Automated generation of residue library entries for CYANA structure calculations in drug design

Abstract

Computational techniques have been important tools in pharmaceutical research and development, e.g. for the predictions of the interactions between drug candidates and target proteins. Among these techniques, the Combined assignment and dynamics algorithm for NMR applications (CYANA) software has been shown to be highly suited for protein structure determination. This manuscript explains a technique for automated generation of residue library entries for the software CYANA structure calculations in drug design. The entries of the PDB mmCIF chemical component dictionary are converted into the specific CYANA residue library format, which then can be used automatically in the structure determination of the CYANA software. One application of this project relies in pharmaceutical industry if Nuclear Magnetic Resonance (NMR) is used for experiments. This project will support new studies in the drug design by allowing the use of CYANA software automatically for any residue, which is present in PDB mmCIF chemical component dictionary. Further applications include the three dimensional structure calculation of any peptides and proteins whose residue entries are present inside the PDB Protein Data Bank.

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