Author: Thomas Desautels; Adam Zemla; Edmond Lau; Magdalena Franco; Daniel Faissol
Title: Rapid in silico design of antibodies targeting SARS-CoV-2 using machine learning and supercomputing Document date: 2020_4_10
ID: kg2j0dqy_31
Snippet: In the absence of a known SARS-CoV-2 spike protein structure, we characterized the surface glycoprotein sequence YP_009724390.1 [13] by constructing a homology-based structural model using the AS2TS system [14] and SARS-CoV-1. To assess regions of sequencestructure conservation or variability between SARS-CoV-1 and SARS-CoV-2 (sequence similarity=71%), we created a set of initial structural models using available templates. The comparative analys.....
Document: In the absence of a known SARS-CoV-2 spike protein structure, we characterized the surface glycoprotein sequence YP_009724390.1 [13] by constructing a homology-based structural model using the AS2TS system [14] and SARS-CoV-1. To assess regions of sequencestructure conservation or variability between SARS-CoV-1 and SARS-CoV-2 (sequence similarity=71%), we created a set of initial structural models using available templates. The comparative analysis between constructed models and all available templates from PDB was performed using the StralSV algorithm [28] , which identifies protein fragments that exhibit structural similarities despite low primary amino acid sequence similarity and regions where some structure conformation uncertainties can be observed. We used results from these searches for modeling missing loop regions and assessment of possible structure conformation diversity in preliminary models.
Search related documents:
Co phrase search for related documents- amino acid and comparative analysis: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70
- amino acid and construct model: 1, 2, 3
- amino acid and homology base: 1, 2
- amino acid and loop region: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23
- amino acid and primary amino acid: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41
- amino acid and primary amino acid sequence: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22
- amino acid and primary amino acid sequence similarity: 1, 2
- amino acid and protein fragment: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26
- amino acid and protein structure: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79
- amino acid and SARS spike: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75
- amino acid and SARS spike protein structure: 1, 2, 3, 4, 5, 6, 7, 8, 9
- amino acid and stralsv algorithm: 1
- amino acid and structural model: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19
- amino acid and structural similarity: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18
- amino acid and structural similarity exhibit: 1
- amino acid and structure conformation: 1, 2, 3, 4, 5, 6, 7
- amino acid and surface glycoprotein: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50
- amino acid and surface glycoprotein sequence: 1, 2
- available template and protein structure: 1, 2
Co phrase search for related documents, hyperlinks ordered by date