AVS

Introduction

Assignment validation suite (AVS) checks the chemical shifts list in BioMagResBank (BMRB) format for a number of possible problems such as consistency to IUPAC labeling, chemical shifts that are grossly outside the typical range for the particular atom/residue, and reports useful statistics information about the examined chemical shift set (e.g. percent assignments, number of stereospecifically assigned methlys, percents aromatic sidechain assignments, etc).   AVS is run on every chemical shift set that is submitted to the BMRB, and can be included as part of the Protein Structure Validation Suite (PSVS) run.  It is advisable to run any chemical shift validation prior to structure determination steps in order to uncover problems with the assignments that could impact the performance of noesy assignments and structure calculation downstream. 

Practical Aspects

A number of version for the standalone AVS routine exist that are adapted for different bmrb versions  (2.1 or 3.1). Two perl scripts can be run from any directory on any computer running perl by either pointing to the local AutoAssign script repository directory or by downloading the scripts linked below.  Here an example script is provideded that generates the bmrb in 2.1 format directly from the sparky resonance list 'rl' and the protein sequences.  The script validates and computes the completeness statistics for the generated chemical shift list.  As modifications are made in the sparky project the operation is repeated until a final bmrb file is achieved.

/Local/AutoAssign1.14/bin/sparkyRL2bmrb.pl HsR50_bb.rl test_bmrb.bmrb 1 MSPIPLPVTDTDDAWRARIAA
HRADKDEFLATHDQSPIPPADRGAFDGLRYFDIDASFRVAARYQPARDPEAVELETTRGPPAEYTRAAVLGFDLGDSHHTLTAFRVEGESSLF
VPFTDETTDDGRTYEHGRYLDVDPAGADGGDEVALDFNLAYNPFCAYGGSFSCALPPADNHVPAAITAGERVDADLEHHHHHH -diasterio
/Local/AutoAssign1.14/bin/missing_shifts.pl -printstats test_bmrb.bmrb > missing_HsR50_101109
/Local/AutoAssign1.14/bin/validate_assignments.pl test_bmrb.bmrb > vali_HsR50_101109
cp test_bmrb.bmrb HsR50_bb.bmrb
rm test_bmrb.bmrb

Three scripts are run: 1) sparkyRL2bmrb.pl, 2) missing_shifts.pl, and 3) validate_assignments.pl. In addition, a bmrb parsing module BMRBParsing.pm is called that interprets the sequence in single letter code and numbers the bmrb residues, ind this case starting from 1.

Newer file versions are available in later versions of the AutoAssign program that should handle bmrb 3.1 format.

Editing in progress

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