About this repository

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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

• Tutorials

  • Substructure Alignment Using OpenEye OEChem RMSD
  • Low-Energy Conformer Generation and Overlay
  • Molecular docking, estimating free energies of binding, and AutoDock's semi-empirical force field

• Scripts and Tools

• Info Sheets

• Literature

• Protein Science Glossary

• Useful Links

I am looking forward to your contributions, suggestions, and ideas

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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.

Tutorials

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Substructure Alignment Using OpenEye OEChem RMSD

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A how-to for extracting a substructure from a molecule and use it as query for an alignment to target molecules.
Link to tutorial

Low-Energy Conformer Generation and Overlay

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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

Molecular docking, estimating free energies of binding, and AutoDock's semi-empirical force field

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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

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Scripts and Tools

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• A useful one-liner cheatsheet for quick and simple commands for working with protein structure files.

• the scripts-and-tools subdirectory with tools for, e.g.,

  • center_of_mass.py - calculating the center of mass of protein and ligands
  • pdb_to_fasta.py - converting PDB files into FASTA strings
  • rmsd.py - calculating the RMSD between two molecules
  • grab_atom_radius.py - extracting coordinates from PDB files
  • renumber_pdb.py - renumbering atoms and residues in PDB files
  • split_multimol2.py - splitting a multi-MOL2 file into individual MOL2 files
  • strip_h.py - stripping Hydrogen atoms for single PDB files or nested directories of PDB files

• smilite - a Python module to download and analyze SMILE strings (Simplified Molecular-Input Line-entry System) of chemical compounds from ZINC

• 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 - A simple command line tool that creates an info table from a list of PDB files.

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Info Sheets

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• Iridium dataset of high-quality protein structures PDB code quickreference

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Literature

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• Literature overview and summaries

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Protein Science Glossary

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Useful Links

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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.