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Hello!
This is more of a question than an issue.
Let's say we want to simulate a protein-ligand complex. For the protein we use the Amber forcefield and for the ligand GAFF. However, the ligand…
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## 🐛 Bug
## To Reproduce
Steps to reproduce the behavior:
1. Running the 14_Modeling_Protein_Ligand_Interactions_With_Atomic_Convolutions
2. Trying to featurize the pdbbind dataset
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SPICE 2 is close to finished, which means this is a good time to discuss possible additions for version 3. Here are some ideas to get things started.
- **Nonbonded interactions between amino acids…
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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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Hi,
CPDB calculates the mean values in the output file "means.txt" as the mean between interaction partner_a & partner_b.
Problem_1:
A high mean might be misleading if partner_a has a very high…
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### Colocar um resumo ou as partes mais importante do abstract (4 linhas máx.) dos seguintes artigos:
- [ ] _P. Zhou et al., A pneumonia outbreak associated with a new coronavirus of probable bat o…
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https://jcheminf.springeropen.com/articles/10.1186/s13321-015-0110-6
_Edit:_
https://doi.org/10.1186/s13321-015-0110-6
>**Background**
A number of algorithms have been proposed to predict the …
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Hi, I got his error while running on this colab tutorial (Part 13): https://colab.research.google.com/github/deepchem/deepchem/blob/master/examples/tutorials/13_Modeling_Protein_Ligand_Interactions.ip…
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This [recent preprint](https://arxiv.org/abs/2305.05475) (from @proteneer @maxentile, and others) shows a really nice method that can greatly accelerate sampling of regions of interest. The basic idea…
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**In broad terms, what are you trying to do?**
On F@H, log a collection of information on (finished) free energy calculations, related to https://github.com/openforcefield/fah-alchemy/issues/2. T…