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.

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