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Hello,
This is a really nice tool, thanks for the hard work.
I am looking to use the tool with molecules output from generative models which do not come with pharmacophore information in the "Pu…
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- [x] Layla: Generate target pharmacophore models
- [ ] Renan: Generate classifier based on clustering of scaffolds
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[Yang, Sheng-Yong. "Pharmacophore modeling and applications in drug discovery: challenges and recent advances." *Drug discovery today* 15, no. 11-12 (2010): 444-450.](https://doi.org/10.1016/j.drudis.…
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Hi! I am trying to follow the Pharmmaker [tutorial](http://prody.csb.pitt.edu/tutorials/pharmmaker/) to generate pharmacophore models for a protein simulated with probes and analyzed using DruGUI. I h…
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[Zoe Cournia, Bryce K. Allen, Thijs Beuming, David A. Pearlman, Brian K. Radak, and Woody Sherman. "Rigorous free energy simulations in virtual screening". *Journal of Chemical Information and Modelin…
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We are working on a generative model to identify new hits that bind the MurD allosteric pocket. This project is a collaboration between the [SBNB](https://sbnb.irbbarcelona.org/) and [Ersilia](https:/…
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### Model Name
Pharmacophore-guided molecular generation
### Model Description
Based on a molecule's pharmacophore, this model generates new molecules de-novo to match the pharmacophore. A graph ne…
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Hi,
I have a question related to results of model building.
In the statistics file, I can see a line like this
cdk8 t1_f7_p0 36 11 94 131 0.766 0.383 0.084 0.511 0.426 0.638 0.65 1.833 4 8.8…
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Hi,
I managed to install the package, but when i run md2pharm using the command
md2pharm -i md_center.xtc -t pharmd.pdb -s 10 -g LIG -o pharmaco/frames.pdb
i got the message:
File "/home/…
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Hello, I have just installed psearch and all the env dependencies in conda. I downloaded the acetylcholinestarase (AChE) dataset to do a test and in the phase of preparing the dataset I came across th…