|A paper describing the PROSIT service has been published in J.Chem.Inf.Comp.Sci. Click here for PDF(500K).|
1. Definition of the dihedral angles
The pseudorotation phase angle P (0°-360°) and the maximum puckering amplitude νmax are calculated according to Altona et al. (J. Am. Chem. Soc. 1972, 94, 8205-8212) using equations 1 and 2. The endocyclic torsions ν0-ν4 are defined as in Figure 1.
In addition to the pseudorotation properties, this tool calculates the main chain torsion angle GAMMA and the glycosyl angle CHI. Definitions for CHI and GAMMA are given in Figure 2.
This script was devised not only to calculate the pseudorotation angles of the natural nucleosides, but also of unnatural nucleoside analoga. Therefore in a first step all non overlapping sugar substructures (see Fig. 3) are mapped in the order of appearance in the molecule file. The bond order is not taken into account for matching.
In the next step all in step 1 obtained sugar structures are distinguished into pyrimidine or purine type nucleosides (analoga) by trying to map them onto the substructures depicted in Figure 4. If no mapping of the sugar structure is possible it is discarded. For the mapped sugar substructures the respective torsion angles and the pseudorotation phase angle is determined.
3. Input/Output Options
To use this tool you need to submit a file with molecule for which you want to have the angles calculated using the field "Input-filename" in the form. All standard chemistry file formats such as PDB, MDL mol and sdf, Sybyl mol2 ... are supported. If the file format supports multiple molecules (e.g. SDF) you can submit one file with multiple molecular ensembles.
For DNA or RNA segments, the default Auto Detect feature automatically searches for the sequence and lists the nucleotides in one strand in the order of 5'->3'.
In addition to the output table, you can request a visual output
of your molecule.
A number of values maybe shown in the result page. These include, for each identified nucleosides, the ID of 1' atom of the sugar, values of ν0-ν4, alpha- or beta-type of nucleoside, sugar pucker, and lots of messages if debugging.
Last updated on Oct. 18, 2004 by GS.