Collaborative Computational Project
for Electron cryo-Microscopy

MRC

Shape Matching for Structural Biology (SMaSB)


Strychnine-sensitive glycine receptor (GlyR). Strychnine bound (EMD-6344) vs glycine bound (EMD-6345).

"Volume matching with SMaSB / PDBeShape", Ardan Patwardhan, May 2016.

The SMaSB software package has been developed to perform volume matching between a query volume (from, for example, single particle reconstruction) and another volume or set of volumes (from e.g. EMDB or generated from PDB structures). The primary aim is to search for similar volumes, rather than to optimise a particular fit. Identification of matching volumes is aided by a set of complementary scoring functions.

The software is primarily a set of Python codes which organise the metadata, control the data flow during volume/shape matching, and load results into a database. Third-party software is called to perform the compute-intensive steps in the process. The software has been developed following an exploration of a range of techniques, and tested against a variety of volume datasets (to be published). The current version of SMaSB is tested extensively in Ubuntu 12.04 and Mac.

SMaSB - download SMaSB (updated 24/5/16).

Dependencies:

UCSF CHIMERA - for map manipulations and volume alignemnt
TEMPy - for map pre-processing and scoring alignments. This in turn requires NumPy, SciPy and BioPython.
GMFIT (optional) - for volume alignment using Gaussian Mixture Model.
lxml. The best way to install lxml is to get the pip package management tool and run the following as super-user (or administrator): 'pip install lxml'.

This software has been written as part of the EU-funded BioMedBridges project. It will underpin a service being developed at PDBe. The authors are Agnel Praveen Joseph, Ingvar Lagerstedt, Ardan Patwardhan and Martyn Winn, with invaluable help from Irene Farabella and Maya Topf.