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...
Saved in:
| Published in: | Brazilian journal of biology Vol. 84; pp. e245592 - 4 |
|---|---|
| Main Authors: | , , , |
| Format: | Journal Article |
| Language: | English |
| Published: |
Brazil
Instituto Internacional de Ecologia
2024
|
| Subjects: | |
| ISSN: | 1519-6984, 1678-4375, 1678-4375 |
| Online Access: | Get full text |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| Abstract | 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.
Resumo Nos últimos anos, o desenvolvimento de tecnologias de alto rendimento para obtenção de dados sequenciais potencializou a possibilidade de análise de dados proteicos in silico. No entanto, quando se trata de estudos de interação de poliproteínas virais, existe uma lacuna na representação dessas proteínas, devido ao seu tamanho e comprimento. Para estudos utilizando técnicas de ponta como o Aprendizado de Máquina, uma boa representação dessas proteínas é imprescindível. Apresentamos uma alternativa para este problema, implementando um protocolo de fragmentação e modelagem para preparar essas poliproteínas na forma de fragmentos de peptídeos. Tal procedimento é feito por diversos scripts, implementados em conjunto no workflow que chamamos de PolyPRep, uma ferramenta escrita em script Python e disponível no GitHub. Este software está disponível gratuitamente apenas para usuários não comerciais. |
|---|---|
| AbstractList | 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. 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. Nos últimos anos, o desenvolvimento de tecnologias de alto rendimento para obtenção de dados sequenciais potencializou a possibilidade de análise de dados proteicos in silico. No entanto, quando se trata de estudos de interação de poliproteínas virais, existe uma lacuna na representação dessas proteínas, devido ao seu tamanho e comprimento. Para estudos utilizando técnicas de ponta como o Aprendizado de Máquina, uma boa representação dessas proteínas é imprescindível. Apresentamos uma alternativa para este problema, implementando um protocolo de fragmentação e modelagem para preparar essas poliproteínas na forma de fragmentos de peptídeos. Tal procedimento é feito por diversos scripts, implementados em conjunto no workflow que chamamos de PolyPRep, uma ferramenta escrita em script Python e disponível no GitHub. Este software está disponível gratuitamente apenas para usuários não comerciais. 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.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. 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. Resumo Nos últimos anos, o desenvolvimento de tecnologias de alto rendimento para obtenção de dados sequenciais potencializou a possibilidade de análise de dados proteicos in silico. No entanto, quando se trata de estudos de interação de poliproteínas virais, existe uma lacuna na representação dessas proteínas, devido ao seu tamanho e comprimento. Para estudos utilizando técnicas de ponta como o Aprendizado de Máquina, uma boa representação dessas proteínas é imprescindível. Apresentamos uma alternativa para este problema, implementando um protocolo de fragmentação e modelagem para preparar essas poliproteínas na forma de fragmentos de peptídeos. Tal procedimento é feito por diversos scripts, implementados em conjunto no workflow que chamamos de PolyPRep, uma ferramenta escrita em script Python e disponível no GitHub. Este software está disponível gratuitamente apenas para usuários não comerciais. |
| Author | Silva, M. L. Dias, M. F. R. Oliveira, F. L. L. Pontes, V. S. |
| AuthorAffiliation | Instituto Nacional de Metrologia, Qualidade e Tecnologia Secretaria Estadual do Espírito Santo Universidade Federal do Rio de Janeiro |
| AuthorAffiliation_xml | – name: Secretaria Estadual do Espírito Santo – name: Instituto Nacional de Metrologia, Qualidade e Tecnologia – name: Universidade Federal do Rio de Janeiro |
| Author_xml | – sequence: 1 givenname: M. F. R. orcidid: 0000-0002-0069-3199 surname: Dias fullname: Dias, M. F. R. organization: Instituto Nacional de Metrologia, Qualidade e Tecnologia, Brasil; Secretaria Estadual do Espírito Santo, Brasil – sequence: 2 givenname: F. L. L. orcidid: 0000-0003-4646-9958 surname: Oliveira fullname: Oliveira, F. L. L. organization: Instituto Nacional de Metrologia, Qualidade e Tecnologia, Brasil – sequence: 3 givenname: V. S. orcidid: 0000-0001-7227-5407 surname: Pontes fullname: Pontes, V. S. organization: Instituto Nacional de Metrologia, Qualidade e Tecnologia, Brasil – sequence: 4 givenname: M. L. orcidid: 0000-0003-4844-7138 surname: Silva fullname: Silva, M. L. organization: Instituto Nacional de Metrologia, Qualidade e Tecnologia, Brasil; Universidade Federal do Rio de Janeiro, Brasil |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/34932622$$D View this record in MEDLINE/PubMed |
| BookMark | eNpdkklrHDEQRkVwiJfknlMQ5JJLT7QvR2MSe8AQ4yxXodZiNNG0Oq3ug_99NG57DgaBVFWvPqpKdQ5OhjIEAD5itMFco6-YY90JrdiGMM41eQPOsJCqY1Tyk_Z-CZ-C81p3CBGOqHoHTinTlAhCzsD95Tjm5OycygBLhHclP97dhxHOpeQKm_Nm-weOU5mDrQGOLfxkpKHCpabhAe5LDm7JdoK-uL_N8x68jTbX8OH5vgC_v3_7dXXT3f643l5d3naOMkI6EpjyXinfS8GddFj3GivLBbJUMxaIUNgiQaKMrPfaR-m4tN6hqHsVqKUXYLvq-mJ3ZpzS3k6PpthknhxlejB2mpPLwdDgPRaK6z54ZonWUjJOpY6MaWejaFqbVau6FHIxu7JMQyve_DzM0BxmSBBhCCHcDsct4cua0Kbxbwl1NvtUXcjZDqEs1RCBiaS0ddLQz6_QozqRWGKmGCeN-vRMLf0--GM_L1_VALQCbiq1TiEeEYzMYRvMsVSzbgP9D_ydok4 |
| Cites_doi | 10.1371/journal.pcbi.1003103 10.1002/jcc.21256 10.1006/jmbi.2000.4018 10.1080/07391102.2017.1417160 10.1109/ACCESS.2018.2807881 10.1016/S1359644602025722 10.1021/jp910958u 10.1186/1758-2946-3-33 10.1006/jmbi.1993.1626 |
| ContentType | Journal Article |
| Copyright | 2024. This work is published under https://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. This work is licensed under a Creative Commons Attribution 4.0 International License. |
| Copyright_xml | – notice: 2024. This work is published under https://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. – notice: This work is licensed under a Creative Commons Attribution 4.0 International License. |
| DBID | AAYXX CITATION CGR CUY CVF ECM EIF NPM 3V. 7QG 7QL 7SN 7SS 7T7 7U9 7X7 7XB 88E 8FD 8FE 8FH 8FI 8FJ 8FK 8G5 ABUWG AEUYN AFKRA ATCPS AZQEC BBNVY BENPR BHPHI C1K CCPQU CLZPN COVID DWQXO FR3 FYUFA GHDGH GNUQQ GUQSH H94 HCIFZ K9. LK8 M0S M1P M2O M7N M7P MBDVC P64 PATMY PHGZM PHGZT PIMPY PJZUB PKEHL PPXIY PQEST PQGLB PQQKQ PQUKI PRINS PYCSY Q9U 7X8 GPN DOA |
| DOI | 10.1590/1519-6984.245592 |
| DatabaseName | CrossRef Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed ProQuest Central (Corporate) Animal Behavior Abstracts Bacteriology Abstracts (Microbiology B) Ecology Abstracts Entomology Abstracts (Full archive) Industrial and Applied Microbiology Abstracts (Microbiology A) Virology and AIDS Abstracts Health & Medical Collection ProQuest Central (purchase pre-March 2016) Medical Database (Alumni Edition) Technology Research Database ProQuest SciTech Collection ProQuest Natural Science Collection Hospital Premium Collection Hospital Premium Collection (Alumni Edition) ProQuest Central (Alumni) (purchase pre-March 2016) Research Library (Alumni Edition) ProQuest Central (Alumni Edition) ProQuest One Sustainability ProQuest Central UK/Ireland Agricultural & Environmental Science Collection ProQuest Central Essentials Biological Science Collection ProQuest Central Natural Science Collection Environmental Sciences and Pollution Management ProQuest One Latin America & Iberia Database Coronavirus Research Database ProQuest Central Korea Engineering Research Database Health Research Premium Collection Health Research Premium Collection (Alumni) ProQuest Central Student Research Library Prep AIDS and Cancer Research Abstracts SciTech Premium Collection ProQuest Health & Medical Complete (Alumni) ProQuest Biological Science Collection Health & Medical Collection (Alumni Edition) Medical Database Research Library Algology Mycology and Protozoology Abstracts (Microbiology C) Biological Science Database Research Library (Corporate) Biotechnology and BioEngineering Abstracts Environmental Science Database ProQuest Central Premium ProQuest One Academic (New) Publicly Available Content Database ProQuest Health & Medical Research Collection ProQuest One Academic Middle East (New) ProQuest One Health & Nursing ProQuest One Academic Eastern Edition (DO NOT USE) ProQuest One Applied & Life Sciences ProQuest One Academic (retired) ProQuest One Academic UKI Edition ProQuest Central China Environmental Science Collection ProQuest Central Basic MEDLINE - Academic SciELO DOAJ Directory of Open Access Journals |
| DatabaseTitle | CrossRef MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) Publicly Available Content Database Research Library Prep ProQuest Central Student ProQuest Central Essentials SciTech Premium Collection ProQuest Central China Environmental Sciences and Pollution Management ProQuest One Applied & Life Sciences ProQuest One Sustainability Health Research Premium Collection Natural Science Collection Health & Medical Research Collection Biological Science Collection Industrial and Applied Microbiology Abstracts (Microbiology A) ProQuest Central (New) ProQuest Medical Library (Alumni) Virology and AIDS Abstracts ProQuest Biological Science Collection ProQuest One Academic Eastern Edition Coronavirus Research Database ProQuest Hospital Collection Health Research Premium Collection (Alumni) Biological Science Database Ecology Abstracts ProQuest Hospital Collection (Alumni) Biotechnology and BioEngineering Abstracts Environmental Science Collection Entomology Abstracts ProQuest Health & Medical Complete Latin America & Iberian Database ProQuest One Academic UKI Edition Environmental Science Database Engineering Research Database ProQuest One Academic ProQuest One Academic (New) Technology Research Database ProQuest One Academic Middle East (New) ProQuest Health & Medical Complete (Alumni) ProQuest Central (Alumni Edition) ProQuest One Community College ProQuest One Health & Nursing Research Library (Alumni Edition) ProQuest Natural Science Collection ProQuest Central ProQuest Health & Medical Research Collection Health and Medicine Complete (Alumni Edition) ProQuest Central Korea Bacteriology Abstracts (Microbiology B) Algology Mycology and Protozoology Abstracts (Microbiology C) Agricultural & Environmental Science Collection AIDS and Cancer Research Abstracts ProQuest Research Library ProQuest Central Basic ProQuest SciTech Collection ProQuest Medical Library Animal Behavior Abstracts ProQuest Central (Alumni) MEDLINE - Academic |
| DatabaseTitleList | MEDLINE Publicly Available Content Database MEDLINE - Academic CrossRef |
| Database_xml | – sequence: 1 dbid: DOA name: Directory of Open Access Journals (DOAJ) url: https://www.doaj.org/ sourceTypes: Open Website – sequence: 2 dbid: NPM name: PubMed url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 3 dbid: PIMPY name: Publicly Available Content Database (ProQuest) url: http://search.proquest.com/publiccontent sourceTypes: Aggregation Database |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Biology |
| DocumentTitleAlternate | Aplicação da ferramenta PolyPRep em poliproteínas de protease de HIV usando docking molecular |
| EISSN | 1678-4375 |
| EndPage | 4 |
| ExternalDocumentID | oai_doaj_org_article_3edd16859bed4a2997745379f449caf6 S1519_69842024000100151 34932622 10_1590_1519_6984_245592 |
| Genre | Journal Article |
| GroupedDBID | --- 23N 2WC 36B 53G 5GY 5VS 7X7 7XC 88E 8FE 8FH 8FI 8FJ 8G5 AAYXX ABUWG ABXHO ACIHN ACPRK ADBBV AEAQA AENEX AEUYN AFFHD AFKRA AFRAH AHMBA ALMA_UNASSIGNED_HOLDINGS APOWU ATCPS AZFZN AZQEC BAIFH BAWUL BBNVY BBTPI BCNDV BENPR BHPHI BPHCQ BVXVI C1A CCPQU CITATION CLZPN CS3 DIK DU5 DWQXO E3Z EBD EBS EJD EMB EMOBN F5P FRP FYUFA GNUQQ GROUPED_DOAJ GUQSH GX1 HCIFZ HMCUK IAO IEA IGS IHR INF INH INR IPNFZ ISR ITC KQ8 LK8 M1P M2O M7P OK1 OVT PATMY PHGZM PHGZT PIMPY PJZUB PPXIY PQGLB PQQKQ PROAC PSQYO PV9 PYCSY RIG RNS RSC RZL SCD SV3 TR2 UKHRP XSB ~02 3V. ALIPV CGR CUY CVF ECM EIF M~E NPM 7QG 7QL 7SN 7SS 7T7 7U9 7XB 8FD 8FK C1K COVID FR3 H94 K9. M7N MBDVC P64 PKEHL PQEST PQUKI PRINS Q9U 7X8 PUEGO GPN |
| ID | FETCH-LOGICAL-c3422-2e48dd88db765c7c19b918a560a3944e2681a062f7f4bd9df7c57adc0f9b8e3a3 |
| IEDL.DBID | M7P |
| ISSN | 1519-6984 1678-4375 |
| IngestDate | Fri Oct 03 12:52:02 EDT 2025 Tue Nov 18 23:23:44 EST 2025 Fri Sep 05 13:52:07 EDT 2025 Sat Nov 29 14:38:24 EST 2025 Thu Jan 02 22:55:43 EST 2025 Sat Nov 29 03:30:19 EST 2025 |
| IsDoiOpenAccess | true |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Keywords | estrutura 3D 3D structures poliproteínas fragmentação modelagem modelling fragmentation polyprotein |
| Language | English |
| License | http://creativecommons.org/licenses/by/4.0 This work is licensed under a Creative Commons Attribution 4.0 International License. http://creativecommons.org/licenses/by/4.0 |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c3422-2e48dd88db765c7c19b918a560a3944e2681a062f7f4bd9df7c57adc0f9b8e3a3 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 |
| ORCID | 0000-0002-0069-3199 0000-0003-4646-9958 0000-0003-4844-7138 0000-0001-7227-5407 |
| OpenAccessLink | https://www.proquest.com/docview/2717148452?pq-origsite=%requestingapplication% |
| PMID | 34932622 |
| PQID | 2717148452 |
| PQPubID | 486387 |
| PageCount | 4 |
| ParticipantIDs | doaj_primary_oai_doaj_org_article_3edd16859bed4a2997745379f449caf6 scielo_journals_S1519_69842024000100151 proquest_miscellaneous_2612733394 proquest_journals_2717148452 pubmed_primary_34932622 crossref_primary_10_1590_1519_6984_245592 |
| PublicationCentury | 2000 |
| PublicationDate | 2024-00-00 |
| PublicationDateYYYYMMDD | 2024-01-01 |
| PublicationDate_xml | – year: 2024 text: 2024-00-00 |
| PublicationDecade | 2020 |
| PublicationPlace | Brazil |
| PublicationPlace_xml | – name: Brazil – name: São Carlos |
| PublicationTitle | Brazilian journal of biology |
| PublicationTitleAlternate | Braz J Biol |
| PublicationYear | 2024 |
| Publisher | Instituto Internacional de Ecologia |
| Publisher_xml | – name: Instituto Internacional de Ecologia |
| References | SU C.T. (ref12) 2018; 36 CHEN H (ref1) 2018; 6 MORRIS G.M. (ref4) 2009; 30 SALI A. (ref10) 1993; 234 CRONK D. (ref2) 2013 O’BOYLE N.M. (ref6) 2011; 3 KÖNNYŰ B. (ref3) 2013; 9 MUHAMMAD S. (ref5) 2021; 83 PEREZ M.A.S. (ref7) 2010; 114 RISHTON G.M. (ref9) 2003; 8 SILVA ML (ref11) 2020 PRABU-JEYABALAN M. (ref8) 2000; 301 CRONK, D.; HILL, R.G.; RANG, H.P. 2013 O’BOYLE, N.M.; BANCK, M.; JAMES, C.A.; MORLEY, C.; VANDERMEERSCH, T.; HUTCHISON, G.R. 2011; 3 SU, C.T.; KWOH, C.; VERMA, C.S.; GAN, S.K. 2018; 36 RISHTON, G.M. 2003; 8 KÖNNYŰ, B.; SADIQ, S.K.; TURÁNYI, T.; HÍRMONDÓ, R.; MÜLLER, B.; KRÄUSSLICH, H.G.; COVENEY, P.V.; MÜLLER, V. 2013; 9 MORRIS, G.M.; HUEY, R.; LINDSTROM, W.; SANNER, M.F.; BELEW, R.K.; GOODSELL, D.S.; OLSON, A.J. 2009; 30 SALI, A.; BLUNDELL, T.L. 1993; 234 MUHAMMAD, S.; MAQBOOL, M.F.; AL-SEHEMI, A.G.; IQBAL, A.; KHAN, M.; ULLAH, S.; KHAN, M.T. 2021; 83 PEREZ, M.A.S.; FERNANDES, P.A.; RAMOS, M.J. 2010; 114 PRABU-JEYABALAN, M.; NALIVAIKA, E.; SCHIFFER, C.A. 2000; 301 CHEN, H; GUO, W; SHEN, J; WANG, L; SONG, J. 2018; 6 SILVA, ML; DIAS, MFR 2020 |
| References_xml | – volume: 9 issue: 6 year: 2013 ident: ref3 article-title: Gag-Pol processing during HIV-1 virion maturation: a systems biology approach publication-title: PLoS Computational Biology doi: 10.1371/journal.pcbi.1003103 – volume: 30 start-page: 2785 issue: 16 year: 2009 ident: ref4 article-title: AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility publication-title: Journal of Computational Chemistry doi: 10.1002/jcc.21256 – volume: 301 start-page: 1207 issue: 5 year: 2000 ident: ref8 article-title: How does a symmetric dimer recognize an asymmetric substrate? a substrate complex of HIV-1 protease publication-title: Journal of Molecular Biology doi: 10.1006/jmbi.2000.4018 – volume: 36 start-page: 4366 issue: 16 year: 2018 ident: ref12 article-title: Modeling the fulllength HIV-1 Gag polyprotein reveals the role of its p6 subunit in viral maturation and the effect of non-cleavage site mutations in protease drug resistance publication-title: Journal of Biomolecular Structure & Dynamics doi: 10.1080/07391102.2017.1417160 – volume: 6 start-page: 11760 year: 2018 ident: ref1 article-title: Structural principles analysis of host-pathogen protein-protein interactions: a structural bioinformatics survey publication-title: IEEE Access doi: 10.1109/ACCESS.2018.2807881 – volume: 83 year: 2021 ident: ref5 article-title: A threefold approach including quantum chemical, molecular docking and molecular dynamic studies to explore the natural compounds from Centaurea jacea as the potential inhibitors for COVID-19 publication-title: Brazilian Journal of Biology – volume: 8 start-page: 86 issue: 2 year: 2003 ident: ref9 article-title: Nonleadlikeness and leadlikeness in biochemical screening publication-title: Drug Discovery Today doi: 10.1016/S1359644602025722 – volume: 114 start-page: 2525 issue: 7 year: 2010 ident: ref7 article-title: Substrate recognition in HIV-1 protease: a computational study publication-title: The Journal of Physical Chemistry. B doi: 10.1021/jp910958u – volume: 3 start-page: 33 issue: 1 year: 2011 ident: ref6 article-title: Open Babel: an open chemical toolbox publication-title: Journal of Cheminformatics doi: 10.1186/1758-2946-3-33 – start-page: 95 volume-title: High-throughput screening. year: 2013 ident: ref2 – year: 2020 ident: ref11 – volume: 234 start-page: 779 issue: 3 year: 1993 ident: ref10 article-title: Comparative protein modelling by satisfaction of spatial restraints publication-title: Journal of Molecular Biology doi: 10.1006/jmbi.1993.1626 – start-page: 95 year: 2013 end-page: 117 publication-title: Drug discovery and development. – volume: 9 issue: 6 year: 2013 article-title: Gag-Pol processing during HIV-1 virion maturation: a systems biology approach publication-title: PLoS Computational Biology – volume: 301 start-page: 1207 issue: 5 year: 2000 end-page: 1220 article-title: How does a symmetric dimer recognize an asymmetric substrate? a substrate complex of HIV-1 protease publication-title: Journal of Molecular Biology – volume: 3 start-page: 33 issue: 1 year: 2011 article-title: Open Babel: an open chemical toolbox publication-title: Journal of Cheminformatics – volume: 234 start-page: 779 issue: 3 year: 1993 end-page: 815 article-title: Comparative protein modelling by satisfaction of spatial restraints publication-title: Journal of Molecular Biology – year: 2020 publication-title: Polyprep – volume: 30 start-page: 2785 issue: 16 year: 2009 end-page: 2791 article-title: AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility publication-title: Journal of Computational Chemistry – volume: 83 year: 2021 article-title: A threefold approach including quantum chemical, molecular docking and molecular dynamic studies to explore the natural compounds from Centaurea jacea as the potential inhibitors for COVID-19 publication-title: Brazilian Journal of Biology – volume: 6 start-page: 11760 year: 2018 end-page: 11771 article-title: Structural principles analysis of host-pathogen protein-protein interactions: a structural bioinformatics survey publication-title: IEEE Access – volume: 8 start-page: 86 issue: 2 year: 2003 end-page: 96 article-title: Nonleadlikeness and leadlikeness in biochemical screening publication-title: Drug Discovery Today – volume: 36 start-page: 4366 issue: 16 year: 2018 end-page: 4377 article-title: Modeling the fulllength HIV-1 Gag polyprotein reveals the role of its p6 subunit in viral maturation and the effect of non-cleavage site mutations in protease drug resistance publication-title: Journal of Biomolecular Structure & Dynamics – volume: 114 start-page: 2525 issue: 7 year: 2010 end-page: 2532 article-title: Substrate recognition in HIV-1 protease: a computational study publication-title: The Journal of Physical Chemistry. B |
| SSID | ssj0025038 |
| Score | 2.3281717 |
| Snippet | Abstract In recent years, the development of high-throughput technologies for obtaining sequence data leveraged the possibility of analysis of protein data in... In recent years, the development of high-throughput technologies for obtaining sequence data leveraged the possibility of analysis of protein data in silico.... Nos últimos anos, o desenvolvimento de tecnologias de alto rendimento para obtenção de dados sequenciais potencializou a possibilidade de análise de dados... |
| SourceID | doaj scielo proquest pubmed crossref |
| SourceType | Open Website Open Access Repository Aggregation Database Index Database |
| StartPage | e245592 |
| SubjectTerms | 3D structures BIOLOGY fragmentation HIV HIV Protease Human immunodeficiency virus Interfaces Libraries Machine learning modelling Molecular docking Molecular Docking Simulation Pathogens Peptides polyprotein Polyproteins Programming languages Protease Proteinase Proteins Representations Scripts Software State-of-the-art reviews Workflow |
| SummonAdditionalLinks | – databaseName: DOAJ Directory of Open Access Journals dbid: DOA link: http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwrV3daxQxEA9SFHwpfve0SgRBfFi7m8xukscqlgpSDj9K30KSSeTgult6V6H_vZPN3rWC4IuPm69NZjaZ3yTZ3zD2JgSCxUmaCiFCBbKDyrQeK5QQOw2AOO7pnn5RJyf67MzMb4X6ynfCCj1wEdyBjIhNp1vjI4KjxZPwSiuVSQAmuDSSbdfKbJypydXKJCfToWRr6gMya6bqjIb3AghCiz-M0MjV_zeAmdlDaYItb1ucowdsd4KK_LB08SG7E_tH7F4JHnn9mH09vDl75kPi82F5PSc8zdfDsFxxSjz-fMpHHgayVPyCsseHRb_i-bb7T36-CY3LkVZFSnnCfhx9-v7xuJoiJFRBAnmRIoJG1Bq96tqgQmO8abQjFOPyD69RdLpxdSeSSuDRYFKhVQ5DnYzXUTr5lO30Qx_3GCdkQFWcByoA3kQtwIMGbMFhgtrN2LuNyOxFIcKw2YEg8dosXpvFa4t4Z-xDlum2XKawHhNIsXZSrP2XYmdsf6MRO82rlRUqB2zX0NI7Xm-zaUbkYw7Xx-GKyhBoU1LSaGbsWdHkticSMl4VVPttUe1N09-2oxCZ9y07ywSVmuf_Yywv2P3caNm62Wc768ur-JLdDb_Wi9Xlq_HT_Q3qr-4f priority: 102 providerName: Directory of Open Access Journals |
| Title | Application of PolyPRep tools on HIV protease polyproteins using molecular docking |
| URI | https://www.ncbi.nlm.nih.gov/pubmed/34932622 https://www.proquest.com/docview/2717148452 https://www.proquest.com/docview/2612733394 http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1519-69842024000100151&lng=en&tlng=en https://doaj.org/article/3edd16859bed4a2997745379f449caf6 |
| Volume | 84 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| journalDatabaseRights | – providerCode: PRVAON databaseName: Directory of Open Access Journals (DOAJ) customDbUrl: eissn: 1678-4375 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0025038 issn: 1519-6984 databaseCode: DOA dateStart: 20010101 isFulltext: true titleUrlDefault: https://www.doaj.org/ providerName: Directory of Open Access Journals – providerCode: PRVPQU databaseName: Biological Science Database customDbUrl: eissn: 1678-4375 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0025038 issn: 1519-6984 databaseCode: M7P dateStart: 20110201 isFulltext: true titleUrlDefault: http://search.proquest.com/biologicalscijournals providerName: ProQuest – providerCode: PRVPQU databaseName: Environmental Science Database customDbUrl: eissn: 1678-4375 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0025038 issn: 1519-6984 databaseCode: PATMY dateStart: 20110201 isFulltext: true titleUrlDefault: http://search.proquest.com/environmentalscience providerName: ProQuest – providerCode: PRVPQU databaseName: Health & Medical Collection customDbUrl: eissn: 1678-4375 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0025038 issn: 1519-6984 databaseCode: 7X7 dateStart: 20110201 isFulltext: true titleUrlDefault: https://search.proquest.com/healthcomplete providerName: ProQuest – providerCode: PRVPQU databaseName: Latin America & Iberia Database customDbUrl: eissn: 1678-4375 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0025038 issn: 1519-6984 databaseCode: CLZPN dateStart: 20110201 isFulltext: true titleUrlDefault: https://search.proquest.com/latinamericaiberian providerName: ProQuest – providerCode: PRVPQU databaseName: ProQuest Central customDbUrl: eissn: 1678-4375 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0025038 issn: 1519-6984 databaseCode: BENPR dateStart: 20110201 isFulltext: true titleUrlDefault: https://www.proquest.com/central providerName: ProQuest – providerCode: PRVPQU databaseName: Publicly Available Content Database (ProQuest) customDbUrl: eissn: 1678-4375 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0025038 issn: 1519-6984 databaseCode: PIMPY dateStart: 20110201 isFulltext: true titleUrlDefault: http://search.proquest.com/publiccontent providerName: ProQuest – providerCode: PRVPQU databaseName: Research Library customDbUrl: eissn: 1678-4375 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0025038 issn: 1519-6984 databaseCode: M2O dateStart: 20110201 isFulltext: true titleUrlDefault: https://search.proquest.com/pqrl providerName: ProQuest |
| link | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwpV1Lb9QwELZoCxIX3tBAWRkJCXEI3diT2D6htmrVSu0SFagWLpFjO1WlJdlutkj994ydbBYkxIWLo_gR2R6P_XnsfEPIW2MQFldcxRYcxMAziFVa2thycJkEsDbYdC9OxWQip1OV9wa3tr9WuZoTw0RtG-Nt5LtMeFfdElL2cX4de69R_nS1d6GxQbY8SwILV_fyYcPlqU4CX2qi4kxJ6I8pUzXeHeI-MEBQzf5YlgJ7_98gp-cTRZWb_b4GHT3839o_Ig969En3uuHymNxx9RNyr_NHefuUnO-tj7NpU9G8md3mCNHpsmlmLcXI45MLGqgdcPGjc0wOL1d1S_0F-kv6Y-Vtl2KdvBX-Gfl6dPjl4DjunS7EhgNuTJkDaa2UthRZaoRJVKkSqREYaf8PrWOZTPQ4Y5WooLTKVsKkQlszrlQpHdf8Odmsm9ptE4pgA4voEjADlMpJBiX2gU1B2wrGOiLvV31ezDtujcLvSVA-hZdP4eVTdPKJyL4XypDPs2KHiGZxWfRKVnBnbZLJVJXOgsaFFrFtyoWqAJTRVRaRnZV0il5V22Itmoi8GZJRyfzJia5dc4N5EAcKzrE1EXnRDYWhJhw8BGZY-l03Ntaf_jy0gnkqOb__RvSVvPx3NV6R-z57Z-fZIZvLxY17Te6an8urdjEiG2IqQihHZGv_cJKf4_Pg9Hs-GQWDAoZn7NMoaAKm5Cdn-bdfgp8G0w |
| linkProvider | ProQuest |
| linkToHtml | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMw1V1Lb9QwEB6VLahceBcWChgJhDiEbuxJYh8QKo9qV92uVlCqcgpO7FSVlmTZbEH7p_iNjPNakBC3HjjGL_nxefyNJ54BeJqmRIszoTyDFj0UIXoqSIxnBNpQIhpT3ekej6PJRJ6cqOkG_GzfwrjfKluZWAlqU6TujnyXRy5Ut8SAv55_81zUKGddbUNo1LA4sKsfpLKVr0bvaH2fcb7__ujt0GuiCnipQNK8uEVpjJQmicIgjVJfJcqXmk5-7R6JWh5KXw9CnkUZJkaZLEqDSJt0kKlEWqEFtXsJNtGBvQeb09Hh9HOn4jnnKpWHVl95oZLYGEYDNdjt0l5yJBrP_zgIq3gBfyO5zoMpbfLZ76fe_vX_bb5uwLWGX7O9ekPchA2b34IrdcTN1W34sLc22LMiY9NitpqSEsKWRTErGSUOR8escl5BxzubU3b1cZaXzD0ROGVf23jCjObA2RnuwKcLGdA29PIit_eAEZ2iKjpBKoCJspJjQnNuAtQmw4Huw4t2jeN57T0kdloX4SF2eIgdHuIaD31440DQlXN-v6uEYnEaN2IkFtYYP5SBSqxBTVSC2HsgIpUhqlRnYR92WjTEjTAq4zUU-vCkyyYx4mxDOrfFOZUhphsJQaPpw90ael1PBDqSz6n28xqL66Y_dqPgzlmeu2Egfunf_3c3HsPW8OhwHI9Hk4MHcNVVrW-1dqC3XJzbh3A5_b48KxePmv3F4MtFQ_QXgKNc5A |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Application+of+PolyPRep+tools+on+HIV+protease+polyproteins+using+molecular+docking&rft.jtitle=Brazilian+journal+of+biology&rft.au=Dias%2C+M.+F.+R.&rft.au=Oliveira%2C+F.+L.+L.&rft.au=Pontes%2C+V.+S.&rft.au=Silva%2C+M.+L.&rft.date=2024&rft.pub=Instituto+Internacional+de+Ecologia&rft.issn=1678-4375&rft.volume=84&rft_id=info:doi/10.1590%2F1519-6984.245592&rft.externalDocID=S1519_69842024000100151 |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1519-6984&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1519-6984&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1519-6984&client=summon |