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


The ConSurf Server

PDB Molecule of the Month

Brian White at the University of Massachusetts Boston has developed several computer based explorations of structural biology:

BioQUEST's ESTEEM Module: Protein Analysis

This Excel workbook allows the analysis of sample or imported protein sequences. The program analyzes five aspects of the protein sequence: the highest potential charge, the amino acid composition, the isoelectric point at varying pHs, the hydrophobicity and membrane spanning regions of the protein sequence.

ESTEEM's: Protein Analysis


StarBiochem is an Java viewer that displays molecules from the Protein Data Bank. It allows users to explore fundamental biological research concepts, select parts of the molecule and control how the selected parts are displayed.

Swami, The Next Generation Biology Workbench

The Next Generation Biology Workbench is a free resource for research and education in Bioinformatics, Genomics, Proteomics, and Phylogenetics. The NGBW is a re-engineering of the Biology Workbench which was designed by Shankar Subramaniam and his group to provide an integrated environment where tools, user data, and public data resources can be easily accessed. It has been re-engineered here using best practices from industry and academia to provide high performance analytical tools to the research and education communities. It is designed to be an organic tool that evolves with the needs of the community.

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.

SwissPDB Viewer

Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.

ExPASy Proteomics and sequence analysis tools

The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) and is dedicated to the analysis of protein sequences. Linked here are tools for secondary structure analysis.

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 is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service. Cn3D runs on Windows, Macintosh, and Unix. Cn3D simultaneously displays structure, sequence, and alignment, and now has powerful annotation and alignment editing features.


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