Biomathematics afternoon in Ljubljana, 2016

Session

First session

Feb 17, 2016, 3:00 PM

2.05 (University of Ljubljana, FMF)

0. Bernhard Thiel (TBI) - Integrating Cryo-EM with Coarse Grained RNA 3D Structure Prediction in ERNWIN

2/17/16, 3:00 PM

Ernwin (Kerpedjiev 2015) is program that performs a Metropolis-Rosenbluth like Monte Carlo sampling of coarse grained RNA 3D structures. Lokal conformations are sampled directly from possible conformations found in crystal structures or structures predicted with very accurate methods. An energy function used in the accept-reject step of the sampling procedure accounts for long-range...

1. Roman Jerala (KI) - Design principles for rapid folding of knotted DNA

2/17/16, 3:20 PM

Knots are some of the most remarkable topological features in nature. Self-assembly of knotted polymers without breaking or forming covalent bonds is challenging, as the chain needs to be steered through the previously formed loops in a predefined order. Here we describe principles to guide the folding of highly knotted single-chain DNA nanostructures as demonstrated on a nano-sized square...

2. Ronny Lorenz (TBI) Constraints in RNA secondary structure predixction

2/17/16, 3:40 PM

Background: A large class of RNA secondary structure prediction programs uses an elaborate energy model grounded in extensive thermodynamic measurements and exact dynamic programming algorithms. External experimental evidence can be in principle be incorporated by means of hard constraints that restrict the search space or by mean of soft constraints that distort the energy model. In...

3. Ajasja Ljubetič (KI) - Designing, modelling and folding protein polyhedra

2/17/16, 4:00 PM

Protein origami is an exciting emerging field, inspired by the success of DNA origami. Proteins however, unlike DNA, have a large number of weak long range interactions which are very difficult to predict and even more to design. This problem can be elegantly solved by using modular components with exactly defined binding partners of which coiled coils are an excellent example (Kočar et al.,...