Bioinformatics Education Dissemination: Reaching Out, Connecting and Knitting-together

TRP Cage Problem Space

Biology WorkBench
Orientation to the Biology Workbench (pdf)

The Biology Workbench is a web-based tool for biologists. The Workbench allows biologists to search many popular protein and nucleic acid sequence databases. Database searching is integrated with access to a wide variety of analysis and modeling tools, all within a point and click interface that eliminates file format compatibility problems.


CAChe Group is a leading provider of computer-aided chemistry software and services for predicting molecular structure, properties, spectra, reactions, thermodynamics and kinetics.


UCSF Chimera is a highly extensible, interactive molecular graphics program. It is the successor to UCSF Midas and MidasPlus ; however, it has been completely redesigned to maximize extensibility and leverage advances in hardware.

Protein Data Bank

The PDB is a worldwide repository for the processing and distribution of 3-D biological macromolecular structure data. The Research Collaboratory for Structural Bioinformatics (RCSB) is a non-profit consortium dedicated to improving our understanding of the function of biological systems through the study of the 3-D structure of biological macromolecules.

National Center for Biotechnology Information (NCBI)

NCBI investigators develop new methods for integrative, computer-based data analysis to mine massive and complex data sets. Once developed, these software tools may then be used by the research community to answer specific scientific questions.

Cn3D -- a 3-dimensional
viewing app for your browser

Entrez -- cross-database search feature

PyMOL is a user-sponsored molecular modeling system with an open-source foundation. Open-Source PyMOL 0.97 has been released for all platforms.

Protein Explorer
Protein Explorer is free software for visualizing the three-dimensional structures of protein, DNA, and RNA macromolecules, and their interactions and binding of ligands, inhibitors, and drugs. It is arguably the easiest-to-use software of its kind. It is suitable for high school and college students (ages 16 years and older), yet it is also widely used by graduate students and researchers.


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