The rapidly growing protein structure repositories have opened up new opportunities for discovery and analysis of functional and evolutionary relationships among proteins. Detecting conserved structural sites that are unique to a protein family is of great value in identification of functionally important atoms and residues. Currently available methods are computationally expensive and fail to detect biologically significant local features. We have developed LFM-Pro (Local Feature Mining in Proteins) as a framework for automatically discovering family specific local sites and the features associated with these sites. Our method uses the distance field to backbone atoms to detect geometrically significant structural centers of the protein. A feature vector is generated from the geometrical and bio-chemical environment around these centers. These features are then scored using a statistical measure, for their ability to distinguish a family of proteins from a background set of unrelated proteins, and successful features are combined into a representative set for the protein family. The utility and success of LFM-Pro are demonstrated on Trypsin-like Serine Proteases family of proteins. The results verify that our method is successful both in identifying the distinctive sites of a given family of proteins, and in classifying proteins using the extracted features.
The software is freely available for academic research use.
ahmet[at]ceng.metu.edu.tr , {ozturk,hakan,yusu}@cse.ohio-state.edu
Ahmet Sacan, Ozgur Ozturk, Hakan Ferhatosmanoglu, and Yusu Wang. LFM-Pro: A Tool for Detecting Significant Local Structural Sites in Proteins. Bioinformatics, 23(6):709-716, 2007
download and unzip the LFMPro software package into folder (The root folder will be denoted as “LFMPro” from here on). When unzipped, you should have the following folders:
in MATLAB:
>> globals_set;
>> rep = mine_family_represent(familyName, 'ptns',ptnNames, 'rand',backgroundPtns);
familyName
is a unique identifier that you can use to refer to the family representation with. ptnNames and backgroundPtns are cell arrays of pdb names for the family members and for the outgroup proteins.
>> signatures_show(pdb, 'familyName',familyName)
For example:
>> data_prepare_batch('help');
Here is a list of sample runs demonstrating some of the available functionality:
See the function reference page for the list of available functions and their usage.
You can view the local features page if you wish to extend LFMPro to incorporate new local features.