Geometrical Pathways in Biomolecules

This applet allows you to find a geometrical pathway between two different protein conformations. It is meant to be very user-friendly and so has few options. After doing a sequence alignment to identify any insertions and deletions, it uses FIRST (Floppy Inclusions and Rigid Substructure Topography) to identify all covalent constraints in the initial and target conformations. A geometric pathway is found using new version of FRODA (Framework Rigidity Optimized Dynamic Algorithm) which preserves the local stereochemistry at every point on the pathway. An earlier version of this applet is available on the Yale morph server.

This software has been developed in the Thorpe group, now at Arizona State University (previously at Michigan State University), by Dan Farrell, Don Jacobs, Leslie Kuhn, Brandon Hespenheide and Kirill Speranskiy. Questions and comments should be sent to Vitaliy Kapko at vkapko@asu.edu.

This applet runs interactively on a dedicated server in Arizona. PDB files are large and life in the southwest is slow, so please be patient after submission - you may have to wait up to 20 minutes to get the result. You can also close your Internet browser and your results will be stored on our server, and you may download the results files to your computer at any time. We hope the wait is worthwhile.

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