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Published online 24 June 2009 | Nature 459, 1038-1039 (2009) | doi:10.1038/4591038b
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New protein structures replace the old
Dutch software to weed out errors in Protein Data Bank.
Protein structures are getting regular makeovers with the help of 're-refinement' software developed by Dutch structural biologists.
The Protein Data Bank (PDB) holds nearly 53,000 three-dimensional structures of protein molecules and nucleic acids that have mainly been deciphered through X-ray crystallography.
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[*] impressive technical achievement, up to the point of the evaluation of non-crystallographic symmetry (NCS) : translation-libration-screw (TLS)-derived displacements can be aided by NCS (Winn, 2001) - this could explain why PDB-REDO cannot achieve the Rfree as low as published for applicable structures - not sure i saw that in the paper. 'a fortiori' that biological macromolecules are *rife* with NCS, in fact symmetry is a fundamental mechanism of biological function - just consider hemoglobin. i do not understand how a massive re-refinement of the pdb can be acceptable without NCS - i suppose we must wait for "Part II" of the paper where autoNCS is brought into play. [*] i can understand that "old" structures like lysozyme can benefit from developments in refinement. the authors claim that scientists "lose interest" in entries after deposition : sure, since now we have sub-Angstroem structures of lysozyme! also, what are scientists to do : dump a quick result in for the paper, then work on it afterwards? i have hard enough time getting the RCSB to change four atoms in a structure for me. [*] "53,000 structures ... 1971" : that's great that we have a date - i presume the author of this column had better things to do than figure out how many structures were there in 1971, or to note the exponential growth of entries, let alone unique folds, etc. Nucleic acids were mentioned - hooray. let's just accept it - they are all macromolecules. [*] "there are definitely errors in the PDB" : not a quote that anyone would think Nature could pass up. [*] it is interesting to note that the phenix developers refine the pdb all the time, yet we probably will never have a publication. [*] default ligand parameters are from the program library, but it is not clear how the scientists evaluated the ligand fit to the data at the level that Kleywegt mentions. many times, this ligand is of the highest interest. [*] many times, the refinement protocol is the critical aspect of the structure : consider the 1.0A structure of calmodulin. scientsts must remember that when they click the re-refine button, you read the paper where the structure was reported.
EDIT : this line should read : "biological macromolecules are rife with ->SYMMETRY<-". only in a *crystal* do they consequently gain NCS.