PyRy3D server

A server for modeling of large macromolecular complexes

by Joanna M. Kasprzak, Mateusz Dobrychłop, Mateusz Susik, Laura Pogorzelska, Rafał Niemiec, Witold Rudnicki and Janusz M. Bujnicki.

http://pyry3d.icm.edu.pl

What is the PyRy3D server?

This service is based on the PyRy3D software for structure prediction and analysis of large macromolecular complexes.

Currently, the server allows to build model of a complex based on the following criteria:

  • sequences of all components
  • structures of some components; here a user can provide experimentally determined structures (from X-ray or NMR),
    theoretical models or even coordinates only for parts of components
  • restraints describing features of the complex such as: distances, surface access etc.
  • shape of the complex e.g. electron density map or raw data from SAXS/SANS

For each modeling task a user selects parameters defining simulation process such as:
  • number of steps
  • sampling algorithm e.g. Genetic, Simmulated Annealing or Replica Exchange
  • frequencies of mutation operations including rotations, translations, exchanges of two components, simulate disorder, rotation around a line
  • weights for penalties assigned for clashes, violation of restraints and empty spaces inside a density map (if provided)
  • grid radius
  • representation of structures here a user can select: full-atom, and several types of reduced representations (implemented for proteins and for nucleic acids)
  • number of models to be saved on disk

To execute your request go to the [submit] section.




The server was tested on the following browsers:
  • Windows: Internet Explorer v. 8 or higher, Firefox v. 4, Google Chrome, Safari 5, Opera v. 10 or higher
  • Linux: Firefox v. 4, Google Chrome, Opera v. 10 or higher
  • Mac OS: Firefox v. 4, Google Chrome, Safari 5, Opera v. 10 or higher