Fibrilizer is composed of four tools: CreateFibril
This tools is the first of its kind in building atomic resolution models of protein fibrils. Starting with the PDB file of an amyloid structure, one can specify the structural parameters needed to build polymorphic fibrils. H-bond distances specify the distances in angstroms between aggregated monomers on a fibril, rotation angele specifies the fibril twist in degrees, and the polymorphism type selects the number and orientation of the filaments making up the fibril. Fibrils can be created in different ways. Specifying the fibril axis (in the JMOL applet) is necessary to aggregate monomers.
The tool uses affine matrix transformations to build the aggregates. A detailed description of this process can be found here
When citing this tool in any scientific publication please refer to it as:
Mohamed Raef Smaoui, Frederic Poitevin, Marc Delarue, Patrice Koehl, Henri Orland, Jerome Waldispuhl, Computational Assembly of Polymorphic Amyloid Fibrils Reveals Stable Aggregates, Biophysical Journal, Volume 104, Issue 3, 5 February 2013, Pages 683-693, ISSN 0006-3495, http://dx.doi.org/10.1016/j.bpj.2012.12.037.
This tool analyzes the stability of proteins by detecting weak points in amyloid strucures. The tool takes in a PDB file and internally extracts Beta strands, Beta sheet regions, hydrphobic residues, hydrophilic residues, charged regions, salt bridges, and amyloid cores.
The tool returns single point mutations that potentially weaken fibril stability, increase the nucleation barrier, and inhibits or leads to shorter fibrils.