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Confronting the problem of interconnected structural changes in the comparative modeling of proteins
R Samudrala1, J T Pedersen, H B Zhou
1Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville 20850, USA.
Proteins
|November 1, 1995
Summary
Protein modeling accuracy was lower than expected due to interconnected structural differences. Future improvements will focus on structure-based alignment and side chain conformation algorithms.
Area of Science:
- Computational biology
- Structural bioinformatics
Background:
- Comparative protein modeling is crucial for understanding protein function.
- Accurate protein models are essential for drug discovery and biological research.
Purpose of the Study:
- To build comparative models for three proteins using computational methods.
- To analyze the accuracy of these models and identify sources of error.
Main Methods:
- Comparative modeling using various computational techniques.
- Extensive use of visual inspection to supplement computational results.
- Detailed analysis of structural differences between target and template proteins.
Main Results:
- The accuracy of the generated protein models was worse than anticipated.
- Interconnectedness of structural differences between target and template proteins was identified as a major cause of poor accuracy.
- Side chain conformations were found to be sensitive to remote sequence details and main chain changes.
Conclusions:
- Modeling interdependent structural regions independently leads to inaccuracies.
- Visual inspection can aid in correcting sequence alignments and selecting appropriate templates.
- Future advancements in structure-based alignment and side chain conformation algorithms are expected to improve modeling accuracy.