Journal of Biomolecular NMR, 23: 85–102, 2002. KLUWER/ESCOM © 2002 Kluwer Academic Publishers. Printed in the Netherlands. 85 PESCADOR: The PEptides in Solution ConformAtion Database: Online Resource Anne Pajon a,∗ , Wim F. Vranken a,∗,∗∗ , Maria Angeles Jimenez b , Manuel Rico b & Shoshana J. Wodak a,∗∗∗ a Service de Conformation des Macromol´ ecules Biologiques, Universit´ e Libre de Bruxelles, Brussels, Belgium; b Instituto de Estructura de la Materia, Consejo Superior de Investigaciones Cient´ ıf´ ıcas, Madrid, Spain Received 3 January 2002; Accepted 29 April 2002 Key words: CD, database, NMR, peptide conformation Abstract In recent years a large body of data has been obtained from Nuclear Magnetic Resonance and Circular Dichroism experiments on the influence of the amino acid sequence and various other parameters on the conformational state of peptides in solution. Interpreting the experimental data in terms of the conformational populations of the peptides remains a key problem, for which current solutions leave appreciable room for improvement. Considering that making this body of data available for surveys and analysis should be instrumental in tackling the problem, we undertook the development of Pescador: The ‘PEptides in Solution ConformAtion Database: Online Resource’. Pescador contains data from NMR and CD spectroscopy on peptides in solution as well as information on the structural parameters derived from these data. It also features specialized Web-based tools for data deposition, and means for readily accessing the stored information for analysis purposes. To illustrate the use of the database in deriving information for the conformational analysis of peptides, we show how the alpha proton δ-values stored in Pescador and measured by NMR for different peptides in different laboratories can be used to derive a new set of ‘random coil’ chemical shift values. Firstly, we show these values to be very similar to those obtained experi- mentally for model peptides in water, and their variation with increasing Tri-Fluoro-Ethanol (TFE) concentration is similar to that reported for model peptides. We show, furthermore, that the chemical shift data in Pescador can be used to derive correction factors that take into account effects of neighboring residues. These correction factors compare favorably with those recently derived from a series of model GGXGG peptides (Schwarzinger et al., 2001). These encouraging results suggest that, as the quantity of NMR data on peptide deposited in Pescador increases, surveys of these data should be a valuable means of deriving key parameters for the analysis of peptide conformation. Introduction Over the past decade a large number of studies have been devoted to the analysis of peptide conforma- tional preferences and interactions in solution. Several of these used peptides with designed amino-acid se- quences in order to elucidate the factors governing ∗ Both authors contributed equally to this work. ∗∗ Current address: European Bioinformatics Institute, Cambridge, U.K. ∗∗∗ To whom correspondence should be addressed. E-mail: shosh@ucmb.ulb.ac.be secondary structure formation. A large body of work was devoted to α-helix formation and conformational equilibrium (Chakrabartty et al., 1991; Padmanabhan and Baldwin, 1994; Baldwin, 1995; Muñoz et al., 1995). With increasing interest in aggregation phe- nomena, believed to involve transitions from helical to extended conformation (Lopez-Hernandez and Ser- rano, 1995, 1996; Taddei et al., 2000; Andersen and Tong, 1997), the focus has recently shifted to- wards peptides forming β-hairpins and small β-sheets (Lacroix et al., 1999; Odaert et al., 1999; Santiveri et al., 2000, 2001; Gellman, 1998; Zerella et al.,