Talk:Protein structure databases

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The following table was taken from a random entry in PDBWiki - it shows just some of the diverse array of protein structure databases that exist. I put it here so that we can extract the important database for the article.

Databases	Visualization tools	Analysis tools	Quarternary structure
Protein Data Bank PDBsum JenaLib NCBI Entrez OCA Proteopedia TOPSAN	RCSB Jmol viewer RCSB KiNG viewer FirstGlance (Jmol) AstexViewer Polyview 3D (Rendered images) PDBCartoon (secondary structure)	Contact Analysis (CSU) Protein cavities (CastP) Domain information (XDom) WHAT IF quality report Functionally important residues (FireDB) Catalytic sites (CSA)	PDB (Download coordinates) PQS PISA ProtBuD PiQSi 3DComplex

Feel free to hack this table to bits / bare bones. --Dan|^(talk) 21:57, 5 April 2008 (UTC)

[edit] Title of this page?

Should this page be Protein structure databases? --Dan|^(talk) 22:04, 5 April 2008 (UTC)

Good start! Title is good, but many databases are missing. You should look here, here, and perhaps a couple of other reviews. The article should also include MODBASE, SCOP, membrane protein databases (such as PDBTM) and others, but it is better to consult with reviews. I can look at this later.Biophys (talk) 04:21, 6 April 2008 (UTC)

Thanks very much for the positive feedback. I'll have a look at the links provide. --Dan|^(talk) 13:34, 6 April 2008 (UTC)

Btw, I am quite familiar with the database issue of the NAR... I created MetaBase :-D --Dan|^(talk) 20:23, 6 April 2008 (UTC)

Right, I added MODBASE, SCOP, PDBTM and some others. The page is begging to grow beyond my ability to look at it all clearly (lame I know), but another pair of eyes on the page at this point would be great. Not sure if I should continue to wikify the database description text, as it may become a bit too confusing. Also a table is probably needed at this stage rather than a description list. --Dan|^(talk) 20:23, 6 April 2008 (UTC)

[edit] Suggestions of pages to add?

Please add suggestions here, or just be bold and add them to the page. Looking here, Category:Bioinformatics_databases, I can immediately identify;

• CATH
• FSSP
• Probably others... we don't want to cross over into the realm of protein sequence databases that happen to integrate structural information.... or do we?

BioModels Database

CATH

Database of Molecular Motions

Orientations of Proteins in Membranes database

Structural Classification of Proteins. These are databases of 3D structures. Biophys (talk) 05:43, 8 April 2008 (UTC)