For more information on BioCoRE, MDTools, NAMD, and VMD

VMD is part of a suite of tools developed by the Theoretical Biophysics group at the University of Illinois.

• BioCoRE
  BioCoRE is a web-based collaborative environment for structural biology which provides tools to allow collaboration between researchers down the hall or around the world. Anyone with access to the internet and a standard web browser can join BioCoRE and create or be added to research projects, and information about a particular project is shared among all members of that project. BioCoRE is accessed through a Java applet which includes instant messaging and notification of project updates.

  BioCoRE currently provides tools in three toolboxes. The Workbench toolbox provides access to structural biology applications such as simulation and visualization programs. The Notebook toolbox supplies a message board where users store project notes. The Conferences toolbox allows interactive text-based chats, which are also archived to the message board for future reference. Soon, the Documents toolbox will provide tools to assist in joint preparation of publications.

  BioCoRE is currently accessible to users through the BioCoRE server at UIUC, and a code release is planned which will allow sites to run their own servers. Because BioCoRE is web-based, updates and new features are automatically available every time the user logs in. More information is available at the BioCoRE home page

• MDTools
  JMV is an easy-to-use Java-based molecular viewer which uses Java3D to provide hardware accelerated 3D rendering of molecules. JMV is designed as component software, and can be used within other programs, or as a standalone application. JMV is implemented as a Java Bean, and can be used in the standard Bean-capable development tools. JMV can be used as an applet to provide in-browser molecular visualization capabilities, in situations where VMD is overkill for the task. More information is available at the JMV home page

• MDTools
  MDTools is a collection of programs, scripts, and utilities provided for researchers to make various modeling and simulation tasks easier, and to provide basic code and utilities which can be built up into larger toolsets. Each tool, script, or library has its own separate distribution, documentation, etc. The programs in this collection are provided for the benefit of the research community, but are not officially supported unless otherwise stated. Each program may have a software license and/or citation suggestions which should be listed on its web page. More information is available at the MDTools home page

• NAMD
  A parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD uses the CHARMM force field and file formats compatible with both CHARMM and X-PLOR. NAMD supports both periodic and non-periodic boundaries with efficient full electrostatics, multiple timestepping, constant pressure and temperature ensemble simulation methods. NAMD provides several methods of steering a simulation through the application of additional forces, including the ability to connect directly to VMD for interactive steering of a live simulation. NAMD is distributed free of charge and includes source code. More information is available at the NAMD home page

• Structural Biology Software Database
  The Structural Biology Software Database contains programs which are thought to be of interest to researchers in the fields of structural biology, quantum chemistry, and bioinformatics. The database entries are contributed by users, and are moderated to provide a high quality resource. More information is available at the Structural Biology Software Database home page

• VMD
  A general molecular visualization program capable of interactive display and concurrent control of a molecular dynamics simulation running on a remote computer. VMD uses an object-oriented design, and is written in C++. This document describes VMD. More information is available at the VMD home page

For more on any of the individual software efforts, BioCoRE, MDTools, NAMD, or VMD, see the Theoretical Biophysics Group WWW home page.