How to validate docking and display findings for 2D-QSAR: prepare, dock, and re-dock in detail

In this video, I will show how to validate docking and display findings for 2D-QSAR: prepare, dock, and re-dock in detail.
(1) AutoDock 4.2.6 / AutoDockTools 1.5.6 - Suite of Automated Docking Tools
Link: mybiosoftware....
(2) AutoDock Vina
Link: vina.scripps.e...
(3) Avogadro
Link: avogadro.cc/
(4) MOE
Link: drive.google.c...
(5) Discovery Studio
Link: discover.3ds.c...
**Data and code available here:
github.com/her...
Detail explain here: doi.org/10.101...

[@duc-hainguyen8499]

Link to download:
1) AutoDock 4.2.6 / AutoDockTools 1.5.6 - Suite of Automated Docking Tools
Link: mybiosoftware.com/autodock-4-2-3-autodocktools-1-5-6-suite-automated-docking-tools.html
2) AutoDock Vina
Link: vina.scripps.edu/downloads/
3) Avogadro
Link: avogadro.cc/
4) MOE
Link: drive.google.com/file/d/1X1c7l-U6yCGcsIElnzDPRw8nUMhsgioM/view
5) Discovery Studio
Link: discover.3ds.com/discovery-studio-visualizer-download

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**Data and code available here:
(1) AutoDock 4.2.6 / AutoDockTools 1.5.6 - Suite of Automated Docking Tools
Link: mybiosoftware.com/autodock-4-2-3-autodocktools-1-5-6-suite-automated-docking-tools.html
(2) AutoDock Vina
Link: vina.scripps.edu/downloads/
(3) Avogadro
Link: avogadro.cc/
(4) MOE
Link: drive.google.com/file/d/1X1c7l-U6yCGcsIElnzDPRw8nUMhsgioM/view
(5) Discovery Studio
Link: discover.3ds.com/discovery-studio-visualizer-download
(6) github.com/herrynguyen1706/Selecting-the-best-molecular-descriptor
(7) Detail explain here: doi.org/10.1016/j.compbiolchem.2023.107872

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Thanks for the video @Dr. Henry Nguyen... Is it necessary to use all the softwares you used? Can't the same process be done with only 2 of these softwares?

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You can use different software. However, you need to check your protein and ligand first.

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Thanks for kind responds. Here is my articles for your references: 1. doi.org/10.1016/j.compbiolchem.2023.107872 2. DOI: 10.1080/07391102.2023.2238068

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anh Hải cho em hỏi em đang học docking nên lặp lại phân tích chất 25 của anh nhưng ra docking score là -6.1 ạ, em thao tác cùng lệnh cmd nhưng kết quả không lặp lại thì do đâu ạ? anh có email thì cho em xin để tiện được hỏi anh. E cám ơn anh.

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Chào bạn, mỗi máy tính sẽ có kết quả hơi khác nhau 1 chút, nhưng không nhiều. Chắc bạn chưa fix protein before docking. Missing residue and atoms, and error in protein structures can explain this reason. Here is two my published papers, can you reference it. Hope it helps. doi: 10.1080/07391102.2023.2238068 and doi.org/10.1016/j.compbiolchem.2023.107872

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@@duc-hainguyen8499 Em cám ơn anh đã trả lời ạ, em có làm hết các bước như anh hướng dẫn mà sau đó em lập lệnh nó chạy ra kết quả khoảng -6.8 nhưng nếu em lặp lại lệnh chạy thì nó lại ra kết quả khác ạ, -6.3. Nên em ko rõ làm như nàođể chuẩn nhất và được phép sai số ra sao ạ.

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