Molmil: a molecular viewer for the PDB and beyond

We have developed a new platform-independent web-based molecular viewer using JavaScript and WebGL. The molecular viewer, Molmil, has been integrated into several services offered by Protein Data Bank Japan and can be easily extended with new functionality by third party developers. Furthermore, the viewer can be used to load files in various formats from the user’s local hard drive without uploading the data to a server. Molmil is available for all platforms supporting WebGL (e.g. Windows, Linux, iOS, Android) from http://gjbekker.github.io/molmil/. The source code is available at http://github.com/gjbekker/molmil under the LGPLv3 licence.

[1]  Philip E. Bourne,et al.  Macromolecular dictionary (mmCIF) , 2006 .

[2]  Klaus Schulten,et al.  Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics , 2013, Nature.

[3]  Akira R. Kinjo,et al.  Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format , 2011, Nucleic Acids Res..

[4]  Gert Vriend,et al.  YASARA View—molecular graphics for all devices—from smartphones to workstations , 2014, Bioinform..

[5]  D. Baker,et al.  Control over overall shape and size in de novo designed proteins , 2015, Proceedings of the National Academy of Sciences.

[6]  Kengo Kinoshita,et al.  eF-site and PDBjViewer: database and viewer for protein functional sites , 2004, Bioinform..

[7]  Haruki Nakamura,et al.  Presto(protein Engineering Simulator): A Vectorized Molecular Mechanics Program for Biopolymers , 1992, Comput. Chem..

[8]  Haruki Nakamura,et al.  Molecular Dynamics Simulations Accelerated by GPU for Biological Macromolecules with a Non-Ewald Scheme for Electrostatic Interactions. , 2013, Journal of chemical theory and computation.

[9]  Randy J. Read,et al.  Overview of the CCP4 suite and current developments , 2011, Acta crystallographica. Section D, Biological crystallography.

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

[11]  Berk Hess,et al.  GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers , 2015 .

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

[13]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[14]  Robert M. Hanson,et al.  Jmol – a paradigm shift in crystallographic visualization , 2010 .

[15]  J. Sussman,et al.  JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia , 2013 .

[16]  Sydney R. Hall,et al.  The STAR file: a new format for electronic data transfer and archiving , 1991, J. Chem. Inf. Comput. Sci..

[17]  Bui Tuong Phong.  Illumination for computer generated pictures , 1975, Commun. ACM.

[18]  Shigeru Endo,et al.  Normal mode analysis based on an elastic network model for biomolecules in the Protein Data Bank, which uses dihedral angles as independent variables , 2013, Comput. Biol. Chem..

[19]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..