC4745020 DOI: 10.1002/pmic.201400633] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 04/17/2015] [Accepted: 05/29/2015] [Indexed: 11/30/2022]
38
Snider NT, Omary MB. Assays for Posttranslational Modifications of Intermediate Filament Proteins. Methods Enzymol 2015;568:113-38. [PMID: 26795469 DOI: 10.1016/bs.mie.2015.09.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
39
Dewhurst HM, Choudhury S, Torres MP. Structural Analysis of PTM Hotspots (SAPH-ire)--A Quantitative Informatics Method Enabling the Discovery of Novel Regulatory Elements in Protein Families. Mol Cell Proteomics 2015;14:2285-97. [PMID: 26070665 PMCID: PMC4528253 DOI: 10.1074/mcp.m115.051177] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Indexed: 11/08/2022]  Open
40
Craveur P, Joseph AP, Esque J, Narwani TJ, Noël F, Shinada N, Goguet M, Leonard S, Poulain P, Bertrand O, Faure G, Rebehmed J, Ghozlane A, Swapna LS, Bhaskara RM, Barnoud J, Téletchéa S, Jallu V, Cerny J, Schneider B, Etchebest C, Srinivasan N, Gelly JC, de Brevern AG. Protein flexibility in the light of structural alphabets. Front Mol Biosci 2015;2:20. [PMID: 26075209 PMCID: PMC4445325 DOI: 10.3389/fmolb.2015.00020] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 04/30/2015] [Indexed: 01/01/2023]  Open
41
Matlock MK, Holehouse AS, Naegle KM. ProteomeScout: a repository and analysis resource for post-translational modifications and proteins. Nucleic Acids Res 2014;43:D521-30. [PMID: 25414335 PMCID: PMC4383955 DOI: 10.1093/nar/gku1154] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]  Open
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