Tool:Neurosnap Tools: New Fully Open Source Package For Molecular Biology
0
2
Entering edit mode
8 days ago
keaun ▴ 40

Hi everyone,

Excited to share a brand new package our team has been working on for parsing and working with structural and sequence data.

Current features include easy ways to:

  • Generate MSAs, including using hmmer + mafft, mmseqs2, and more methods coming in the near future.
  • Easily parse structures and complexes.
  • Remove waters and non-biopolymers.
  • Align and compute RMSDs.
  • Find structural features such as salt bridges, disulfide bonds, hydrophobics, and more.
  • Easily extract coordinates for all atoms, specific segments of a structure, or even just the backbone.
  • Easy to access dataframe corresponding to the loaded structure (similar to biopandas).
  • Ability to generate diverse conformers using RDkit in a compute friendly way.
  • Calculate Sequence Identity.
  • Generate static and animated pseudo 3D plots of your proteins.
  • Calculate lDDT between proteins.
  • Calculate AlphaFold2 derived metrics such as iPAE.
  • And much more!

We are also planning on actively developing this package so if you are looking for a feature that hasn't been added yet. Definitely, let us know as there's a good chance we can implement.

Demo Notebook: https://colab.research.google.com/github/NeurosnapInc/neurosnap/blob/main/example_notebooks/protein.ipynb

Github: https://github.com/NeurosnapInc/neurosnap

Full disclosure Neurosnap is a for profit company and the collection of tools outlined in this post are intended to be fully open source and free to use for everyone!

msa protein docking ligand pdb • 151 views
ADD COMMENT

Login before adding your answer.

Traffic: 1694 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6