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We should switch to openMM for minimization after structural models have been built.
- Need to minimize structures with small molecules bound
- Want to score structures with both protein+ligand …
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## Motivation
Pangenomes are key to understanding the distribution of gene content and synteny across closely related genomes. Currently, the driving force behind this strategy is sequence alignmen…
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Hi, I used rfaa to test the posebuster set, but the precision I got was not as good as the 42% docking success rate mentioned in the article. I think my test protocol is not consistent with yours. Cou…
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Hi,
I'm interested in capturing the exact state of the receptor after flexible docking.
It seems there is no description about that on docs, but is there any way to do that with vina?
If not…
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Hi,
I've heard of this strong model which can learn atomic coordinates. Now I want to adapt this model for my project, but I find the code is a bit complicated and hard to follow. (The paper also c…
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Hi all
I'm interested in generating contact maps from the ESM2 attention heads as described in the following github notebook:
https://github.com/facebookresearch/esm/blob/main/examples/contact_predi…
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While working with the hif2a system and the current protein.pdb file I figured out that it differs to the pdb structure used in the merck benchmark study (Please see the pictures). When using the prot…
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### Team Name:
Lindwurm
### Team Member:
Sangwoo Park ( shadow1229@naver.com / shadow1229@snu.ac.kr )
### Project Description:
The goal of the project is building quantum machine lea…
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Thank you for providing an example showing how to run DiffDock-PP inference with PDB files. I was able to run the example you provided, but I'm confused by the output. The pdb files generated by th…
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## *Hosting Details*
*The Request will be deployed on the infrastructure requested through the latest on-boarding request. Please raise an updated on-boarding request if extra resources are required …