Here we provide a brief description of the analyzed parameters and used definitions. For details and references please see the MINT manual.pdf.

A hydrogen bond is formed if a hydrogen atom is placed close to an acceptor atom, and if the angle between the donor atom, hydrogen and acceptor is ideally close to 180 degrees (Figure 1). The user may define both parameters: minimal angle and maximal distance between the acceptor and donor or the acceptor and hydrogen.

We defined a list of all possible acceptors and donors for all four nucleotides. The acceptors and donors are assigned to the edges of the nucleotide, as shown in Figure 2. MINT determines the interacting edges of every pair of nucleotides from the names of the interacting atoms. However, several atoms are placed in the corners of a molecule and therefore participate in more than one edge. In such cases, the rest of bonds are classified, and the prevailing edge is chosen. If there is only one hydrogen bond, both names are returned.

After detecting the hydrogen bonds and defining the interacting sites, the cis/trans configuration is computed. MINT measures the torsion angle formed by the four atoms and depending on its value, the configuration is assigned. Both cis and trans configurations are shown in Figure 3.

MINT maps all hydrogen bonds for all nucleotide pairs that are within the cutoff distance. The cutoff is measured between the C1' carbons of every nucleotide.

In the output description file the user will find description of the WC-WC bonds with atom names and distances

and non-WC-WC pairs:

MINT detects all kinds of motifs that are defined as a set of unpaired nucleotides with the surrounding pairs. For clarity MINT uses the numerical description of the motifs. Figure 4(b) shows a four nucleotide loop at the end of a hairpin, represented by a single number 4. Figure 4(c) shows a symmetrical bulge loop, with bulge length of three and is represented by two numbers: 0-3. The three-way junction, shown in Figure 4(d), without unpaired nucleotides is represented by the three zeros: 0-0-0. The numbers correspond to the number of unpaired nucleotides between pairs. Therefore the multibranched loop in Figure 4(e) is denoted as 1-2-3.

MINT describes all secondary structural motifs and lists them in the _description output file. First, the output lists all the helices:

then MINT provides a list of motifs than can be easily visualized in the VMD program in its graphical representation window:

The same is done for all other motifs:

From all Watson-Crick pairs, a list representation of the RNA secondary structure is created. Each nucleotide may have only one Watson-Crick partner. If the second WC-WC partner is encountered all three nucleotides are added to the triplets list. Index of the list represents the number of the nucleotide and the stored value is the number of its Watson-Crick partner.

The internal representation of the RNA structure contains also information about other higher-order structures such as pseudo-knots. A pseudo-knot is also formed by the Watson-Crick interactions but creates three-dimensional folds. MINT detects the pseudo-knot fold when the arcs intersect. A pseudo-knot is a symmetrical structure - three pairs 6-17 7-16 8-15 shown in Figure 5 form the pseudo-knot as well as two pairs: 12-19 13-18; the natural way of solving this conflict is to choose the shorter list, in that case pairs 12-19 13-18.

In the _description output pseudo-knots will be described as following:

If there is more than one partner for a certain nucleotide, MINT puts them in the Triplets list. Exemplary triplet is shown in Figure 6.

Triplets will be enlisted in the _description file as follows:

We estimate stacking between two bases by calculating the energy of electrostatic (Coulomb) and van der Waals interactions, applying the equations used in molecular mechanics. We consider two bases as stacked if the value of the VDW interaction energy between them is smaller than a given parameter vdw_cutoff_stacking by default set to [-0.5 kcal/mol]. Only pairs that satisfy this condition will be printed in the _description and _stacking_in_time.csv files. Calculations of the interaction energy are performed only for pairs for which the distance between the centers of mass of the bases is smaller than user defined cutoff stacking (default 5.5 [Å]). An example of the stacking pairs is shown in Figure 7.

In the description_ output the stacking pairs are outlined as follows:

MINT can also detect the interactions termed ion-pi. This is an arrangement in which one of the phosphorus atoms is placed close to a nucleotide ring, as presented in Figure 8. For details and references please see the MINT manual.pdf.

The list of these conformational arrangements will appear in the _descriptiom output file:

[1]  Lescoute and E Westhof. The interaction networks of structured RNAs. Nucleic acids research, 34(22):6587-604, January 2006.