Protein Structure Theory Group

Using PyMOL as a Protein Structure workbench

This page focuses on PyMOL. More about the Protein Structure Theory Group can be found at www.charite.de/bioinf.

PyMOL Plugins Tips from the PyMOL mailing list Columba - Database of Protein Structure Annotation PDBList.py - A tool for tracking changes in the PDB PyMOL links

For structure-based studies, the most essential component of a work environment is a molecular display and modeling tool. PyMOL is an open-source molecular modeling program written in the Python language. For achieving a high picture quality and performance, basic parts of the software were implemented in C. As all the user interaction can be handled through a Python programming interface, extending the PyMOL platform is very straightforward. Python code is inherently quick to be written and easy to maintain. Thus, connecting the PyMOL environment to other high-performance software is very easy. Columba is a web based query system for comparing annotation of protein structures. For Columba, lots of data sources like SCOP, CATH, SWISS-PROT, DSSP, KEGG, PISCES and ENZYME were collected into a single relational database.

Affiliation:

The tools presented here are offspring to a major research effort at the
Protein Structure Theory Group at the Charite Berlin. Our group is member to the Berlin Center of Bioinformatics (BCB). Visit our websites for further information.

Contact:

AG Proteinstrukturtheorie
Institut für Biochemie
an der Charite Berlin
Monbijoustraß 2
10117 Berlin
Humboldt Universität Berlin