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1. Definition of the dihedral angles

Figure 1. Definition of endocylic pseudorotation torsions ν₀-ν₄ in nucleosides.

The pseudorotation phase angle P (0°-360°) and the maximum puckering amplitude ν_max 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.

(Notice: It has come to our attention that there is a typo in the FIRST print of Saenger's book where v₂ is misspelled as v₀ in eq. 2.)

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.

Figure 2. Definition of CHI and GAMMA for purines and pyrimidines.

2. Method

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.

Figure 3. Substructure for first identification of all sugar type structures (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.

Figure 4. Substructures for identification of pyrimidine type and purine type bases (bond order is not taken into account for matching).

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'.

Other choices include the "single strand" or "double strand" representation in the output table. To identify the distinct strands the number of base pairs is assumed to be half the number of bases. If the value for number of bases/2 is odd a single strand table is generated.i

In addition to the output table, you can request a visual output of your molecule.
"2D display" generates a GIF picture with the mapping of the substructures in Fig. 4 - this works well for smaller molecules.
"3D display" displays the molecule with help of MDL's Chime plug-in. The base index and the pseudorotation phase angle P are used as labels.
Default is "no display".

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.