wwPDB task force-X-Ray Validation

wwpdb mx validation

Info

The wwPDB X-Ray Validation Task Force (XVTF) was convened by the wwPDB to recommend a new generation of crystallographic validation criteria for the PDB archive. Its landmark report - Read et al., “A new generation of crystallographic validation tools for the Protein Data Bank,” Structure 19(10):1395-1412 (2011) - defined the validation metrics now embedded in wwPDB validation reports, PHENIX, CCP4, MolProbity, and Coot. The workshop was supported financially and logistically by RCSB PDB (NSF DBI 0829586) and EMBL-EBI.

Membership (2011 Structure paper)

Member	Affiliation (2011)	Role / Known for
Randy Read	CIMR, University of Cambridge	Phaser molecular replacement
Paul Adams	Lawrence Berkeley National Laboratory	PHENIX consortium lead
W. Bryan Arendall, III	Duke University Biochemistry	MolProbity
Axel T. Brunger	Stanford University / HHMI	XPLOR / CNS lineage
Paul Emsley	University of Oxford Biochemistry	Coot
Robbie P. Joosten	CMBI, Radboud Nijmegen	PDB-REDO
Anastassis Perrakis	Netherlands Cancer Institute	ARP/wARP, PDB-REDO
Gerard Kleywegt	Uppsala University (until 31 May 2009)	Uppsala Software Factory; later PDBe (UK, EMBL-EBI)
Eugene B. Krissinel	CCP4 / Rutherford Appleton Laboratory	CCP4 project leader
Thomas Lütteke	Justus-Liebig University Giessen	pdb-care glycan validation
Zbyszek Otwinowski	UT Southwestern Medical Center	HKL / DENZO / SCALEPACK
Jane S. Richardson	Duke University Biochemistry	MolProbity, ribbon diagrams
William H. Sheffler	University of Washington / Baker Lab	RosettaHoles
Janet L. Smith	University of Michigan LSI	LS-CAT at APS
Ian J. Tickle	Astex Therapeutics	BUSTER-TNT; fragment-based drug discovery
Gert Vriend	CMBI, Radboud Nijmegen	WHAT_CHECK / WHAT IF
Peter H. Zwart	Lawrence Berkeley National Laboratory	PHENIX / cctbx / SAXS

Funding acknowledged

• NIH P01 GM063210 (to P.D.A., R.J.R., J.S.R.)
• NIH R01-DK42303 and R01-GM81544 (to J.L.S.)
• NIH R01-GM073919 and R01-GM073930 (to W.B.A. and J.S.R.)
• Howard Hughes Medical Institute (to A.T.B.)
• Wellcome Trust grant 082961 (to R.J.R.)
• Netherlands Organization for Scientific Research (NWO) via NCF supercomputer facilities (to R.P.J. and G.V.)
• NBIC BioRange / BSIK Netherlands Genomics Initiative (to R.P.J. and T.L.)
• EU FP6 EMBRACE Grid LUNG-CT-2004-512092 (to G.V.)
• BBSRC via CCP4 (to E.K.)
• EMBL (to E.K.)
• Uppsala University, Royal Swedish Academy of Sciences (K.V.A.), Swedish Research Council (V.R.) (to G.J.K. until May 2009)

Primary source

• Read et al., “A new generation of crystallographic validation tools for the Protein Data Bank,” Structure 19(10):1395-1412 (2011): https://www.cell.com/structure/fulltext/S0969-2126(11)00285-1