During my work and hobbies, I started accumulating useful material about different topics in Protein-Science, which I wanted to collect in a central place and share with others in hope that it might serve as a useful reference one day.
If you have any suggestions or want to make additions, I would be very happy if you could send me
- an email,
- leave me a message on google+,
- or even send me a tweet on twitter (given you can fit it within the 140 character limit ;)).
Or even better: It would be great if you would simply fork this project and send me a pull request.
A how-to for extracting a substructure from a molecule and use it as query for an alignment to target molecules.
Link to tutorial
Tutorial and script to generate low-energy conformers of query and target molecules and overlay them to choose the highest-scoring hit using OpenEye software.
Link to tutorial
Useful scripts for working with protein files in FASTA, PDB, and MOL2 formats
Please visit scripts-and-tools subdirectory for documentation and examples.
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smilite - a Python module to download and analyze SMILE strings (Simplified Molecular-Input Line-entry System) of chemical compounds from ZINC
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pyprot - a Python package for working with protein structure files formats. It comes with a collection of ready-to-use scripts for the most common file operations and protein analyses.
- Iridium dataset of high-quality protein structures PDB code quickreference
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ZINC
A free database for > 35 million purchasable chemical compounds for virtual screening. -
RCSB Protein Data Bank (PDB)
The world's largest repository for downloadable 3D structures of biological molecules, including protein nucleic acid (DNA) structures. -
EMBL-EBI PDBsum
A Pictorial database of 3D structures in the Protein Data Bank that provides additional useful information, e.g., visualization between protein-ligand interactions. -
Ligscore - Pose & Rank
A web server for scoring protein-ligand complexes based on statistical potentials.