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PDP specifications


Unique identifier OMICS_13713
Name PDP
Alternative name Protein Domain Parser
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability No
Maintained No


No version available


This tool is not available anymore.

Publication for Protein Domain Parser

PDP citations


Template‐based quaternary structure prediction of proteins using enhanced profile–profile alignments

PMCID: 5836938
PMID: 29178285
DOI: 10.1002/prot.25432

[…] quence identity of 40% using CD‐HIT, based on the domain definition provided by the PDB. In all, we had 46,194 protein domains. The domain definition originates from the updated definition by SCOP or protein domain parser (PDP). We retrieved domain boundary information from the RCSB PDB and generated domain structures using BioJava. To develop reliable profiles, we performed all‐against‐all struct […]


An ambiguity principle for assigning protein structural domains

Sci Adv
PMCID: 5235333
PMID: 28097215
DOI: 10.1126/sciadv.1600552

[…] 0-residue-long domain delineations. Thus, each PU merging event defines a domain partitioning level, which is evaluated using two criteria: the separation (σ) and the compactness (κ), inspired by the PDP () and PUU [Parser for protein Unfolding Units ()] methods, respectively. The separation criterion σi,j measures the independence between two PUs, i and j, and can be written as followsσi,j=pi,j/( […]


Extending Protein Domain Boundary Predictors to Detect Discontinuous Domains

PLoS One
PMCID: 4621036
PMID: 26502173
DOI: 10.1371/journal.pone.0141541

[…] boundaries.Some methods such as SnapDRAGON[], RosettaDom[] and OPUS-DOM[] first constructed a 3D model and then extracted domain boundaries with structure-based domain partition tools such as DAIL[], PDP[] and DomainParser []. Although these methods can detect discontinuous domains, the success of the domain assignments relies on the correctness of the predicted models, which are applicable only t […]


Tools for macromolecular model building and refinement into electron cryo microscopy reconstructions

PMCID: 4304694
PMID: 25615868
DOI: 10.1107/S1399004714021683

[…] ive approach is fold recognition, where the density is searched for features resembling known protein domains and motifs. Two approaches have been described: FREDS (Khayat et al., 2010), which uses a protein-domain parser, PDP (Alexandrov & Shindyalov, 2003), to prepare a library of folds directly from the PDB that are then searched against the density map, and SPI-EM (Velázquez-Muriel et al., 200 […]


Optimization and revision of the production process of the Necator americanus glutathione S transferase 1 (Na GST 1), the lead hookworm vaccine recombinant protein candidate

PMCID: 4186034
PMID: 25424799
DOI: 10.4161/hv.28872

[…] urvival of the parasite within the host is under development by the Sabin Vaccine Institute and Texas Children’s Hospital Center for Vaccine Development, a non-profit product development partnership (PDP).One of the leading hookworm antigens currently under development as a recombinant vaccine is a glutathione s-transferase (GST) cloned from N. americanus and expressed in P. pastoris (yeast). Hook […]


PepBind: A Comprehensive Database and Computational Tool for Analysis of Protein–peptide Interactions

PMCID: 4357787
PMID: 23896518
DOI: 10.1016/j.gpb.2013.03.002

[…] tional annotation . For a structure similarity search, we take advantage of the web service of PDB, which employs the FATCAT algorithm to recognize homologous domains available at PepBind, SCOP and PDP . […]


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PDP institution(s)
Ceres Inc, Malibu, CA, USA; San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA

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