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Hi, I am a beginning user of openmm toolkit. I followed [this tutorial](https://htmlpreview.github.io/?https://github.com/openmm/pdbfixer/blob/master/Manual.html) and everything seems good. However, I…
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[Hayes, Joseph M., and Georgios Archontis. "MM-GB (PB) SA calculations of protein-ligand binding free energies." Molecular Dynamics-Studies of Synthetic and Biological Macromolecules (2012): 171-190](…
cramg updated
3 years ago
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Hi! This is a great package with many useful resources!
After looking into it, we were wondering if it can also be used to model cellular communication. More precisely, we would like to extend INDRA…
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Hi
I was wondering if one can use groamcs-ramd to get binding events instead of unbinding. Is it possible to change the parameters in which the ligand approaches the binding site instead of getti…
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https://doi.org/10.1109/BIBM.2016.7822515 (https://arxiv.org/abs/1611.05777)
> Transcription factors (TFs) are macromolecules that bind to \textit{cis}-regulatory specific sub-regions of DNA promot…
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Hi,
I wanted to express my excitement about the team's plans to release the training code for OpenFold-Multimer (press report [here](https://www.businesswire.com/news/home/20240219658831/en/OpenFol…
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I'm currently working with fingerprints calculation in molecular dynamics trajectories.
To do this I need to convert protein and ligand in a pdb file for every single frame, and then reopen every fil…
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Dear Dr. Huang, I have encountered following errors when applying the sample_for_pdb.py . Would you please help me with it? Many thanks.
python -u sample_for_pdb.py --ckpt pretrained/500.pt --pdb_p…
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- MDFP (https://pubs.acs.org/doi/10.1021/acs.jcim.6b00778), a package for extracting features from molecular dynamics trajectories, which can be used for machine learning applications.
- LigGrep (htt…
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When I use your full_atom.ckpt to sample for the protein pockets in the test set of CrossDocked dataset, the following error occured.
```
File "DiffSBDD/equivariant_diffusion/dynamics.py", line 14…