VVTAK Mn(II)
Download VVTAK Mn(II) as a self-extracting archive
This algorithm is for prediction of coordination spheres for Manganese (II) cations.
The algorithm works with PDB files which should contain both coordinates of each atom in 3D space and also description of secondary structure elements (in lines "HELIX" and "SHEET").
Amino acid sequence in FASTA format should also be provided.
Instructions
Enter amino acid sequence in FASTA format (the one from www.pdb.org site) in the designated line of "Chain" list. Don't forget to delete all the lines left from the previous protein.
Enter all the text from PDB file into the "PDB" list. Don't forget to delete all the lines left from the previous protein.
The information on all the amino acid residues predicted as "active binders" on the basis of primary and secondary structure will appear in the table from the "PREDICTIONS" list.
The information on all the Asp, His and Glu residues situated near those "active binders" will appear in the table on "Coordination spheres" list.
The longest distance between "active binder" and "passive binders" is set at 6 Angstroms, while user may enter other threshold in the special cell on "Coordination spheres" list (under the table).
The minimal number of amino acid residues sufficient to form a single coordination sphere is equal to 3. However, coordination spheres with lower number of binders (2 or 1) may theoretically bind Mn(II) ions at higher concentrations or in the presence of special ligands.
Copy the information from "PDB OUTPUT" list and save it as PDB file (for example, by NotePad).
Open that saved PDB file by RasMol (www.rasmol.org) and visualize predicted Mn(II) binding atoms (use "Temperature" in "Colours" menu and "Ball & Stick" in "Display" menu).
Please, cite:
Khrustaleva T. A., Khrustalev V. V. , Barkovsky E. V. Structural context around amino acid residues binding Mn+2 ions in bacterial proteins // Moscow Conference on Computational Molecular Biology (MCCMB'13): Proceedings. – 2013 - http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/124.pdf