Protein Geometrical Pathways

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 common constraints between the initial and target conformations, and then identifies the rigid regions. A geometric pathway is found using FRODA (Framework Rigidity Optimized Dynamic Algorithm) which preserves the local stereochemistry at every point on the pathway. An earlier version of this applet, which does not do sequence alignment and only preserves covalent constraints, 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 Don Jacobs, Leslie Kuhn, Brandon Hespenheide, Dan Farrell and Kirill Speranskiy. Questions and comments should be sent to Kirill Speranskiy at kirill@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. We hope the wait is worthwhile.