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liuyihua

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[资源] 【分享】Molecular Biology Toolkit 及其衍生软件

Molecular Biology Toolkit（MBT）是一个三维大分子可视化工具箱。基于它构建的软件有很多，既有web版的，又有单机版的，其中最有名的可能就是RCSB Protein Data Bank上用于观察大分子结构的protein workshop了。其他的还有Sirius、Epitope Viewer、ligand explorer、PKR Explorer等等。个人感觉大部分基于MBT的软件与其他免费开源软件（jmol、rasmol、webmol、KiNG ）相比，最突出的特点就是图形显示质量高，适合文章图片的使用。我认为其图像显示质量和那些大型商业软件路如DS studio、MOE、Molegro Virtual Docker、Jchem等相比一点都不逊色。但他们的功能与pymol、VMD相比，除了Sirius都显得有些薄弱，不过，由于它是based on java，使得它在构建网络数据库方面有着重要的作用。
Description
The Molecular Biology Toolkit (MBT) is a Java-based protein visualization and analysis toolkit. The toolkit provides classes for efficiently loading, managing and manipulating protein structure and sequence data. The MBT also provides a rich set of graphical 3D and 2D visualization components which can be easily "plugged together" to produce applications having sophisticated graphical user interfaces. Yet, with all of the GUI components provided in the toolkit, the core data i/o and manipulation classes may be used to write completely non-graphical applications (say, for implementing pure analysis codes, or, for producing a non-graphical "back end" for web-based applications).

Background
There are a large number of very powerful and popular stand-alone applications for the visualization and analysis of protein data. Be sure that we have no intention to reproduce their functionality in order to compete head-to-head with those applications. But, when we began the MBT project there were few if any well documented and easy to use developer's toolkits to enable the creation of custom molecular biology visualization and analysis applications.

Vision
With many major biological research resources being deployed via the web, none of the toolkits enabled applications themselves to be easily deployable both as stand-alone applications OR directly through a web interface. Even fewer packages enabled applications to run seamlessly on multiple computer platforms.
Since this project was undertaken as a "companion" project to the Protein Data Bank project, we had the additional desire to create a toolkit which could ultimately integrate seamlessly with that resource. One of our goals is to enable the transparent network access of protein data from the PDB site as well as interactive database query capability into the PDB site. For example, imagine being able to select a 3D structure in an MBT application and then be able to select a menu to find other similar structures in the PDB database.
MBT主页：http://mbt.sdsc.edu/ 里面有详细的介绍和大量的例子
源代码及工具箱下载：http://mbt.sdsc.edu/software/downloads 供有兴趣的人自己去build
Sirius下载：http://sirius.sdsc.edu/ 要注册，我试用了一下，感觉它比web版的protein workshop、Epitope Viewer、MBT GlExplorer、MBT SimpleViewer、MBT Explorer 功能强大了不少，可以做一些简单的计算（RMSD），画Ramachandran plot，BLAST search，还可作为Modeller9v2的图形界面进行同源建模。
ligand explorer：http://www.kukool.com/ligand 这是MBT主页提供的链接，但好像已经失效。
PKR Explorer ：http://pkr.genomics.purdue.edu/pkr/explorer.do 无法安装，不知何故
EpitopeViewer：http://www.immuneepitope.org

Example Applications：
MBT GlExplorer (run)：http://mbt.sdsc.edu/files-mbt/apps/GlExplorer.jnlp
MBT SimpleViewer (run) ：http://mbt.sdsc.edu/files-mbt/apps/SimpleViewer.jnlp
MBT Explorer (run) ：http://mbt.sdsc.edu/files-mbt/apps/Explorer.jnlp

Reference：The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications：http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=548701
EpitopeViewer: a Java application for the visualization and analysis of immune epitopes in the Immune Epitope Database and Analysis Resource (IEDB)
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1810240

[ Last edited by fegg7502 on 2009-12-9 at 23:17 ]

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