Application of PolyPRep tools on HIV protease polyproteins using molecular docking
Abstract In recent years, the development of high-throughput technologies for obtaining sequence data leveraged the possibility of analysis of protein data in silico. However, when it comes to viral polyprotein interaction studies, there is a gap in the representation of those proteins, given their...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Instituto Internacional de Ecologia
2021-12-01
|
| Series: | Brazilian Journal of Biology |
| Subjects: | |
| Online Access: | http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1519-69842024000100151&tlng=en |
| _version_ | 1798021414883688448 |
|---|---|
| author | M. F. R. Dias F. L. L. Oliveira V. S. Pontes M. L. Silva |
| author_facet | M. F. R. Dias F. L. L. Oliveira V. S. Pontes M. L. Silva |
| author_sort | M. F. R. Dias |
| collection | DOAJ |
| description | Abstract In recent years, the development of high-throughput technologies for obtaining sequence data leveraged the possibility of analysis of protein data in silico. However, when it comes to viral polyprotein interaction studies, there is a gap in the representation of those proteins, given their size and length. The prepare for studies using state-of-the-art techniques such as Machine Learning, a good representation of such proteins is a must. We present an alternative to this problem, implementing a fragmentation and modeling protocol to prepare those polyproteins in the form of peptide fragments. Such procedure is made by several scripts, implemented together on the workflow we call PolyPRep, a tool written in Python script and available in GitHub. This software is freely available only for noncommercial users. |
| first_indexed | 2024-04-11T17:13:30Z |
| format | Article |
| id | doaj.art-3edd16859bed4a2997745379f449caf6 |
| institution | Directory Open Access Journal |
| issn | 1678-4375 |
| language | English |
| last_indexed | 2024-04-11T17:13:30Z |
| publishDate | 2021-12-01 |
| publisher | Instituto Internacional de Ecologia |
| record_format | Article |
| series | Brazilian Journal of Biology |
| spelling | doaj.art-3edd16859bed4a2997745379f449caf62022-12-22T04:12:49ZengInstituto Internacional de EcologiaBrazilian Journal of Biology1678-43752021-12-018410.1590/1519-6984.245592Application of PolyPRep tools on HIV protease polyproteins using molecular dockingM. F. R. Diashttps://orcid.org/0000-0002-0069-3199F. L. L. Oliveirahttps://orcid.org/0000-0003-4646-9958V. S. Ponteshttps://orcid.org/0000-0001-7227-5407M. L. Silvahttps://orcid.org/0000-0003-4844-7138Abstract In recent years, the development of high-throughput technologies for obtaining sequence data leveraged the possibility of analysis of protein data in silico. However, when it comes to viral polyprotein interaction studies, there is a gap in the representation of those proteins, given their size and length. The prepare for studies using state-of-the-art techniques such as Machine Learning, a good representation of such proteins is a must. We present an alternative to this problem, implementing a fragmentation and modeling protocol to prepare those polyproteins in the form of peptide fragments. Such procedure is made by several scripts, implemented together on the workflow we call PolyPRep, a tool written in Python script and available in GitHub. This software is freely available only for noncommercial users.http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1519-69842024000100151&tlng=enpolyproteinfragmentationmodelling3D structures |
| spellingShingle | M. F. R. Dias F. L. L. Oliveira V. S. Pontes M. L. Silva Application of PolyPRep tools on HIV protease polyproteins using molecular docking Brazilian Journal of Biology polyprotein fragmentation modelling 3D structures |
| title | Application of PolyPRep tools on HIV protease polyproteins using molecular docking |
| title_full | Application of PolyPRep tools on HIV protease polyproteins using molecular docking |
| title_fullStr | Application of PolyPRep tools on HIV protease polyproteins using molecular docking |
| title_full_unstemmed | Application of PolyPRep tools on HIV protease polyproteins using molecular docking |
| title_short | Application of PolyPRep tools on HIV protease polyproteins using molecular docking |
| title_sort | application of polyprep tools on hiv protease polyproteins using molecular docking |
| topic | polyprotein fragmentation modelling 3D structures |
| url | http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1519-69842024000100151&tlng=en |
| work_keys_str_mv | AT mfrdias applicationofpolypreptoolsonhivproteasepolyproteinsusingmoleculardocking AT flloliveira applicationofpolypreptoolsonhivproteasepolyproteinsusingmoleculardocking AT vspontes applicationofpolypreptoolsonhivproteasepolyproteinsusingmoleculardocking AT mlsilva applicationofpolypreptoolsonhivproteasepolyproteinsusingmoleculardocking |