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The PMDB Protein Model Database.

Tiziana Castrignanò¹, Paolo D'Onorio De Meo, Domenico Cozzetto

¹CASPUR, Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Università e Ricerca. Via dei Tizii, 6/b, I-00185 Rome, Italy.

Nucleic Acids Research

|December 31, 2005

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The Protein Model Database (PMDB) offers a public repository of manually curated 3D protein models. It provides access to validated scientific literature models and experimental data for researchers.

Area of Science:

Structural biology
Bioinformatics
Computational biology

Background:

Protein structure determination is crucial for understanding biological function.
Publicly accessible, curated databases are essential for scientific research.
Existing resources may lack comprehensive collections of manually built protein models.

Purpose of the Study:

To establish a public resource for manually built 3D protein models.
To provide access to validated protein models and supporting experimental data.
To facilitate the submission and retrieval of protein models and evidence.

Main Methods:

Development of a relational database system.
Implementation of a user-friendly interface for model submission and download.

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Integration of model data with validating experimental evidence.

Main Results:

The Protein Model Database (PMDB) currently houses over 74,000 models for approximately 240 proteins.
The database provides direct access to models via unique identifiers.
Users can navigate and retrieve models for specific target proteins or protein regions.

Conclusions:

PMDB serves as a valuable public resource for 3D protein models.
The database supports scientific discovery by providing curated and validated structural data.
PMDB enhances accessibility to protein structure information for the research community.