CYLIB

CYANA library preparation

CYLIB (© by Peter Güntert) can be used to prepare new entries for the CYANA residue library starting from molecular topology descriptions given as Tripos Mol2 or PDB Chemical Component Dictionary mmCIF files.

CYLIB is an algorithm for converting molecular topology descriptions in MOL2 format or from the PDB

   Chemical Component Dictionary into CYANA residue library entries.

Setting up CYANA residue library entries therefore involves, besides straightforward format conversion, the non-trivial step of defining a suitable tree structure of torsion angles, and to re-order the atoms in a way that is compatible with this tree structure. This can be done manually for small numbers of ligands but the

   process is time-consuming and error-prone. An automated method is necessary in order to handle the
   large number of different potential ligand molecules to be studied in drug design projects. CyLib is
   an algorithm for this purpose.
   The CYANA structure calculation algorithm uses torsion angle molecular dynamics for the efficient
   computation of three-dimensional structures from NMR-derived restraints. For this, the molecules have
   to be represented in torsion angle space with rotations around covalent single bonds as the only
   degrees of freedom. The molecule must be given a tree structure of torsion angles connecting rigid
   units composed of one or several atsoms with fixed relative positions. Setting up CYANA residue
   library entries therefore involves, besides straightforward format conversion, the non-trivial step
   of defining a suitable tree structure of torsion angles, and to re-order the atoms in a way that is
   compatible with this tree structure. This can be done manually for small numbers of ligands but the
   process is time-consuming and error-prone. An automated method is necessary in order to handle the
   large number of different potential ligand molecules to be studied in drug design projects. CyLib is
   an algorithm for this purpose.

   The input topology-file must be either in MOL2 format (with extension .mol2) or in the mmCIF format
   of the PDB Chemical Component Dictionary (with extension .cif).
 

With CYLIB you can easily:

• Convert between different data file formats

Availability

• CYLIB is available free-of-charge. The current version is CYLIB 2.2.

References

• Maden Yilmaz, E. & Güntert, P. NMR structure calculation for all small molecule ligands and non-standard residues from the PDB Chemical Component Dictionary. J. Biomol. NMR 63, 21-37 (2015)

Reports or publications of results obtained with CYLIB should cite this paper.