https://github.com/rasbt/protein-science
A collection of useful tutorials for Protein Science
https://github.com/rasbt/protein-science
protein-data-bank protein-science python
Last synced: 5 months ago
JSON representation
A collection of useful tutorials for Protein Science
- Host: GitHub
- URL: https://github.com/rasbt/protein-science
- Owner: rasbt
- License: gpl-3.0
- Created: 2014-01-31T17:49:29.000Z (over 11 years ago)
- Default Branch: master
- Last Pushed: 2015-06-29T17:22:25.000Z (over 10 years ago)
- Last Synced: 2025-03-30T13:23:17.459Z (7 months ago)
- Topics: protein-data-bank, protein-science, python
- Language: Python
- Size: 14.9 MB
- Stars: 105
- Watchers: 13
- Forks: 41
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
#### About this repository
[[back to top](#about-this-repository)]
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.
- [Software Quick Guides](./scripts-and-tools/more_protein-science_tools.md)
- [Tutorials](#tutorials)
- [Substructure Alignment Using OpenEye OEChem RMSD](#substructure-alignment-using-openeye-oechem-rmsd)
- [Low-Energy Conformer Generation and Overlay](#low-energy-conformer-generation-and-overlay)
- [Molecular docking, estimating free energies of binding, and AutoDock's semi-empirical force field](#molecular-docking-estimating-free-energies-of-binding-and-autodocks-semi-empirical-force-field)
- [Scripts and Tools](#scripts-and-tools)
- [Info Sheets](#info-sheets)
- [Literature](#literature)
- [Protein Science Glossary](#protein-science-glossary)
- [Useful Links](#useful-links)
#### I am looking forward to your contributions, suggestions, and ideas
[[back to top](#about-this-repository)]
If you have any suggestions or want to make additions, I would be very happy if you could send me
- an [email](mailto:se.raschka@gmail.com),
- leave me a message on [google+](https://plus.google.com/118404394130788869227/),
- or even send me a tweet on [twitter](https://twitter.com/rasbt) (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.
# Tutorials
[[back to top](#about-this-repository)]
### Substructure Alignment Using OpenEye OEChem RMSD
[[back to top](#about-this-repository)]
A how-to for extracting a substructure from a molecule and use it as query for an alignment to target molecules.
[Link to tutorial](./tutorials/substructure_alignment/README.md)
### Low-Energy Conformer Generation and Overlay
[[back to top](#about-this-repository)]
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](./tutorials/low_energy_conformer_overlay/README.md)
### Molecular docking, estimating free energies of binding, and AutoDock's semi-empirical force field
[[back to top](#about-this-repository)]
Discussions and questions about methods, approaches, and tools for estimating (relative) free binding energies of protein-ligand complexes are quite popular, and even the simplest tools can be quite tricky to use. Here, I want to briefly summarize the idea of molecular docking, and give a short overview about how we can use AutoDock 4.2's hybrid approach for evaluating binding affinities.
[Link to tutorial](./tutorials/scoring_functions_and_autodock/2014_autodock_energycomps.md)
# Scripts and Tools
[[back to top](#about-this-repository)]
- A useful [one-liner cheatsheet](./scripts-and-tools/oneliner.md) for quick and simple commands for working with protein structure files.
- the **[`scripts-and-tools`](./scripts-and-tools)** subdirectory with tools for, e.g.,
- [`center_of_mass.py`](./scripts-and-tools/center_of_mass) - calculating the center of mass of protein and ligands
- [`pdb_to_fasta.py`](./scripts-and-tools/pdb_to_fasta) - converting PDB files into FASTA strings
- [`rmsd.py`](./scripts-and-tools/rmsd) - calculating the RMSD between two molecules
- [`grab_atom_radius.py`](./scripts-and-tools/grab_atom_radius) - extracting coordinates from PDB files
- [`renumber_pdb.py`](./scripts-and-tools/renumber_pdb) - renumbering atoms and residues in PDB files
- [`split_multimol2.py`](./scripts-and-tools/split_multimol2) - splitting a multi-MOL2 file into individual MOL2 files
- [`strip_h.py`](./scripts-and-tools/strip_h) - stripping Hydrogen atoms for single PDB files or nested directories of PDB files
- **[smilite](https://github.com/rasbt/smilite)** - a Python module to download and analyze SMILE strings (Simplified Molecular-Input Line-entry System) of chemical compounds from ZINC
- **[pyprot](https://github.com/rasbt/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.
- **[PDB Info Table](https://github.com/rasbt/datacollect/tree/master/pdb_infotable)** - A simple command line tool that creates an info table from a list of PDB files.
# Info Sheets
[[back to top](#about-this-repository)]
- Iridium dataset of high-quality protein structures [PDB code quickreference](./info_sheets/Iridium_pdb_codes.md)
# Literature
[[back to top](#about-this-repository)]
- [Literature overview and summaries](./literature/literature_summaries.md)
# [Protein Science Glossary](./glossary/README.md)
[[back to top](#about-this-repository)]
# Useful Links
[[back to top](#about-this-repository)]
- [ZINC](http://zinc.docking.org)
A free database for > 35 million purchasable chemical compounds for virtual screening.
- [RCSB Protein Data Bank (PDB)](http://www.rcsb.org)
The world's largest repository for downloadable 3D structures of biological molecules, including protein nucleic acid (DNA) structures.
- [EMBL-EBI PDBsum](http://www.ebi.ac.uk/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](http://modbase.compbio.ucsf.edu/ligscore/)
A web server for scoring protein-ligand complexes based on statistical potentials.