Recoord 07
12
RECOORD REcalculated COORdinates Database Nederveen et al., Proteins 2005
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christiane-riedinger -
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This is a presentation about a paper published in Proteins in 2005 by Nederveen et al. It's about a tool to standardise NMR structure calculations in order to decrease user - and software dependent bias (REcalculated COORdinates Database). RECOORD has been developed at the Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands and is really useful tool for anyone who has to face solving an NMR structure on their own (and other people, too). Those guys in Utrecht are doing a great job, I can specially recommend the NMR course they organise every year. Thank you!!!!
Transcript of Recoord 07
RECOORD
REcalculated COORdinates Database
Nederveen et al., Proteins 2005
Recalculation of > 500 NMR Structures
• decrease user - and software dependent bias • better comparison
• provide database for development of… - validation tools - calculation protocols - statistical approaches - modelling
NMR Data?!?
Three types of restraints:
1. distance restraints (NOEs !!!!)
2. dihedral angle restraints (coupling constants or chemical shift)
3. orientational restaints (RDCs, relaxation data)
NMR Structure Calculation !?!?
XPLOR/CNS: Molecular Dynamics in Cartesian Space Simulated Annealing Refinement (put in solvent!)
DYANA: Torsion Angle Dynamics Simulated Annealing No force field, energy minimisation necessary
Find a model that fits with your data and the known chemistry of your protein!
• used CNS and CYANA for recalculation
• > 8000 processors used
• total CPU time: 31,169h (~3.5 years on single computer!)
How it was done….
• restraints obtained from BMRB database
• water refinement: restrained molecular dynamics (CNS)
• extensive quality assessment (PROCHECK and WHAT-CHECK)
Results
Quality-assessment of recalculated structures
o Packing o Ramachandran appearance
One standard deviation closer to mean!
Results continued…
o Number of restraints per residue o Agreement with experimental restraints o RMSD (positional root mean square deviation) o Comparison CNS and CYANA o Relation NMR data quality and structural quality
Quality-assessment of recalculated structures
CNS vs. CYANA (no water ref.)
Z-score: standard deviation away from the mean
CNS before and after water ref.
Why am I telling you this?
www.ebi.ac.uk/msd-srv/docs/NMR/recoord/main.html
… you can use the scripts!
