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Open Access Technical Note

mmView: a web-based viewer of the mmCIF format

Petr Čech1 and Daniel Svozil2*

Author Affiliations

1 Department of Computing and Control Engineering, Faculty of Chemical Engineering, Institute of Chemical Technology, Technická 5, CZ-166 28 Prague, Czech Republic

2 Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, Institute of Chemical Technology, Technická 5, CZ-166 28 Prague, Czech Republic

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BMC Research Notes 2011, 4:121  doi:10.1186/1756-0500-4-121

Published: 12 April 2011

Abstract

Background

Structural biomolecular data are commonly stored in the PDB format. The PDB format is widely supported by software vendors because of its simplicity and readability. However, the PDB format cannot fully address many informatics challenges related to the growing amount of structural data. To overcome the limitations of the PDB format, a new textual format mmCIF was released in June 1997 in its version 1.0. mmCIF provides extra information which has the advantage of being in a computer readable form. However, this advantage becomes a disadvantage if a human must read and understand the stored data. While software tools exist to help to prepare mmCIF files, the number of available systems simplifying the comprehension and interpretation of the mmCIF files is limited.

Findings

In this paper we present mmView - a cross-platform web-based application that allows to explore comfortably the structural data of biomacromolecules stored in the mmCIF format. The mmCIF categories can be easily browsed in a tree-like structure, and the corresponding data are presented in a well arranged tabular form. The application also allows to display and investigate biomolecular structures via an integrated Java application Jmol.

Conclusions

The mmView software system is primarily intended for educational purposes, but it can also serve as a useful research tool. The mmView application is offered in two flavors: as an open-source stand-alone application (available from http://sourceforge.net/projects/mmview webcite) that can be installed on the user's computer, and as a publicly available web server.