Hi Fellows,
Christian Weichenberger has updated the Twilight ligand database and program. Data are now current to January 2017. http://www.ruppweb.org/twilight/default.htm Note that there may be slight differences in ranking due to map downloads changed from retired EDS to PDBe. There are also a few new earlier entries included now in the update that were not included before due to absence of EDS maps. http://www.ruppweb.org/twilight/CHANGELOG.txt Disclaimers: Before you start to gloat about a 'bad ligand' please understand the following: a. The unsupervised Twilight data mining is ignorant of any context. To judge whether low evidence (high ranking) is relevant to the claims made in a publication, you first need to look at the map AND read the paper carefully. Monomers can be bona fide ligands that are important and relevant for the story, or can be solvent components irrelevant to the core claims of the paper. The latter are sometimes modeled more enthusiastically and fall under the category of 'something is there' and the opinions are split if and how such should or should not be modelled. Examples are sugar units, amino acids, various cocktail additives etc. We do not look at UNLs and UNKs. b. The problem is in part caused by the fact that the PDB is identifying particularly amino acids and sugars independent of whether they are single units (possibly ligands of relevance), parts of a separate polymer ligand, or an attached glycosylation. Again, one needs to look at the map AND read the story before rendering judgement. In principle, an amino acid is chemically NOT the same as an amino acid residue; similar for sugars and other polymers. An unresolved general issue. Peptide Twilight will be updated in due course. Best regards, BR ----------------------------------------------------------------- Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 [email protected] <http://www.ruppweb.org/> http://www.ruppweb.org/ http://www.hofkristallamt.org/ ----------------------------------------------------------------------- The road to scientific serfdom is paved with Nature papers -----------------------------------------------------------------------
