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Structural Alignment

Title: Structural Alignment and Superposition

Lecturer: J. Rodríguez-Guerra, A. Volkamer

Maximum number of participants: 5

Period/preliminary appointment: 1. March - 30. April 2020  (preliminary meeting t.b.a.)

Location: Institute of Physiology, 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, will be 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 will fill that gap with a modern Python package designed under the current best practices for development, testing and deployment. Ultimately, the tool could be integrated into a web-application for increased impact and reach.

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://github.com/volkamerlab/structuralalignment/blob/master/20200131%20Structural%20Alignment.pdf

Language: English

eVV WiSe 20/21