W16 - Workshop on Tools and Techniques for Analysis and Design of Macromolecular Structures



September 6th 2014


Samuel C. Flores (Uppsala University, Sweden)

Grzegorz Chojnowski (International Institute of Molecular and Cell Biology, Poland)


In this 1-day workshop, we will present techniques to analyze, design, and optimize models of proteins, DNA, RNA, and their complexes for scientific and industrial applications. The workshop will comprise two parts, a lecture session and hands-on exercises with participants laptops. Invited speakers 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 interactions and 3D structures of RNA and protein-RNA complexes, e.g. from low-resolution density maps and biochemistry.

Why you should attend this workshop

Several fast-growing fields in academic and industrial research are centered around nanotechnology and macromolecular analysis and design. Many protein and RNA complexes (e.g. the ribosome) are known structurally, but their dynamics are not well understood. RNA Origami structures to deliver drugs are under development. There is a boom in antibodies and alternative scaffolds, which are designed to bind proteins in human patients for therapy and diagnosis. Enzymes can be engineered for stability and specificity. In many of these applications, development based only on experiments is possible, but very laborious and often unreliable. On the other hand, the quality of computer methods has improved to the point that a non-specialist can get quantitative predictions from modeling which can save months of time in the laboratory. Participants in this workshop will learn to use these tools to become more effective modelers, or to complement their experimental work with modeling.

Target audience

Advanced undergraduates, MS, or PhD students, postdocs, and faculty in Molecular Biology, Biochemistry, Bioinformatics, Biotechnology, or related fields. Anyone with an interest in macromolecular structure and dynamics.



9:00 Opening remarks

9:10 Eric Westhof, "RNAPuzzles: Recent comparisons between Predictions and Structures"

9:30 Mark Bathe, "Computational Design Principles for Functional Nucleic Acid Nanostructures"

9:50 Ian Moal, ‚ÄúTools for the protein-protein interaction design, docking and affinity prediction.‚ÄĚ

10:10 Samuel Flores, "Evaluating the effect of mutations in protein-protein interfaces with a multiscale approach"

10:30 Coffee

11:00 Grzegorz Chojnowski (Bujnicki Lab) ‚ÄúRNA Bricks - a database of RNA 3D motifs and their interactions‚ÄĚ

11:20 Francois Major, ‚ÄúStructural dynamics control the microRNA maturation pathway‚ÄĚ

11:40 Jo√£o Rodrigues (Bonvin Lab), ‚ÄúIntegrative Modeling of Protein Interactions‚ÄĚ

12:00 Lunch


1:00 Using HADDOCK to model protein interactions (Jo√£o Rodrigues)

2:00 Predict RNA 2D and 3D structure over the Internet using MC-Tools (Francois Major) [download tutorial]

3:00 Modeling Large Macromolecular Complexes with PyRy3D (Grzegorz Chojnowski) [download tutorial]

4:00 MMB (MacroMoleculeBuilder) tutorial (Samuel Flores)


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