Structural Modeling for Large Macromolecular Complexes

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   IMPORTANT DATES for this Course
   Deadline for applications: May 20th 2014 (extended deadline)
  Latest notification of acceptance: May 21st 2014
   Course date: June 11th - June 13th 2014

Candidates with adequate profile will be accepted in the next 72 hours (in working days) after the application until we reach 20 participants.


Joanna Kasprzak started her scientific career in 2006 when she obtained a Master's degree in bioinformatics, focusing on the analysis of enzymes responsible for RNA modifications. She then specialized in protein and RNA structure prediction and phylogenetic analysis. In 2013 she was awarded a PhD from Adam Mickiewicz University in Poznan, Poland under a supervision of Prof. Janusz M. Bujnicki. A major element of her thesis was the development of PyRy3D, a software tool for the modeling of large macromolecular complexes, and its application to the prediction of structure for a complex involved in DNA repair pathways. This software has been shortlisted by the "Killer Application" Award Committee at the ISMB/ECCB conference in Vienna, Austria, in 2011 and has been received with enthusiasm by its first group of users.
In 2013 she was hired in the International Institute of Molecular and Cell Biology in Warsaw as a PostDoc. Her research now focuses mainly on modeling of large macromolecular complexes. In her work, apart from using common modeling tools and pipelines, she continues development of PyRy3D program. To understand and predict function and mechanism of action of complexes of interest, Joanna collaborates a lot with experimental biologists who deliver her data from cryo-EM, SAXS, chemical cross-linking and FRET experiments.

Affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, PL and Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznań, PL.

Grzegorz Chojnowski obtained his PhD in biophysics from the University of Warsaw in 2010, under the supervision of Prof. Matthias Bochtler. He is currently a PostDoc in the group of Prof. Janusz M. Bujnicki at the International Institute of Molecular and Cell Biology in Warsaw. His main research interests are the development of new tools for the macromolecular crystallography ( and structural studies of RNA and protein-RNA complexes ( He is also an experienced user of both experimental (x-ray crystallography, SAXS) and computational methods for protein and RNA structure determination.

Affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, PL.

Course description

One of the major challenges in structural biology is to determine the structures of macromolecular complexes and to understand their function and mechanism of action. However, structural characterization of macromolecular assemblies is very difficult. To begin addressing this problem, we have developed PyRy3D.
In a nutshell, PyRy3D employs a hybrid computational approach that incorporates spatial information from a variety of experimental methods into the modelling procedure to build low-resolution models of large macromolecular complexes. The PyRy3D model building procedure uses a Monte Carlo approach to sample the solutions-space. It uses spatial restraints to define components interacting with each other, and a simple scoring function is applied to pack them tightly into contours of the entire complex (e.g. cryoEM density maps).

Target Audience

The course is oriented to structural biologists and bioinformaticians interested in modeling of multi-subunit biological complexes, mainly at the graduate and post-graduate levels. Minimal computational skills are required. We anticipate that this course is attended by people with a rather wide variety of interests in biological complex structures, and that will make its delivery more challenging, while ensuring richer experiences to the participants. It is likely that they may also aim at getting involved in generating their own structural models for complexes of their interest, but that does not have to be the case for all the participants: they may, for example, just want to explore publicly available data.

Course Pre-requisites

Graduate level knowledge in the Life Sciences. Minimum familiarity with Linux command line level usage is useful, but NOT strictly required. Scripting in Python is also useful, to enable the discovery of the full potential usage of the techniques. Basic understanding of molecular biology and no particular computing expertise will be assumed.

Detailed Program

Instituto Gulbenkian de Ciência,

Apartado 14, 2781-901 Oeiras, Portugal

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Last updated:  Apr 14th 2014