The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications
By J. Moreland, A. Gramada, O. Buzko, Qing Zhang, Philip E. Bourne. BMC Bioinformatics, 2005
304 citations recorded by the source corpus.
BackgroundThe large amount of data that are currently produced in the biological sciences can no longer be explored and visualized efficiently with traditional, specialized software. Instead, new capabilities are needed that offer flexibility, rapid application development and deployment as standalone applications or available through the Web.ResultsWe describe a new software toolkit – the Molecular Biology Toolkit (MBT; http://mbt.sdsc.edu) – that enables fast development of applications for protein analysis and visualization. The toolkit is written in Java, thus offering platform-independence and Internet delivery capabilities. Several applications of the toolkit are introduced to illustrate the functionality that can be achieved.ConclusionsThe MBT provides a well-organized assortment of core classes that provide a uniform data model for the description of biological structures and automate most common tasks associated with the development of applications in the molecular sciences (data loading, derivation of typical structural information, visualization of sequence and standard structural entities).
Subfields: Information Systems and Management, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/55b568118856bbf99f5d50dbe7aef2733a3d4a0f
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Citations in the corpus
- The RCSB Protein Data Bank: new resources for research and education (2012, methodology): “In addition, options to export high-resolution images with custom sizes for publications and posters are available for the three RCSB PDB viewers: Protein Workshop, Simple Viewer and Ligand Explorer.”
- ProViz—a web-based visualization tool to investigate the functional and evolutionary features of protein sequences (2016, methodology): “…have been developed including Java applet based tools (JalView2 Lite (24), STRAP (25), PFAAT (26)), resource specific tools (PDB viewers (27,28), Pfam (3), webPrank (29)) and general alignment / feature viewers (Alignment-Annotator (30), MView (31), JSAV (32)) (Supplementary Table S1).”
- Computational prediction of secondary and supersecondary structures. (2013, background): “The secondary structure, which is assigned from the tertiary structure, is used for a variety of applications, including visualization (61-63) and classification of the protein folds (64-67), and as a ground truth to develop and evaluate the secondary and SSS predictors.”
- The RCSB Protein Data Bank: views of structural biology for basic and applied research and education (2014, methodology): “(c) Interactive 3D visualization using Ligand Explorer (33) (ligand in stick and ball style, and some of the interacting binding site residues in green; dashed lines, hydrogen bonds and metal coordination with distance, and transparent binding site surface color-coded by hydrophobicity of the closes”