Buildproteinlib is an implementation for CYANA and allows to create a ‘‘pseudoprotein residue’’ composed by as many pseudoatoms as the number of atoms of the protein starting from the pdb of the protein itself. These pseudoatoms have coordinates equal to the coordinates of the corresponding atoms in the model structure and no van der Waals radius. A library defining the “pseudoprotein residue” and the upper distance limits between all the heteroatoms of the protein and the corresponding atoms of the “pseudoprotein residue” are generated.
This program can be used to generate a model as close as possible to a X-ray structure using the library of CYANA. Therefore the “pseudoprotein residue” is linked to the protein sequence through dummy residues, which have the function of allowing the pseudoprotein residue to freely move with respect to the protein residues.
When the program is executed, it requires:
- the pdb of the protein without the header and the tail;
- the name of the pseudoresidue that we want to generate (three letters, i.e.: CAT);
- the number of the pseudoresidue in the sequence (it has to follow the sequence of the protein to which it is attached, i.e.: if the protein ends with the residue 161 and the number of introduced dummy atoms is 40, the pseudoresidue number is 202);
- the name to give to the library (i.e.: CAT.lib);
- the name to give to the upl file (i.e.: CAT.upl);
- the range of the upl (i.e.: 0.1)
Once the .lib file has been generated the head and tail have to be copied from the "HeaderAndTailToLibraryFile" inside the .lib file: the first lines correspond to the head
RESIDUE RMZ 1 1191 4 1188 #attention: RMZ=residue name
1 LB 0 0 0.0000 2 3 1189 1190 0
1 Q1 DUMMY 0 0.0000 0.0000 0.0000 0.0000 0 0 0 0 0
2 Q2 DUMMY 0 0.0000 1.4142 0.0000 -1.4142 0 0 0 0 0
3 Q3 DUMMY 0 0.0000 2.8284 0.0000 0.0000 0 0 0 0 0
and the last lines to the tail; these lines have to be renumbered according to the numeric progression of the file.
1189 Q1 DUMMY 0 0.0000 0.0000 0.0000 0.0000 0 0 0 0 0
1190 Q2 DUMMY 0 0.0000 1.4142 0.0000 -1.4142 0 0 0 0 0
1191 Q3 DUMMY 0 0.0000 2.8284 0.0000 0.0000 0 0 0 0 0
The four highlighted numbers in the head of the file have to be changed (the first represents the total number of atoms and the second number represents the last number of the residue's library before adding the tail).
The upl file is already in the correct cyana format
202 CAT NN06 6 ASN N 0.10 0.10E+00
where the first decimal number is the tolerance on the distance between the atoms of the proteins and the pseudoresidue and the second decimal number (0.10E+00) is the weigth to give to the distance costraints.
Download the files:
REFERENCE
I. Bertini, V. Calderone, L. Cerofolini, M. Fragai, C.F.G.C. Geraldes, P. Hermann, C. Luchinat, G. Parigi, J.M.C. Teixeira, “The catalytic domain of MMP-1 studied through tagged lanthanides”, FEBS Letters (2012) 586, 557-567.