v4.0The SIB Swiss Institute of Bioinformatics presents:
Swiss-PdbViewer
DeepView
v4.04
by Nicolas Guex , Alexandre Diemand , Manuel C. Peitsch , & Torsten Schwede
DeepView - Swiss-PdbViewer: New Website Design!
The design of the website has been modified to meet the new Web design guidelines of the Swiss Institute of Bioinformatics.
While every effort has been made to ensure a smooth transition, some issues may have been overlooked.
Thank you for reporting these.
Description
Swiss-PdbViewer (aka DeepView) 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.
Swiss-PdbViewer (aka DeepView) has been developped since 1994 by Nicolas Guex. Swiss-PdbViewer is tightly linked to SWISS-MODEL, an automated homology modeling server developed within the Swiss Institute of Bioinformatics (SIB) at the Structural Bioinformatics Group at the Biozentrum in Basel.
Working with these two programs greatly reduces the amount of work necessary to generate models, as it is possible to thread a protein primary sequence onto a 3D template and get an immediate feedback of how well the threaded protein will be accepted by the reference structure before submitting a request to build missing loops and refine sidechain packing.
Swiss-PdbViewer can also read electron density maps, and provides various tools to build into the density. In addition, various modeling tools are integrated and residues can be mutated.
Finally, as a special bonus, POV-Ray scenes can be generated from the current view in order to make stunning ray-traced quality images. An example can be found here.
News: end of sporadic service interruptions
- The hardware running the Swiss-PdbViewer website and computing service (alignment and motif search) has been successfully upgraded and all services are now back on line.
News: sporadic service interruptions during the first week of January 2012
- Please note that the Swiss-PdbViewer website might be sporadically unavailable during the first week of January 2012, as various servers will be upgraded.
- The Swiss-PdbViewer application will continue to work as expected, including the import function of the file menu and the connection to SwissModel.
- The Align with Muscle service (from the Fit menu) and the Submit 3Dmotif search (from the tool menu) might experience hang-ups during this period.
- We apologize for the inconvenience but wish you a happy Holidays season.
News: version 4.0.4 has been released on Sept 14th 2011
- The blast against Uniprot feature has been fixed
- Improved the readibility of the Motif search feature.
News: version 4.0.2 has been released on April 13th 2011
- The URLs to import uniprot entries have been updated
- Fixed the Select AAkind submenu issues on the PC version
News: version 4.0.1 has been released on October 7th 2008
- The Thymine C6 atom is now correctly loaded
- Fixed the POV-Ray output endless loop on the PC version
- The occasional crash while saving PDB files (such as 2i37) on the PC has been fixed
- Updated the address of the Uppsala Electron Density Map Server
News: version 4.0 has been released on June 27th 2008
- First of all, and most importantly, PC and Mac versions have been resynchronized.
- Support for direct login modelling submissions and result retrieval to/from the SwissModel Workspace
- Enhanced Import Menu
- Enhanced user interface with taxonomy support, and new sequence alignment features.
- Beta version of 3D Motif Searching feature
- Easy access to external user defined scripts directly from the interface
- Revised Help files accessible from the interface