Introducing a two‐dimensional graph of docking score difference vs. similarity of ligand‐receptor interactions
Observation of molecular docking results was generally performed by analyzing the docking score and the interacting amino acid residues separately either in tables or graphs. Sometimes it was not easy to rank the tested ligands’ docking results, especially if there were many ligands. This study aims...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Universitas Gadjah Mada, Yogyakarta
2021-03-01
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| Series: | Indonesian Journal of Biotechnology |
| Subjects: | |
| Online Access: | https://jurnal.ugm.ac.id/ijbiotech/article/view/62194 |
| _version_ | 1828041246272126976 |
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| author | Mohammad Rizki Fadhil Pratama Hadi Poerwono Siswandono Siswodihardjo |
| author_facet | Mohammad Rizki Fadhil Pratama Hadi Poerwono Siswandono Siswodihardjo |
| author_sort | Mohammad Rizki Fadhil Pratama |
| collection | DOAJ |
| description | Observation of molecular docking results was generally performed by analyzing the docking score and the interacting amino acid residues separately either in tables or graphs. Sometimes it was not easy to rank the tested ligands’ docking results, especially if there were many ligands. This study aims to introduce a new way to analyze docking results with a two‐dimensional graph between the difference in docking score and the similarity of ligand‐receptor interactions. Molecular docking was performed with one reference ligand and several test ligands. The docking score difference was obtained between the test and the reference ligands as the graph’s x‐axis. Meanwhile, the y‐axis contains the similarity of ligand‐receptor interactions, obtained from the ratio of amino acid residues and the types of interactions between the test and reference ligands. Docking result analysis was more straightforward because two critical parameters were presented in one graph. This graph could be used to support the analysis of the docking results. |
| first_indexed | 2024-04-10T17:06:25Z |
| format | Article |
| id | doaj.art-99442a5122284b6fb77c8cd226962117 |
| institution | Directory Open Access Journal |
| issn | 0853-8654 2089-2241 |
| language | English |
| last_indexed | 2024-04-10T17:06:25Z |
| publishDate | 2021-03-01 |
| publisher | Universitas Gadjah Mada, Yogyakarta |
| record_format | Article |
| series | Indonesian Journal of Biotechnology |
| spelling | doaj.art-99442a5122284b6fb77c8cd2269621172023-02-06T03:00:10ZengUniversitas Gadjah Mada, YogyakartaIndonesian Journal of Biotechnology0853-86542089-22412021-03-01261546010.22146/ijbiotech.6219429528Introducing a two‐dimensional graph of docking score difference vs. similarity of ligand‐receptor interactionsMohammad Rizki Fadhil Pratama0Hadi Poerwono1Siswandono Siswodihardjo2Doctoral Program of Pharmaceutical Science, Faculty of Pharmacy, Universitas Airlangga, Surabaya, East JavaDepartment of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Airlangga, Surabaya, East JavaDepartment of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Airlangga, Surabaya, East JavaObservation of molecular docking results was generally performed by analyzing the docking score and the interacting amino acid residues separately either in tables or graphs. Sometimes it was not easy to rank the tested ligands’ docking results, especially if there were many ligands. This study aims to introduce a new way to analyze docking results with a two‐dimensional graph between the difference in docking score and the similarity of ligand‐receptor interactions. Molecular docking was performed with one reference ligand and several test ligands. The docking score difference was obtained between the test and the reference ligands as the graph’s x‐axis. Meanwhile, the y‐axis contains the similarity of ligand‐receptor interactions, obtained from the ratio of amino acid residues and the types of interactions between the test and reference ligands. Docking result analysis was more straightforward because two critical parameters were presented in one graph. This graph could be used to support the analysis of the docking results.https://jurnal.ugm.ac.id/ijbiotech/article/view/62194analysisdockingdocking scoreinteractiontwo‐dimensional graph |
| spellingShingle | Mohammad Rizki Fadhil Pratama Hadi Poerwono Siswandono Siswodihardjo Introducing a two‐dimensional graph of docking score difference vs. similarity of ligand‐receptor interactions Indonesian Journal of Biotechnology analysis docking docking score interaction two‐dimensional graph |
| title | Introducing a two‐dimensional graph of docking score difference vs. similarity of ligand‐receptor interactions |
| title_full | Introducing a two‐dimensional graph of docking score difference vs. similarity of ligand‐receptor interactions |
| title_fullStr | Introducing a two‐dimensional graph of docking score difference vs. similarity of ligand‐receptor interactions |
| title_full_unstemmed | Introducing a two‐dimensional graph of docking score difference vs. similarity of ligand‐receptor interactions |
| title_short | Introducing a two‐dimensional graph of docking score difference vs. similarity of ligand‐receptor interactions |
| title_sort | introducing a two dimensional graph of docking score difference vs similarity of ligand receptor interactions |
| topic | analysis docking docking score interaction two‐dimensional graph |
| url | https://jurnal.ugm.ac.id/ijbiotech/article/view/62194 |
| work_keys_str_mv | AT mohammadrizkifadhilpratama introducingatwodimensionalgraphofdockingscoredifferencevssimilarityofligandreceptorinteractions AT hadipoerwono introducingatwodimensionalgraphofdockingscoredifferencevssimilarityofligandreceptorinteractions AT siswandonosiswodihardjo introducingatwodimensionalgraphofdockingscoredifferencevssimilarityofligandreceptorinteractions |