MViewer: Visualization of Protein Molecular Structures Stored in the PDB, mmCIF and PDBML Data Formats

Molecular viewers allow visualization of spatial structures of proteins and other biological molecules. However, most of them are not able to read molecular structures stored in the PDBML format provided by the world-wide Protein Data Bank (PDB). In the paper, we present main features of the MViewer that we have designed and developed in order to support a man-protein structure interaction. The unique feature of the MViewer is the ability to open, read and visualize structures stored in all three formats (i.e. PDB, mmCIF, and PDBML) available from the PDB repository.

[1]  Philip E. Bourne,et al.  [30] Macromolecular crystallographic information file , 1997 .

[2]  J. Gasteiger,et al.  Chemoinformatics: A Textbook , 2003 .

[3]  John D Westbrook,et al.  The PDB format, mmCIF, and other data formats. , 2003, Methods of biochemical analysis.

[4]  E. Pietka,et al.  Information Technologies in Biomedicine , 2008 .

[5]  J D Gans,et al.  Qmol: a program for molecular visualization on Windows-based PCs. , 2001, Journal of molecular graphics & modelling.

[6]  Haruki Nakamura,et al.  PDBML: the representation of archival macromolecular structure data in XML , 2005, Bioinform..

[7]  C W Hogue,et al.  Cn3D: a new generation of three-dimensional molecular structure viewer. , 1997, Trends in biochemical sciences.

[8]  Tadeusz Burczyński,et al.  Topological evolutionary computing in the optimal design of 2D and 3D structures , 2007 .

[9]  Dariusz Mrozek,et al.  Protein Molecular Viewer for Visualizing Structures Stored in the PDBML Format , 2008, Information Technologies in Biomedicine.

[10]  D. Oxender,et al.  The regulation of neutral amino acid transport by amino acid availability in animal cells , 1983 .

[11]  Marco Masseroli,et al.  Clinical Bioinformatics: challenges and opportunities , 2012, BMC Bioinformatics.

[12]  W. Delano The PyMOL Molecular Graphics System , 2002 .

[13]  John W. R. Schwabe Art and architecture of proteins , 2000 .

[14]  Philip E. Bourne,et al.  The Macromolecular Crystallographic Information File (mmCIF) , 2001 .

[15]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[16]  Dariusz Mrozek,et al.  search GenBank: interactive orchestration and ad-hoc choreography of Web services in the exploration of the biomedical resources of the National Center For Biotechnology Information , 2013, BMC Bioinformatics.