MINT is an automatic standalone tool for analyzing three-dimensional structures of RNA and DNA molecules, their full-atom molecular dynamics trajectories or other conformation sets (e.g. X-ray or NMR-derived structures). You can also draw your structure (using VARNA) and colour it according to the computed parameters.

Output files

MINT produces multiple output files. In all of them nucleotides are described in a manner that allows to identify them unambiguously. We use the representation containing a chain name, a residue name and a residue number. For example: the N|GUA:521 represents residuum number 521 from the chain N, with the name GUA. The values posted in the chain name|residue name:residue number code are derived from the input PDB file. The zipped package contains the following files:

_description – the main file containing the complete description of the structure. The file content starts from the list of all of the used parameters, followed by the list of helices, motifs, triplets and pseudo-knots. One can also find the list of both Watson-Crick (WC-WC) and non-Watson-Crick interactions, with the exact parameters of the hydrogen bonds. Additionally there is a simple dot-bracket representation of the secondary structure that can be used for visualization or energy computation by other tools.

_helices.csv – a file that contains a list of the deceted helices.

_ion_pi.csv – a file that contains a list of the recognized ion-pi interactions (i.e., detected if a phosphorus atom in one nucleotide is placed close to the nucleobase of the second nucleotide) with their interaction energy values.

_motifs.csv – a file that contains list of the all RNA structural motifs.

_nucleotides_eval.csv – a file that contains the number of the WC-WC hydrogen bonds, non-WC-WC hydrogen bonds, Coulomb energy, van der Waals energy and their sum per nucleotide. The content gives the energetic description of the state of every nucleotide.

_pairs.csv – a file that contains list of all detected pairs along with its classification according to edge (WC, Hoosteen, Sugar) and configuration (Cis or Trans).

_pseudo.csv – a file that contains list of the all detected pseudo-knot.

_stacking.csv – a file that contains a list of all recognized stacking pairs with their interaction energy values.

_triplets.csv – a file that contains the number of the recognized triplets.

_MINT.xls – a multiple sheets file that combines the above .csv files.

.pdb files – the analyzed structure with the column containing the beta-factors replaced with: the number of WC-WC hydrogen bonds (_2D.pdb), non-WC-WC hydrogen bonds (_3D.pdb), energy of the Coulomb interactions (_Coulomb.pdb), van der Waals interactions (_VDW.pdb) and their sum (_stacking_sum.pdb). These files may be used for 3D visualizations, e.g., in VMD or Chimera.

.png files – pictures with 2D visualizations of computed parameters from Varna. Naming convention is similiar to the .pdb files.

Here we provide a brief description of the analyzed parameters and used definitions. For details please see the MINT_manual.

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

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