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Pescador: the PEptides in Solution ConformAtion Database: Online Resource.
Anne Pajon1, Wim F Vranken, Maria Angeles Jimenez
1Service de Conformation des Macromolécules Biologiques, Université Libre de Bruxelles, Brussels, Belgium.
Journal of Biomolecular NMR
|August 3, 2002
Summary
A new database, Pescador, centralizes peptide conformation data from Nuclear Magnetic Resonance (NMR) and Circular Dichroism (CD) experiments. This resource aids in analyzing peptide structures and deriving crucial conformational parameters.
Area of Science:
- Biophysics
- Structural Biology
- Computational Chemistry
Background:
- Interpreting peptide conformation data from NMR and CD experiments is challenging.
- Existing methods for analyzing peptide solution structures require improvement.
Purpose of the Study:
- To develop Pescador, a database for peptide conformation data from NMR and CD spectroscopy.
- To provide tools for data deposition and analysis of peptide structures in solution.
Main Methods:
- Collected and curated data from NMR and CD spectroscopy on peptides in solution.
- Developed web-based tools for data deposition and retrieval.
- Utilized stored NMR alpha proton delta-values to derive new 'random coil' chemical shift values.
Main Results:
- Pescador database established with NMR and CD data, including structural parameters.
- Derived 'random coil' chemical shift values comparable to experimental data in water.
- Developed correction factors for neighboring residue effects, showing favorable comparison with existing methods.
Conclusions:
- Pescador serves as a valuable resource for peptide conformational analysis.
- The database facilitates the derivation of key parameters for understanding peptide structures.
- Future data accumulation in Pescador will enhance its utility for biophysical studies.