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