BioBlender: Fast and Efficient All Atom Morphing of Proteins Using Blender Game Engine

TL;DR

BioBlender is a software tool that leverages Blender's game engine to create fast, realistic animations of protein conformational changes, aiding the visualization and analysis of molecular motions based on NMR data.

Contribution

It introduces a novel method for generating all-atom protein transition states using computer graphics technology, specifically Blender, which was not previously applied in this context.

Findings

Successfully generated intermediate conformations of Calmodulin

Enabled visualization of protein motions based on NMR data

Provided an accessible tool with tutorials and examples

Abstract

In this and the associated article 'BioBlender: A Software for Intuitive Representation of Surface Properties of Biomolecules', (Andrei et al) we present BioBlender as a complete instrument for the elaboration of motion (here) and the visualization (Andrei et al) of proteins and other macromolecules, using instruments of computer graphics. A vast number of protein (if not most) exert their function through some extent of motion. Despite recent advances in higly performant methods, it is very difficult to obtain direct information on conformational changes of molecules. However, several systems exist that can shed some light on the variability of conformations of a single peptide chain; among them, NMR methods provide collections of a number of static 'shots' of a moving protein. Starting from this data, and assuming that if a protein exists in more than 1 conformation it must be able to transit between the different states, we have elaborated a system that makes ample use of the computational power of 3D computer graphics technology. Considering information of all (heavy) atoms, we use animation and game engine of Blender to obtain transition states. The model we chose to elaborate our system is Calmodulin, a protein favorite among structural and dynamic studies due to its (relative) simplicity of structure and small dimension. Using Calmodulin we show a procedure that enables the building of a 'navigation map' of NMR models, that can help in the identification of movements. In the process, a number of intermediate conformations is generated, all of which respond to strict bio-physical and bio-chemical criteria. The BioBlender system is available for download from the website www.bioblender.net, together with examples, tutorial and other useful material.