Applications
Submitted by siteadmin on Fri, 2006-10-20 10:14.
Description
This page presents a collection of applications written using the Molecular Biology Toolkit (MBT). These application represent a cross-section of the kinds of programs that can be developed using the toolkit. They hopefully serve to demonstrate the possibilities of the toolkit and provide some inspiration for further application development by its users.
Example Applications
MBT includes a number of pre-written applications which you might find useful as-is or to be used as a starting point for your own custom applications. You can run each application directly from this page by clicking the appropriate link below.
| MBT GlExplorer (run) | John Moreland (SDSC) |
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The MBT GlExplorer program is a visualization application. It offers a more complete set of molecule visualization capabilities than the SimpleViewer program. |
| MBT SimpleViewer (run) | John Moreland (SDSC), Apostol Gramada (UCSD) |
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The SimpleViewer program is a basic 3D structure viewing application. It offers a quick and easy means of viewing a molecule with little fuss or features. |
| MBT Explorer (run) | John Moreland (SDSC), Apostol Gramada (UCSD) |
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The MBT Explorer program is a visualization application. It offers a more complete set of molecule visualization capabilities than the SimpleViewer program. |
User Applications
MBT has been designed to be a flexible software base upon which 3rd party extensions can be built. The toolkit provides toolkit-wide events (changes to application state) to be shared among multiple viewers. Each viewer has complete and equal access to all active data sets.
To date we have had a number of ideas for applications and extensions
of our own as have many of our colleagues. Below are some of the ideas
for which people have expressed an interest or for which they have
already produced applications. While the development team will try to
do its best to incorporate some of the ideas from MBT contributors,
we can not guarantee that they will be included as MBT deliverables.
| Protein Workshop | John Beaver (UCSD) |
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The protein workshop is a tool for quickly generating high quality images of large macromolecular structures. The workshop provides easy-to-use controls for manipulating structural presentation based on features such as hydrophobicity, residue and conformation. |
| Sirius | Sasha Buzko, PhD (SDSC) |
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Sirius is a component-based visualization framework designed for application in molecular modeling, drug discovery, protein structure analysis, as well as database mining and sequence-based work. |
| PKR Explorer | Sasha Buzko, PhD, Dr. Roland Hannes Niedner, MD (UCSD, PKR) |
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Based upon the existence of an annotation extension and a query by example extension, a tool is being developed to enable Kinase-specific structural sequence features to be interactively, visually, and analytically compared. By producing an alignment matrix for each Kinase into a common reference coordinate system, scientists would be able to visually preview the structural alignment of all kinase structures in 3D. |
| Ligand Explorer | Dr. Qing Zhang, PhD (unknown) |
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A "holy grail" of structural biology is to to understand the structure-function relationship. A portion of this research envolves the understanding of how ligands (small biologically active molecules) interact with proteins. Researchers have begun to develop new tools to better visualize Protein-Ligand interactions. |
| PDB Image Generation | Wayne Townsend-Merino (UCSD, PDB) |
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One of the many architectural advances incorporated into the newest PDB web site is the use of Java to orchestrate many of the back-end database and presentation layer functions. This design choice has also enabled the PDB site design team to encorporate features of the MBT toolkit directly into the back-end of the presentation layer for the site. Currently the PDB team is testing the automatic production of 3D image rendering of each structure using MBT as a pure library component. |
| Single Nucleotide Polymorphism (SNP) Viewer | Michael Barker (UCSD, PDB) |
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A custom tool has been written using MBT to visualize single nucleotide polymorphisms (SNPs or "snips"). SNPs are DNA sequences having a single altered nucleotide (ie: A,T,C,or G) yet account for the majority of human genetic variation and potentially predispose people to certain kinds of disease. |
| Epitope Viewer | John Beaver (UCSD) |
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A custom tool has been written using MBT to visualize Epitopes. An Epitope is a unique shape or marker carried on an antigen's surface which provideds a localized region on the surface of an antigen to which antibody molecules can identify and bind. This binding process then triggers a corresponding antibody immune response. Epitopes are also known as antigenic determinants. |
| Visual Protein Fold Atlas | Louise Fairweather (UCSD, PDB) |
| tbd | Protein folds (as represented by domains) are the fundamental building blocks of all proteins, and yet our current understand of fold space is relatively limited - at the time this text was written there were 800 folds in the latest SCOP release. While SCOP as a definitive source of folds it is limited. The aim of this MBT application is to begin by creating a gallery of all representative folds that is organized by basic classes - all alpha, all beta etc. From this overview we should be able to drill down to the data in the PDB associated with each fold - superfamily and family members etc. Ultimately, we can do an all by all structure comaprison to establish interfold relationships. |
| Scripting | Goran Neshich (Embrapa Brazil) or Paul Craig, PhD (RIT) |
| tbd | The ability to write scripts to drive the MBT API is very appealing because it would enable algorithmic content generation or modification, plus user-triggered interactions and animation. Many scriptible applications exist (Chime, Molscript, etc) which could be used as the basis for potential scripting language features. |
| Query By Example | Wayne Townsend-Merino (UCSD, PDB) |
| tbd | One of the long-term visions of the MBT project is to enable a tight coupling of user interaction across different visual representations and sources of protein data. For example, imagine being able to select an important structural component of a protein from a 3D view (say, a helix or an active site) and then selecting a menu which causes a database search for similar structures. This "Query-By-Example" ability when coupled with a live database would be of great value to many scientists. |
| Annotation | Jianwen Su (UCSB), Yuan-Fang Wang (UCSB) |
| tbd | Many researchers have expressed an interest in being able to add annotation (eg: 3D labels/pointers, descriptive text, and even hyper-links) to existing protein data sets. The ability to then store, retrieve and view these authored "scenes" would serve to extend raw data with scientifically meaningful "visual comments" about important regions of interest in the raw data. The Sticky Notes project is an example of a tool which enables adding/storing/retrieving/viewing of protein annotations. The group of researchers at UCSB have already begun prototyping such a system and have begun discussions to use the MBT toolkit for the underlying infrastructure. |
| Collaboration | John Moreland (SDSC, UCSD) |
| tbd | The Interactive Collaboration Environment (ICE) package is a general purpose collaboration toolkit used by the MICE project. |