Abstract:
Recent advances in highly performant investigation methods contribute to obtain information about cells, from molecules to tissues, acros 4 orders of magnitude: from cell shape and composition to atomic structure of macromolecules. Our aim is to integrate available information about biomolecules activities and present them in an intuitive, animated form ( www.scivis.it). The cellular environment and its components are recreated in Blender, a free, open-source, 3D modelling, animation and rendering package. 

We focused on atomic scale visualization and developed BioBlender (www.bioblender.eu), a package dedicated to biological work, that comprise two major features: elaboration of proteins' motions using the game engine and the simultaneous visualization of physico-chemical features on molecular surface. Blender's Game Engine is used to calculate protein motions by interpolating between different conformations according to specific rules. Transition between NMR collections or different X-rays structures of the same protein are obtained, as physically plausible sequence of intermediate conformations that are the basis for the subsequent visual elaboration.

A new visual, photo-realistic code, is introduced for MLP visualization: a range of optical features, from dull-rough-dark surfaces for hydrophilic areas to shiny-smooth-clear for lipophilic.

EP is represented as animated line particles that flow along field lines, from positive to negative, proportional to the total charge of the protein.

BioBlender is a new and fast system to calculate conformational changes of proteins between known conformations. It also includes a novel code for their intuitive representation, which contributes to gain insight into the function of molecules by drawing viewer's attention to the most active regions of the protein. A more direct visualization can result in an increased understanding of biological activities.

For further details or to contact Monica while she is visiting BSC, please contact Fernando, fernando.cucchietti@bsc.es

www.bsc.es/marenostrum-support-services/hpc-education-and-training/severo-ochoa-research-seminar/0307-sors