BionanoMetaserver

Run

Required:

email (to access your results later):	Job title:

PDB
id: or file

If you specify the PDB id (e.g. 3LOA) the .pdb file will be automatically downloaded from the PDB database and the structure will be protonated using Reduce. Due to the last changes in the wwPDB Archive this option works only for the PDB codes which refer to the actual .pdb files in the PDB database. We are working on a solution for the new type PDB entries (containing >62 chains and/or 99999 ATOM lines).

Note that if you upload your own PDB file, the structure must contain hydrogens. You can use the tool on the MOL probility website to protonate your structure.

If you find MINT useful please cite: A. Górska, M. Jasiński, J. Trylska, Nucleic Acids Res. 2015, 43 (17): e114

Optional parameters:

If you leave these fields empty, MINT will run using default values.

chains_names (default: all| e.g. A B C)

Select the chains to be analyzed. Take into account that in the output MINT treats all provided RNA or DNA molecules as one part.

Select a force field:
AMBER ff10
CHARMM 36

If you want to use different/own force field, use a standalone version.

Select a atom to measure the distance for detection of hydrogen bond:
donor atom
hydrogen atom

See the documentation if you would like to visulalize the hydrogen bond.

hydrogen bond maximal length (default: 3.5 [Å] for acceptor-donor hydrogen bond definition)

hydrogen bond minimal angle (default: 150 degrees)

Note that these two above are only geometric criteria an may in some structures result in detection of more than 3 hydrogen bonds for a GC pair and more than 2 for an AU pair.

cutoff (default: 20 [Å])

Distance measured between the C1' carbons of every nucleotide. If the distance is larger than cutoff, the program does not search for hydrogen bonds.

cutoff stacking (default: 10.5 [Å])

Distance measured between centers of mass of every nucleobase. If the distance is larger than cutoff, the program does not search for stacking interaction.

vdw cutoff stacking (default: -0.5 [kcal/mol])

If the calculated value of the van der Waals interaction energy between two nucleobases is higher than the above given value, MINT does not consider the interaction as stacking.

π_stacking_distance_cutoff (default: 4.5 [Å])

The maximal length between backbone phosphate group and nucleobase ring for ion-π interaction to be detected.

For details see user manual: MINT_manual.pdf