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STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins
Matthias Heinig1, Dmitrij Frishman
1Department of Genome Oriented Bioinformatics, Technical University of Munich, Wissenschaftszentrum Weihenstephan, 85354 Freising, Germany.
Nucleic Acids Research
|June 25, 2004
Summary
STRIDE is a software tool that assigns protein secondary structures using hydrogen bond energy and backbone torsional angles. The STRIDE web server offers visualization tools and a database for protein structure analysis.
Area of Science:
- Structural biology
- Bioinformatics
- Computational chemistry
Background:
- Accurate assignment of protein secondary structure is crucial for understanding protein function and dynamics.
- Existing methods may not fully leverage the wealth of information available in atomic resolution structures.
Purpose of the Study:
- To introduce STRIDE, a knowledge-based software tool for secondary structure assignment.
- To provide a user-friendly web server for accessing STRIDE and related analyses.
Main Methods:
- STRIDE employs a knowledge-based algorithm combining hydrogen bond energy and statistically derived backbone torsional angle information.
- The STRIDE web server accepts Protein Data Bank (PDB) files for analysis.
- The server includes visualization of secondary structure, contact maps, and Ramachandran maps.
Main Results:
- STRIDE assignments are optimized for maximal agreement with crystallographers' designations.
- The web server provides access to the STRIDE tool, visualization features, and a searchable database of assignments for the latest PDB release.
Conclusions:
- STRIDE offers a robust method for secondary structure assignment from protein atomic resolution structures.
- The STRIDE web server enhances accessibility and utility for researchers in structural biology and bioinformatics.