PDP: protein domain parser

By N. Alexandrov, Ilya N. Shindyalov. 2003

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Analysis of CASP8 targets, predictions and assessment methods (2009, methodology): “Domain parses by DOM (11), DOMAK (12), DomainParser (13), PDP (14) and PUU (15) were also analyzed.”
The RCSB Protein Data Bank: new resources for research and education (2012, methodology): “Figure 2 highlights how the residues listed in the sequence (SEQRES) and in the atom records (ATOM) map onto the relevant parts of the UniProtKB sequence, along with annotations from DSSP (32), SCOP, PDP (29) and Pfam (33).”
Optimal contact definition for reconstruction of Contact Maps (2010, background): “[5,6], in structural modelling by the extraction of contactbased empirical potentials [7-10] or for the identification of residues critical for folding [11], stability [12] and function [13].”
mTM-align: a server for fast protein structure database search and multiple protein structure alignment (2018, methodology): “An option is provided to automatically cut the query structure into domains by the PDB program (20).”