PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids

By Roman A. Laskowski, Victor V. Chistyakov, Janet M. Thornton. Nucleic Acids Res., 2004

435 citations recorded by the source corpus.

PDBsum is a database of mainly pictorial summaries of the 3D structures of proteins and nucleic acids in the Protein Data Bank. Its pages aim to provide an at-a-glance view of the contents of every 3D structure, plus detailed structural analyses of each protein chain, DNA–RNA chain and any bound ligands and metals. In the past year, the database has been significantly improved, in terms of both appearance and new content. Moreover, it has moved to its new address at http://www.ebi.ac.uk/thornton-srv/databases/pdbsum.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ef8b447288111b47b912545db66844976d24fe1f

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Citations in the corpus

ProFunc: a server for predicting protein function from 3D structure (2005, background): “The PDBsum database (28) already has a feature that enables upload of a structure for the generation of secure PDBsum pages and its analyses could greatly help in the study of any newly solved protein structure.”
Crystal structure of the archaeal heat shock regulator from Pyrococcus furiosus: a molecular chimera representing eukaryal and bacterial features. (2007, methodology): “In fact the cavity at the interface of the two subunits on the coiled coil region forms the largest cleft as analyzed by the PDBsum server.(29)”
SPACE: a suite of tools for protein structure prediction and analysis based on complementarity and environment (2005, background): “A number of web-based servers, including our own [LPC/CSU (3)], provide information on inter- and intramolecular contacts in proteins [PDBsum (4,5), GRASS (6), Relibase (7), RankViaContact (8), STING CONTACTS (9) and Monster (10)].”
AffinDB: a freely accessible database of affinities for protein–ligand complexes from the PDB (2005, methodology): “Accordingly, secondary databases, such as Relibase (14,15) and PDBsum (16,17), have been developed which provide more convenient access to specific information about protein–ligand complexes (e.”
PDBsum new things (2008, background): “We focus on changes made to it since it was last described (9), and specifically concentrate on features that are unique to it.”
OPM database and PPM web server: resources for positioning of proteins in membranes (2011, background): “The database provides links to TCDB (6), Pfam (32) from family and superfamily pages and to SCOP (33), PDB (3), PDBsum (39), PDBe (29), OCA (40), MMDB (41) from protein pages.”
Conformation Dependence of Backbone Geometry in Proteins (2009, background): “The secondary structure is taken from PDBsum (Laskowski et al., 2005).”