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Structural Alignment

Title: Structural Alignment and Superposition

Lecturer: J. Rodríguez-Guerra, tba, A. Volkamer

Maximum number of participants: 4

Period/preliminary appointment: tba, (likely March 2021)

Location: virtual (Institut für Physiologie, CCO, Charité Campus Mitte)

Short description of content:

In this internship, an open-source structural alignment Python package for biopolymers, i.e. proteins and ligands, that we started implementing in 2020 will be further developed and released. While diverse structural alignment implementations can be found in visualization software such as PyMol, VMD or UCSF Chimera, a standalone package is currently missing in the Python ecosystem. We have started filling that gap with a modern Python package designed under the current best practices for development, testing and deployment. 

The main focus of this year’s course will be on finalizing the package. This will include, getting familiar with the current code base, working on alignment-specific issues such as automatic structural renumbering as well as benchmarking the tool.

Quantitative allocation (in %):

Practical programming work: 60%

Soft skills: 40%

Programming language(s) used: Python

Difficulty level (Eight stars distributed over three areas):

A Programming: 4*

B Biology/Chemistry: 2*

C Projekt management: 2*

Required previous knowledge: Python 3 und Git

Contact address, website / link:

·        http://volkamerlab.org/

·        https://github.com/volkamerlab/

Presentation: https://volkamerlab.org/2021/01/structural-alignment-2021/

Language: English