Pdb database manual#

'The RCSB PDB information portal for structural genomics.' Nucleic Acids Res 34(Database issue): D302-5. 'IntAct-open source resource for molecular interaction data.' Nucleic Acids Res 35(Database issue): D561-5. 'iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions.' Bioinformatics 21(3): 410-2. (2010) 'The Negatome Database: a reference set of non-interacting protein pairs', Nucleic Acids Researchįinn, R.

Smialowski, P., Pagel, P., Wong, P., Brauner, B., Dunger, I., Fobo, G., Frishman, G., Montrone, C., Rattei, T., Frishman, D.,

Pdb database manual#

'Negatome 2.0: a database of non-interacting proteins derived by literature mining, manual annotation,Īnd protein structure analysis', submitted to Nucleic Acids Research. īlohm, P., Frishman, G., Smialowski, P., Goebels, F., Wachinger, B., Ruepp, A., Frishman, D. The supplement to the Negatome 2.0 paper can be downloaded here. Compared to the first version the contents of the database have grown by over 300%. Potential non-interactions were proposed by a modified version of a text mining tool calledĮxcerbt. Negatome 2.0 was created by use of an advanced text mining procedure to guide the manual annotation process. Thus, the negatome is complementary to such random data for training protein interaction prediction algorithms. The Negatome is much less biased towards functionally dissimilar proteins than the negative data derived by randomly selecting proteins from different cellular locations. More stringent lists of non-interacting pairs were derived from these two datasets by excluding interactions from IntAct. The database currently contains experimentally supported non-interacting protein pairs derived from two distinct sources: by manual curation of literature and byĪnalysing protein complexes from the PDB. The Negatome is a collection of protein and domain pairs which are unlikely engaged in direct physical interactions.