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PROGEN: an automated modelling algorithm for the generation of complete protein structures from the alpha-carbon
1Center for Macromolecular Design, College of Veterinary Medicine, Texas A&M University, College Station 77843-4467.
Journal of Computer-Aided Molecular Design
|April 1, 1993
Summary
A new algorithm, PROGEN, generates complete protein atomic coordinates from alpha-carbon data using an optimal geometry parameter database. This method accurately models protein structures, including proline configurations.
Area of Science:
- Computational Biology
- Structural Bioinformatics
- Protein Modeling
Background:
- Generating complete protein atomic coordinates is crucial for structural biology.
- Existing methods may require extensive input or lack automation.
Purpose of the Study:
- To describe a novel algorithm, PROGEN, for generating protein atomic coordinates from alpha-carbon coordinates.
- To validate PROGEN's accuracy and efficiency in protein structure modeling.
Main Methods:
- Development of the PROGEN algorithm utilizing an optimal geometry parameter (OGP) database.
- Establishing the OGP database from 19 known proteins in the Brookhaven Protein Data Bank (BPDB).
- Refinement of generated models using energy minimization and molecular dynamics.
Main Results:
- PROGEN successfully generated complete atomic coordinates for 60 diverse proteins.
- Achieved low root-mean-square deviation (r.m.s.d.) values for main-chain atoms (average 0.53 Å) and all non-hydrogen atoms (1.44–1.93 Å).
- Accurately assigned cis/trans proline configurations.
Conclusions:
- PROGEN provides an automated and efficient method for protein structure modeling from alpha-carbon coordinates.
- The algorithm demonstrates high accuracy comparable to experimental structures.
- PROGEN requires no specialized input, making it broadly applicable.