PDBsum: a Web-based database of summaries and analyses of all PDB structures.

By Roman A. Laskowski, E. Hutchinson, A. Michie, Andrew C. Wallace, Martin L. Jones, Janet M. Thornton. 1997

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Citations in the corpus

ShapeNet: An Information-Rich 3D Model Repository (2015, methodology): “Though we ﬁrst use WordNet due to its popularity, the ShapeNet UI is designed to allow multiple views into the collection of shapes that it contains, including different taxonomy views and faceted navigation.”
The Uppsala Electron-Density Server. (2004, background): “There are websites that run validation software on all coordinate entries in the PDB (Hooft et al., 1996; Laskowski et al., 1997) and report outliers.”
An overview of the structures of protein-DNA complexes (2000, unknown): “A2(103-160), B1(5-75), B2(102-161) 1oct C1(5-75) Oct-1 POU domain H.”
PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids (2004, methodology): “The PDBsum database was created at University College London in 1995 (1,2).”
CATHEDRAL: A Fast and Effective Algorithm to Predict Folds and Domain Boundaries from Multidomain Protein Structures (2007, methodology): “Functional sites are identiﬁed using the PDBsum database [41], and the alignments are manually adjusted to ensure that conserved residues and secondary structure elements are correctly aligned.”
Practical limits of function prediction (2000, methodology): “…corresponding to each PDB structure were retrieved from the pdbtosp.txt ﬁle (release 37.0) of the SWISS-PROT database 27 or from the PDBsum database 28 for PDB entries corresponding to more than one SWISS-PROT ﬁle, i.e., multi-chain structures, mutants of natural proteins, different ligands or…”
PDBsum additions (2013, methodology): “PDBsum has been available since 1997 (2), with various improvements made since (3–5).”
Residue centrality, functionally important residues, and active site shape: Analysis of enzyme and non‐enzyme families (2006, methodology): “using the ConSurf server (Glaser et al. 2003). where”
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.”
PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach (2010, methodology): “The target annotations were extracted from DrugBank, PDBSum (24), UniProt (25) and in-house TargetBank (our unpublished data) and were categorized as follows: UniProt access ID, target name, target function and indication/disease involved.”
Dynamic Fluctuations Provide the Basis of a Conformational Switch Mechanism in Apo Cyclic AMP Receptor Protein (2013, background): “R180, E181 and R185 are the key residues of the HTH motif involved in specific protein-DNA interactions [6], whereas the nonspecific DNA binding residues are R169, Q170 and S179 [7] with the other DNA binding sites [8] D138, V139, T168, C178, T182, G184, K188, H199, and G200.”
Evolution of function in protein superfamilies, from a structural perspective. (2001, methodology): “, 1997), PDBsum (Laskowski et al., 1997), SWISS-PROT (Bairoch & Apweiler, 2000) and ENZYME (Bairoch, 2000) databases, and the literature.”