OSCAR (Open Source Cluster Application Resources) is a snapshot of the best known practices for building, programming and using a cluster. The toolkit is geared towards a modest sized cluster (50+ nodes) and features a wizard-based GUI for cluster installation.
The SPADE provides community tools for development and deployment of essential structure and sequence equipment. Includes a chemical probing suite to support experimental verification of predicted structural models.
Deacon J. Sweeney, Gerald M. Alter, and Michael L. Raymer
Introducing SPADE, the Structural Proteomics Application Development Environment.
Ohio Collaborative Conference on Bioinformatics (OCCBIO), 2-4 June 2008, University of Toledo.
Molecules is an application for the iPhone, iPod touch, and now iPad that allows you to view three-dimensional renderings of molecules and manipulate them using your fingers. You can rotate the molecules by moving your finger across the display, zoom in or out by using two-finger pinch gestures, or pan the molecule by moving two fingers across the screen at once.
The Maxit Program Suite was developed by the PDB (Protein Data Bank) and NDB (Nucleic Acid Database) to assist in the processing and curation of macromolecular structure data.
CellExplorer is a package of computer programs to process and analyze 3D confocal image stacks of the model animal C. elegans, and can be applied to several other model systems such as fruit fly embryo/larvae as well. Some other applications include 3D cell/nuclei segmentation, quantification, gene expression analysis, automatic cell naming/annotation, cell targeting, etc.
OpenMM Zephyr is a molecular simulation application for studying molecular dynamics of proteins, RNA, and other molecules. Zephyr guides the user through a work flow for setting up and running a specialized version of the molecular dynamics application gromacs. This version of gromacs uses the OpenMM API for GPU-accelerated molecular simulations.
iMol is a free molecular visualization application for Mac OS X operating system. The program is an indispensable tool for chemists and molecular biologists. iMol supports several file formats. It can easily handle small and large molecules, loads multiple molecules, can move and rotate them independently, or displays a molecular dynamics trajectory.