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For: Orlando G, Raimondi D, Khan T, Lenaerts T, Vranken WF. SVM-dependent pairwise HMM: an application to protein pairwise alignments. Bioinformatics 2018;33:3902-3908. [PMID: 28666322 DOI: 10.1093/bioinformatics/btx391] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 06/12/2017] [Indexed: 12/27/2022]  Open
Number Cited by Other Article(s)
1
Crauwels C, Díaz A, Vranken W. GPCRchimeraDB: A Database of Chimeric G Protein-Coupled Receptors (GPCRs) to Assist Their Design. J Mol Biol 2025;437:169164. [PMID: 40268234 DOI: 10.1016/j.jmb.2025.169164] [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: 12/16/2024] [Revised: 04/11/2025] [Accepted: 04/16/2025] [Indexed: 04/25/2025]
2
Donvil L, Housmans JAJ, Peeters E, Vranken W, Orlando G. In silico identification of archaeal DNA-binding proteins. Bioinformatics 2025;41:btaf169. [PMID: 40315131 PMCID: PMC12065626 DOI: 10.1093/bioinformatics/btaf169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2024] [Revised: 03/17/2025] [Accepted: 03/31/2025] [Indexed: 05/04/2025]  Open
3
Orlando G, Raimondi D, Codice F, Tabaro F, Vranken W. Prediction of disordered regions in proteins with recurrent Neural Networks and protein dynamics. J Mol Biol 2022;434:167579. [DOI: 10.1016/j.jmb.2022.167579] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/21/2022] [Accepted: 03/31/2022] [Indexed: 10/18/2022]
4
Orlando G, Raimondi D, Duran-Romaña R, Moreau Y, Schymkowitz J, Rousseau F. PyUUL provides an interface between biological structures and deep learning algorithms. Nat Commun 2022;13:961. [PMID: 35181656 PMCID: PMC8857184 DOI: 10.1038/s41467-022-28327-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 01/18/2022] [Indexed: 11/09/2022]  Open
5
Kagami L, Roca-Martínez J, Gavaldá-García J, Ramasamy P, Feenstra KA, Vranken WF. Online biophysical predictions for SARS-CoV-2 proteins. BMC Mol Cell Biol 2021;22:23. [PMID: 33892639 PMCID: PMC8062939 DOI: 10.1186/s12860-021-00362-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/01/2021] [Indexed: 12/26/2022]  Open
6
Orlando G, Raimondi D, Kagami LP, Vranken WF. ShiftCrypt: a web server to understand and biophysically align proteins through their NMR chemical shift values. Nucleic Acids Res 2020;48:W36-W40. [PMID: 32459331 PMCID: PMC7319548 DOI: 10.1093/nar/gkaa391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/21/2020] [Accepted: 05/04/2020] [Indexed: 02/06/2023]  Open
7
Zhang D, Guan ZX, Zhang ZM, Li SH, Dao FY, Tang H, Lin H. Recent Development of Computational Predicting Bioluminescent Proteins. Curr Pharm Des 2020;25:4264-4273. [PMID: 31696804 DOI: 10.2174/1381612825666191107100758] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 11/04/2019] [Indexed: 12/22/2022]
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