BALL-SNPgp

BALL-SNPgp is the extension of the proof-of-concept tool BALL-SNP, a software tool based on the Biochemical Algorithms Library (BALL), a molecular modeling framework, providing robust and sophisticated algorithms on structural bioinformatics (paper)(webpage).
Our new tool BALL-SNPgp enables the assessment of multiple non-synonymous single nucleotide polymorphisms (nsSNPs) in a single protein by visualizing the mutated residues within the wild type structure, collecting available pathogenicity information from different databases, predicting binding pockets, protein stability changes and pathogenicity, as well as performing a cluster analysis on comprised amino acid substitutions (paper). Based on the generated information and the three-dimensional visualization, a user can assume whether the amino acid substitutions can have a quantitative effect due to mutual interaction or have an influence on binding and stability.

 

BALL-SNP workflow

We currently offer two different input formats:

Since three-dimensional structure information is essential for the analysis of nsSNP accumulations within one single protein, we automatically extract the PDB identifier of the largest available three-dimensional structure from UniProt. The chosen PDB structure, then is automatically loaded from the Protein Data Bank (PDB).
To maintain flexibility, we also provide the possibility to state a preferred PDB identifier within both input formats.
In cases, where no PDB structure is available, we offer automated 3D homology modelling to generate a 3D model.

Example Data from Cardiomyopathy Study

In a Next Generation Sequencing Data set on dilated cardiomyopathy (DCM) (paper), we detected nsSNPs clustering in potentially interesting locations within the genes JUP, VCL and SMYD2. The input files for the BALL-SNP analysis can be downloaded below:

Tutorial

Detailed information how to work with BALL-SNPgp:Tutorial

 

Installation

Details how to install BALL-SNPgp: here

NOTE: The sources for the actual version are available below. If you have a version older than 10th March 2016, please download the actual version.

Source: BALL-SNPgp_src

Pre-build version (Ubuntu trusty): BALL-SNPgp_pre_build

 

Support

If you encounter problems please write to the following mailing list: ballsnp@milaman.cs.uni-saarland.de