Proteopedia
.Proteopedia contains one page for every entry in the World Wide Protein Data Bank, which contained >148,000 entries in January, 2019. Proteopedia is updated weekly with new entries shortly after they are released by the Protein Data Bank. Most of these pages, which are titled with a four-character PDB identification code, are "seeded" automatically to include a default view of the quaternary assembly ("biological unit", or if not provided by PDBe, the asymmetric unit), the abstract of the publication, green links to highlight sites and ligands, and molecule-specific links to other viewers and databases. If you click "Random" in the "navigation" box at the upper left, usually you will get an article titled with a PDB code, since they outnumber human-authored articles
From the Source
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 developed since 1994 by Nicolas Guex. Swiss-PdbViewer was initially 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. However, the SWISS-MODEL web interface evolved to a point where it is now possible to use it directly for advanced modeling. Maintaining a direct interface with Swiss-PdbViewer is too complex and no longer supported.
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 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
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BIOVIA Draw
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ChemDraw
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A chemistry communication suite, ChemOffice+ Cloud Standard transforms your chemical drawings into chemical knowledge by facilitating the management, reporting and presenting of your Chemistry research."
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ChemDoodle
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MarvinSketch & MarvinView
Marvin is one of the world’s most widely used and trusted chemical drawing software, utilized daily by over 100,000 scientists, researchers, start-ups and Fortune 500 organizations, including top 20 pharmaceutical companies.
In one application, you can simply and intuitively produce customizable illustrations, search for chemical structures online and perform advanced chemical calculations. Marvin can handle a large variety of chemical structures and file formats, so it’s robust enough for any use case.
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RasMol and OpenRasMol
"RasMol is a program for molecular graphics visualisation originally developed by Roger Sayle. This site is provided for the convenience of users of RasMol and developers of open source versions of RasMol. The site itself is provided courtesy of Bernstein + Sons. Maintenance of RasMol, much of the development, and integration of modifications provided by the community is done at the ARCiB project at RIT."
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Accelrys Draw
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