PyRy3D Tutorial

Modeling of human polymerase gamma complex structure

In this tutorial you can learn how to use PyRy3D commands to build a simple complex model. In particular you will learn how to e.g.

• Prepare input files for analysis
• Manipulate simulation parameters
• Analyse results

[ Go to polymerase gamma modeling tutorial ]

Modeling of 1NIC complex structure using PyRy3D Chimera Extension

• First steps in using PyRy3D UCSF Chimera Extension
• Automatic complex scoring
• Model analysis
• Running PyRy3D Simulations in UCSF Chimera
• Preparing input files for a command line version of the program
• Generating a ranking of models
• Recording a movie from simulation
• Clustering of obtained models

Modeling solution conformation of a non-coding RNA molecule using PyRy3D web-server

• Tutorial

Additional materials about PyRy3D

• PyRy3D Manual
• PyRy3D concepts
• PyRy3D in practice

​Support from PyRy3D authors

If you have any comments, recommendations, ideas how to improve the workshop or the software please do not hesitate to contact us:

Joanna Kasprzak: This email address is being protected from spambots. You need JavaScript enabled to view it.
Mateusz Dobrychłop: This email address is being protected from spambots. You need JavaScript enabled to view it.
Janusz Bujnicki: This email address is being protected from spambots. You need JavaScript enabled to view it.

Acknowledgments

We would like to acknowledge people who helped us to prepare this tutorial for all recommendations, comments and exhaustive testing of our software: Damien Larivière, PhD (Fourmentin-Guilbert Scientific Foundation, Noisy-Le-Grand, France), Mateusz Koryciński, MSc (Department of Protein Evolution, Max-Planck Institute for Developmental Biology, Tübingen, Germany) and Grzegorz Chojnowski, PhD (Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland)