UENO, M.

I tried to check out `features.pkl` generated by running AlphaFold to find which templates are used. When `--model_preset=monomer` is used I could find `template_domain_names` as a key name of the...

What is the difference between ADFR and flexible docking using vina?

2

Dear all, Upon reading a tutorial on partially protein-flexible docking using Vina, I couldn’t understand how it differs from ADFR. I’ve read both of the papers on Vina v1.2.0 and...

prepare_receptor causes `ValueError: Could not find atomic number for Hn Hn`

1

I tried to validate the accuracy of Vina on the DUD-E dataset according to the AutoDock Vina v1.2.0 paper and the supporting information description. After adding hydrogens to the receptor...

I noticed `vinardo` lacks in docstrings for `Vina` class though the scoring function is available for docking using AutoDock vina now. Users might know its availability if they read vina's...

After `ns preview` I got this message and could not see the preview. @halfnelson Can you investigate this problem? ``` ReferenceError: navigator is not defined at standardBrowserEnv (file:///var/mobile/Containers/Data/Application/5145D892-1D78-4984-B2AB-6D78652D5C96/Library/preview/vendor.js:48608:41) at Object../node_modules/axios/lib/helpers/isURLSameOrigin.js...

Fix _assign_element to deal with 4 characters atom with last number.

2

- [X] I hereby agree to dual licence this and any previous contributions under both the _Biopython License Agreement_ **AND** the _BSD 3-Clause License_. - [X] I have read the...

### Setup I am reporting a problem with Biopython 1.83, Python 3.11.7, and Linux-6.1.64-09049-g010fe86d9eae-x86_64-with-glibc2.36 as follows: When running `_assign_element` in `PDB/Atom.py`, elements are not correctly assigned for atoms with 4...

Hi, Building docker image using the dockerfile fails because `mamba config` is not implemented. ```shell $ mamba config Currently, only install, create, list, search, run, info, clean, remove, update, repoquery,...

How can I get `tfrecord` data of proteins?

2

Thank you for your work to help train/fine-tune AF2/OpenFold/pLMFold models. I tried to run pLMFold's training using my own protein datasets, but couldn't figure out how proteins' tfrecord data can...

Thank you for your work. I tested this RMSD calculation script. I found a wrong usage in README.md and corrected it. Also, a variable `ref_obj` is defined after its use,...