Andrzej Kolinski Research Group

Coarse-grained protein modeling

Modeling Software & Servers

Biomolecules — dynamics & interactions

CABS-NMR

Short description: 
toolkit for protein modeling with the use of NMR data

 

A toolkit of useful tools for NMR data formats conversion and utilizing sparse NMR data in protein structure modeling. It includes bash scripts for conversion of NMRSTAR format to DipoCoup and TALOS formats. An efficient tool called TRANSFORM translates all atom cooridinates of psi and phi dihedral angles into theta and gamma pseudoangles defined in reduced coordinates of C-alpha backbone trace. Protein structure modeling is performed by CABS-NMR, a modified version of the CABS algorithm, and NMR_FILTER tool which is used to discriminate protein models with respect to such sparse NMR data as: backbone chemical shifts, RDCs, NOEs (including also methyl-methyl NOEs), H/D exchange rates and hydrogen bonds. CONTACT_FILTER is an additional tool which enables to discriminate protein models with respect to predicted contact maps. In case of any questions, please contact: pledor at chem.uw.edu.pl