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Fragment Finder: a web-based software to identify similar three-dimensional structural motif
P Ananthalakshmi1, Ch Kiran Kumar, M Jeyasimhan
1Bioinformatics Centre, Indian Institute of Science, Bangalore 560 012, India.
Nucleic Acids Research
|June 28, 2005
Summary
Fragment Finder (FF) is a web tool for finding similar 3D protein structural fragments. It aids molecular modeling by comparing protein backbone angles and superimposing structural motifs.
Area of Science:
- Structural Biology
- Bioinformatics
- Computational Chemistry
Background:
- Identifying similar 3D structural fragments in proteins is crucial for understanding protein function and evolution.
- Existing methods may lack efficient tools for searching and comparing specific structural motifs within large protein datasets.
Purpose of the Study:
- To develop and present Fragment Finder (FF), an interactive web-based search engine.
- To enable users to retrieve similar 3D structural fragments from protein datasets based on conformational angles.
Main Methods:
- The FF engine compares main chain backbone conformational angles (phi and psi) of protein structures.
- It allows searching within selected subsets of non-homologous protein chains (25% or 90%).
- The system supports superposition of queried motifs to assess structural similarity.
Main Results:
- FF provides an interactive platform for retrieving user-defined similar 3D structural fragments.
- The engine facilitates the visualization of superposed or individual 3D structures on the client machine.
- The tool is freely accessible via a web server.
Conclusions:
- Fragment Finder (FF) offers an effective solution for identifying and analyzing similar 3D protein structural fragments.
- The web server enhances molecular modeling by providing accessible tools for structural comparisons.
- FF supports structural biology research through its interactive search and visualization capabilities.