We created this Protein Geometrical Pathways web portal to help in the study of large scale protein conformational changes. A very fast software algorithm allows one to obtain a non-clashed, stereo-chemically correct trajectory between the initial and final conformations of a biomolecule containing protein, DNA, RNA, ligands and water. This portal provides a very efficient way to visualize large conformational transformations, usually within minutes. The creation of this web portal is the result of further development of the FIRST/FRODA software used in Flexweb portal.
Two input files are needed - any hydrogens present will be stripped off and a complete set positioned using Reduce. The default is that only common residues of protein, DNA and RNA are targeted. There is an option to also include any ligands and heterogens in the targeting. However, this feature does not work for ions or waters, and the user must remove these from the PDB files before submitting.
The major areas of focus for Protein Geometrical Pathways can be reached by
following the links in the left-hand menus. These menus will be present on all pages on this
site. You can run Pathways as a guest or as a registered user. If you registered you will be able to use the personal File Cabinet and download the software. This registration is separate and distinct from Flexweb registration. If you have already registered
please proceed to Software. You will find helpful information on how to use this website in the Software link. Please feel free to contact us at akumar67@asu.edu with any suggestions, comments or questions. If the connection is lost, it will continue running on our servers, and can be retreived through the file cabinet.
The software available on this site has been written by Daniel Farrell, Mykyta Chubynsky, Brandon Hespenheide, Don Jacobs, Scott Menor, A.J. Rader and Stephen Wells. The Protein Geometrical Pathways site was developed by Kirill Speranskiy, with help from Brandon Hespenheide and Scott Menor. If you used this Protein Geometrical Pathways website please follow Citation link to find the proper information, as we appreciate being cited.
