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

TRP Cage Problem Space
Tools

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.

http://workbench.sdsc.edu


CAChe

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


http://www.CACheSoftware.com


Chimera

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.

http://www.cgl.ucsf.edu/chimera/


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.

http://www.rcsb.org/pdb/


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.

http://www.ncbi.nlm.nih.gov/

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

http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml

Entrez -- cross-database search feature
http://www.ncbi.nlm.nih.gov/Entrez/index.html


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

http://pymol.sourceforge.net/


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.

http://molvis.sdsc.edu/protexpl/frntdoor.htm

 

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