Structural Modelling for Large Macromolecular Complexes

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   IMPORTANT DATES for this Course
   Deadline for applications: April 18th 2015
   Latest notification of acceptance: April 20th 2015
   Course date: April 27th - April 30th 2015

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


Joanna Kasprzak started her scientific career in 2006. She obtained Master degree in bioinformatics analysis of enzymes responsible for RNA modifications. She specialised in protein structure prediction and phylogenetic analysis. In 2013 she got her PhD at the Adam Mickiewicz University in Poznań, Poland under a supervision of Prof. Janusz M. Bujnicki. Her thesis focused mainly on development of a software tool for modelling of large macromolecular complexes, PyRy3D, and applying it to prediction of structure for a complex involved in DNA rapair pathways. The program has been rewarded by Killer Application Award Committee during ISMB/ECCB conference in Vienna in 2011 and has already gained the trust of the first group of users. In 2013 she has been hired in International Institute of Molecular and Cell Biology in Warsaw as a Postdoc. Presently, her research focuses mainly on the modelling of large macromolecular complexes, in particular those involved in DNA repair but also RNA polymerases.
In her work, apart from using common modelling tools and pipelines, she continues with the development of PyRy3D program. To understand and predict function and mechanism of action of the 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, Warsaw, PL
Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznań

Mateusz Dobrychłop is a PhD student in Adam Mickiewicz University in Poznań. In 2010, he started developing PyRy3D Chimera Extension - a plugin that integrates PyRy3D with a popular molecular viewer UCSF Chimera. His MSc thesis, defended in 2014, focused on the modelling of highly disordered SF3b complex engaged in splicing, using the PyRy3D suite.
In 2014, Mateusz started PhD studies under Prof. Janusz Bujnicki's supervision. He is developing a new method for comparative modelling of protein structures, including post translational modifications and ligands.

Affiliation: Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznań


We will present a range of techniques to generate, analyse, and optimise models of proteins, RNA, and their complexes. We will talk about new approaches to structure determination of macromolecules and macromolecular complexes. During the practical sessions participants will learn how to use methods for modelling protein and RNA 3D structures such as Modeller and ModeRNA. Also we will focus on methods dedicated to protein-RNA complexes modelling, e.g. by combining data from low-resolution density maps, SAXS and biochemistry. In particular, we will present how to use PyRy3D, a computational tool to build models of macromolecular complexes based on data from various sources.
Participants will be able to bring-in specific biological questions and/or their on data to work with during the course.

Target Audience

The course has been designed for molecular and structural biologists, bioinformaticians and biotechnologists and other scientists interested in modelling of biological complexes. The content is suitable for researchers, both at the graduate and post-graduate levels.
Minimal levels of computer usage skills are required. We anticipate the participants to have a wide diversity of interests in biological complexes and their structures. It is likely that they may also aim at getting involved in generating structural models for complexes of 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 Life Sciences, interest in structural biology.


Detailed Program

Instituto Gulbenkian de Ciência,

Apartado 14, 2781-901 Oeiras, Portugal

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Last updated:  Mar 15th 2015