Small molecule binder design

[wangzaimieyoutou]

When performing small molecule binder design using rfd3, can the results from docking be utilized? Since the small molecule I'm using is custom-designed, I aim to design a protein that will encapsulate it.

[rclune]

First, I would highly recommend posting your question on Foundry's slack, you can join by following this link. Your question will be seen by more scientists in the community if you post it there.

Second, using the results from a previous docking calculation: If you have a structure saved in a PDB or CIF file, you can use that structure as the input and specify which pieces of it you would like to see in your final design via several different options. If you haven't already, I would look at the small molecule binder design examples provided in Foundry's documentation.
The small molecule being custom-designed should not be an issue. If the label you gave it in your PDB/CIF file causes issues, try replacing it with something like L:G to avoid any overlaps with existing molecules in the PDB. (See Issue 91.)

[wangzaimieyoutou]

首先，我强烈建议你在Foundry的Slack上发帖提问，你可以点击这个链接加入。如果你把问题发到那里，社区里会有更多科学家看到。

其次，利用之前对接计算的结果：如果你在PDB或CIF文件中保存了结构，你可以将该结构作为“，并通过多种选项指定你希望在最终设计中看到的部分。如果你还没看过，建议看看Foundry文档里提供的小分子结合剂设计示例。小分子是定制设计的，应该不会成为问题。如果你在PDB/CIF文件中给出的标签出现问题，可以试着用类似的标签替换，以避免与PDB中已有的分子重叠。（参见第91期。）input``L:G

Thank you for your response.The Slack link has expired. Could you please send me a new one？

[r-krishna]

Here is an updated link!