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A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Analyzing the performance of conformational search programs on compound databases
Markus J Loferer1, István Kolossváry, András Aszódi
1In Silico Sciences Unit, Informatics and Knowledge Management, Novartis Institutes for Biomedical Research Vienna, Brunnerstrasse 59, A-1235 Vienna, Austria.
Journal of Molecular Graphics & Modelling
|July 4, 2006
Summary
We evaluated conformational search programs for sampling low-energy, diverse molecular structures. LMOD excels in energy criteria, while other programs offer broader geometric diversity. OMEGA is the fastest program.
Area of Science:
- Computational Chemistry
- Drug Discovery
- Molecular Modeling
Background:
- Conformational search programs are crucial for identifying low-energy molecular structures.
- Effective conformational searching requires balancing energetic and geometric diversity.
- Evaluating program performance is essential for selecting appropriate tools in molecular modeling.
Purpose of the Study:
- To assess the sampling performance of five conformational search programs: DGEOM, QXP, ROTATE, LMOD, and OMEGA.
- To compare programs based on energetic and geometric criteria for conformational diversity.
- To identify optimal programs for high-quality conformational search applications.
Main Methods:
- Geometric analysis using multidimensional scaling and eigenvalue analysis of covariance matrices.
- Energetic analysis by comparing conformer energy distributions after semi-empirical quantum mechanics optimization.
- Application of methodologies to a diverse 604-compound subset of the LeadQuest library.
Main Results:
- LMOD demonstrated superior performance based on the energetic criterion.
- Other programs (DGEOM, QXP, ROTATE, OMEGA) sampled a wider range of geometrically diverse conformations.
- OMEGA was identified as the fastest program, though with higher median conformer energies.
Conclusions:
- No single program optimally satisfies both energetic and geometric criteria.
- LMOD is recommended for applications prioritizing energetic quality.
- OMEGA is recommended for applications requiring speed and broad geometric sampling.
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