GORBTURN (v3.0)

The program GORBTURN (v 3.0) is a user-freiendly piece of software written in Fortran77. The original program, known as BTURNPRED, was described in two publications (Thornton 1988, Thornton 1990). It was consisted of 2 different programs, BTURN (v2.0) and GORBTURN (v1.0), which predicted the position of ß-turns from an amino acid sequence. In 1988, it was shown that types I and II turns exhibit differential positional sequence preferences. BTURN (v 2.0) and GORBTURN (v1.0) differentially predicted type I and II beta-turns, as well as a non-specific category to cover all remaining turn types. These programs uses the directional parameters of Gibrat et al. in combination with equivalent parameters produced from work by Garrett et al., to eliminate potential helix and strand forming residues from the ß-turn prediction. This led to improved prediction power. In 1994, a revised set of potentials for ß-turn formation in proteins was published by Gail Hutchinson and Janet Thornton based on the exponential growth in the number of atomic resolution protein structures solved by X-ray crystallography and NMR. These potentials have been incorporated into a new version of GORBTURN (v 3.0) which allows the differential prediction of 5 beta-turn types (I,II,I',II',VIII).

The program initially predicts the possible positions of helix or strand residues using the GOR method of Gibrat et al. The predictions for helix and strand are included in output. It uses a 17 residue window in the algorithm, which makes it less suitable for the prediction of beta-turns in short peptide sequences than in proteins.

A. Positional frequencies for Type I turns

B. Positional frequencies for Type II turns

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