Welcome to Gront lab laboratory protocols

This repository provides notes, protocols and tutorials related to multiscale modeling of biomacromolecules, primarily proteins and their complexes, that are used in daily research tasks by Gront lab (http://bioshell.pl). While documentation related to BioShell package (bioinformatics and biosimulation tools) can be found on a separate website: http://bioshell.readthedocs.io/, these pages provide practical solutions to common calculations and modelling scenarios.

We make these protocols available under Apache 2.0 license 1.

BioShell protocols

Protocols that utilize mainly BioShell applications:

Rosetta protocols

These pages provide information about Rosetta protocols used by the Gront lab, including Rosetta flag-files and handy one liners that can be copied & pasted into your terminal. To see the full documentaion however, visit rosettacommons.org website

Modeller protocols

Modeller is a widely recognized tool for homology modelling of protein structures.

PyMOL notes

Modeller is a widely recognized tool for homology modelling of protein structures.

Bioinformatic tools

This section desribes common bioinformatics tools such as psiblast or HH-suite