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.

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 molecules but is time-consuming and error-prone. CYLIB automates this process.

The tree structure of torsion angles is needed by the CYANA structure calculation algorithm because it 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.

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).

Availability

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

Reference

• 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.