YASARA related links

If you try one of the external developments below, please be aware that we cannot provide support ourselves. If you are working with YASARA yourself and have a website to show, please add it here.

CMBI - The Center for Molecular and Biomolecular Informatics at the Radboud University Medical Centre in Nijmegen, the Netherlands has kindly hosted YASARA development in the early days from 2000 to 2004. It has made extensive use of YASARA for research and teaching (image on the right courtesy of Bart van Dieken), often combined in the Twinset with Gert Vriend's WHAT IF program.

WHAT IF - The legendary molecular modeling program developed by Gert Vriend and his students since the 1980s, mostly at the EMBL in Heidelberg and the CMBI in Nijmegen. Since 2005, a joint distribution of WHAT IF and YASARA is available as the Twinset, which makes classic WHAT IF functions available with the latest Vulkan 3D graphics and virtual reality headsets. In the mean time, WHAT IF development has moved to a tropical island.

Bio-Prodict - Developer of 3DM, a tool that can automatically generate super-family specific databases designed to guide scientific research in the field of protein engineering, drug design and DNA-diagnostics, and employs YASARA as an interactive database interface.

FoldX plugin - A YASARA interface to FoldX free energy predictions developed at the Centre for Genomic Regulation in Barcelona.

YAMACS plugin - A YASARA interface to run GROMACS.

YAPyCon - A real-time Python console for YASARA with examples.

YAPlTemp - A cookiecutter template to kickstart YASARA plugin development.

Binding-site definition - A collection of macros and shell scripts to pre-process existing complexes for re-docking.

Videos related to YASARA

The following videos feature YASARA, were created with YASARA, or with the help of YASARA (combined with other 3D animation software):

Introductory video on amino acids by Reinhard Wimmer
Introductory video on peptide conformation by Reinhard Wimmer
Introductory video on the Ramachandran plot by Reinhard Wimmer
Scientific animation: protein production and folding by Spronk Studio
How to study the impact of entropy on enzyme catalysis by Kürten and Syren, KTH Royal Institute of Technology
WeNMR Small Angle X-ray Scattering by Spronk Studio
Bio-NMR information campaign on structural biology by Spronk Studio
Asper Biotech - Arrayed Primer Extension technology by Spronk Studio