Hi Lucas, this book ( http://www.amazon.com/Structural-Bioinformatics-Methods-Biochemical-Analysis/dp/0471201995/ref=sr_1_2?s=books&ie=UTF8&qid=1382044405&sr=1-2&keywords=structural+bioinformatics) brings nice examples of protein structures with "unusual features" in the structure validation chapter . I used it on my "protein modeling"course and it is definitely worth buying.
I small list taken from the book (unless I am very much mistaken) includes these structures: 1. 2ABX 2. 1GMA 3. 1CYC 4. 3PGM 5. 1CTX 6. 2GN5 7. 2ATC 8. 1PYP 9. 4RCR 10. 1TRC HTH, --asn [ ]s --alessandro 2013/10/17 Lucas <lucasbleic...@gmail.com> > Dear all, > > I've been lecturing in a structural bioinformatics course where graduate > students (always consisting of people without crystallography background to > that point) are expected to understand the basics on how x-ray structures > are obtained, so that they know what they are using in their bioinformatics > projects. Practices include letting them manually build a segment from an > excellent map and also using Coot to check problems in not so good > structures. > > I wonder if there's a list of problematic structures somewhere that I > could use for that practice? Apart from a few ones I'm aware of because of > (bad) publicity, what I usually do is an advanced search on PDB for entries > with poor resolution and bound ligands, then checking then manually, > hopefully finding some examples of creative map interpretation. But it > would be nice to have specific examples for each thing that can go wrong in > a PDB construction. > > Best regards, > Lucas >
