Dear all,
Twice a year, the Protein Data Bank in Europe (PDBe; http://pdbe.org)
releases new and improved tools and services. Our first website update
of 2013 features:
1. A new weekly overview of new biology in the PDB
2. Improved searching of EMDB entries with rapid filtering of results
3. New features for visual analysis of EMDB entries
4. Improved pages with chemical-shift-validation information for NMR entries
5. Easy sharing of PDBe pages
--------------------
1. A new weekly overview of new biology in the PDB.
You can now view instances of new biology in the PDB including Pfam
families, GO terms and UniProt entries that appear in the archive for
the first time. For example, this week's release includes the first
structure ever from a member of the "Alternative Oxidase" Pfam sequence
family
(http://www.ebi.ac.uk/pdbe/searchResults.html?display=latest&tab=xref).
Note that two kinds of "new biology" are shown: cases where an existing
Pfam family etc. maps to a newly released structure in the PDB for the
first time, and cases where an existing PDB entry maps to a new entry in
Pfam, GO, UniProt, CATH or SCOP.
2. Improved searching of EMDB entries with rapid filtering of results.
We have made searching the EMDB easier by implementing search filters
that enable you to rapidly narrow down the set of search results.
Filters based on experimental details, journal, organism etc. can be
applied when searching (http://pdbe.org/emsearch) or browsing the
contents of the archive (http://pdbe.org/embrowse).
3. New features for visual analysis of EMDB entries.
We have introduced several new features to aid visual analysis and
validation of EMBD entries, including:
* A volume-estimate graph that shows how the enclosed volume of a
map varies with the contour level (e.g.
http://pdbe.org/emd-5357/analysis).
* A Fourier-shell correlation (FSC) curve used to estimate the
resolution of single particle maps (e.g.
http://pdbe.org/emd-5357/analysis).
* A residue-based atom-inclusion chart that can be used to assess
the quality of fit of PDB models to an EMDB map (e.g.
* http://pdbe.org/emd-2017/analysis).
* An image showing the overlay of any deposited masks on a map, that
show segmentations or some particular feature of an entry (e.g.
http://pdbe.org/emd-1206/analysis).
(Note that not all features are available or applicable for all entries.)
4. Improved pages with chemical-shift-validation information for NMR
entries.
We have improved the presentation of information on the validation of
chemical shifts with VASCO. The redesigned webpages now show statistics
on the assigned chemical shifts, any referencing corrections and a list
of atoms with unusual chemical shifts values (e.g.
http://www.ebi.ac.uk/pdbe-apps/nmr/vasco/searchEntry?pdbCode=2knr).
5. Easy sharing of PDBe pages.
Regular visitors of the PDBe website may have noticed some small changes
to the headers of our pages. The new headers include feedback and
sharing buttons on every PDBe webpage. If you want to share what you
find on one of our pages with friends or colleagues, use the share
button to post the URL on Facebook, Twitter, etc. or to email it. If you
have suggestions for improvements, please let us know by using the
feedback button.
You may also have noticed our new logo. Based on a motif that is found
at all levels of structure, we hope that our new logo will quickly
become synonymous with the provision of high-quality information about
3D molecular and cellular structure. Our new logo and guidelines for its
use are available from our website at http://pdbe.org/logo
As always, we welcome your comments and suggestions through the feedback
button at the top of every PDBe webpage.
Gary.
--
Gary Battle
Protein Data Bank in Europe (PDBe)
http://www.facebook.com/proteindatabank
http://twitter.com/PDBeurope
