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Protein Structure Viewer

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These are a collection of protein structure viewer and display sites.

[info] Protein Data Bank 3DB Browser
[info] QuickPDB - Sequence/Structure Search and Display
[info] Swiss 3D Protein Images
[info] Swiss-PdbViewer
[info] Convert PBD file to animated GIF image
[info] MatrixPlot - make high quality matrix plots
[info] RbDe - Residue-based Diagram editor

Detailed information on the above options

Protein Data Bank 3DB Browser
Search and display information from the PDB database.

QuickPDB - Sequence/Structure Search and Display
This is a Java program that allows you to search the PDB protein structure database by keywords or sequence. The sequence and structure of entries found are displayed in 3D and secodary structure regions are displayed in colours.

Swiss 3D Protein Images
This is an image database which strives to provide high quality pictures of biological macromolecules with known three-dimensional structure. The database contains mostly images of experimentally elucidated structures, but also provides views of well accepted theoretical protein models. The images are provided in several useful formats; both mono and stereo pictures are generally available.

Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyse 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.

Moreover, Swiss-PdbViewer is tightly linked to Swiss-Model, an automated homology modelling server running in the Geneva Biomedical Research Center. Working with these two programs greatly reduces the amount of work necessary to generate homology 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.

Finally, as a special bonus, POV-Ray scenes can be generated from the current view in order to make stunning ray-traced quality images.

Convert PBD file to animated GIF image
This utility converts PDB files to animated GIF images by using RasMol2 for rendering the images.

It also includes information on using JavaScript for the clever use of animated images in a web page.

MatrixPlot - make high quality matrix plots
MatrixPlot is a program for making high quality matrix plots, such as mutual information plots of sequence alignments and distance matrices of sequences with known three-dimensional coordinates. The user can add information about the sequences (e.g. a sequence logo profile) along the edges of the plot, as well as zoom in on any region in the plot. The user can also type in the name of a PDB entry and receive the distance matrix directly. It is also illustrated how output generated from other web servers can be exported to the MatrixPlot server.

RbDe - Residue-based Diagram editor
Makes pictures of proteins presented as pearls on a string.

Any Comments, Questions? Support@hgmp.mrc.ac.uk