New on the NCBI Structure Group pages

17 Jun 2002 CDD in Entrez: The Conserved Domain Database has been made an integral part of the Entrez retrieval system. Conserved Domains are indexed for retrieval by keywords; links between Conserved Domains and Proteins, PubMed, and Taxonomy have been added. Conserved Domains are also linked to other Conserved Domains by two different neighboring mechanisms. "Similar" domains are defined as those giving overlapping annotations on sets of protein sequences, "Co-occurring" domains are defined as those giving non-overlapping annotations on sets of protein sequences.

11 Jun 2002 CDD v1.57: The most recent update of domain models in the Conserved Domain Database goes along with changes in the presentation. The new CD-server software supports visualization with Cn3D v4.0.

1 Mar 2001 DART: The Domain Architecture Retrieval Tool allows protein neighboring by domain architecture. Use pre-calculated CD-Search results to find proteins which contain a set of domains similar to that of your query.

25 Sep 2000 Domain Guess by Size: Empirical distributions of domain sizes and segmentation patterns can be used to guess domain composition and boundaries based only on the length of a globular protein chain.

7 Aug 2000 Conserved Domain Database: A collection of sequence alignments and profiles, representing protein domains conserved in molecular evolution, is now available via CD-Search.

18 May 2000 Get Cn3D 3.0 now! A new version of Entrez's structure viewer is available. Cn3D 3.0 offers better quality graphics, more user display options, improved sequence and alignment viewers, coloring by alignment conservation, and the ability to save display settings and alignments.

20 Dec 99 An on-line version of the paper describing MMDB in the 1/2000 issue of Nucleic Acids Research is available here.

21 July 99 Get Cn3D 2.5 now! A new version of Entrez's structure viewer is available. Cn3D 2.5 offers feature editing to set and save annotations and display styles for user-defined residue sets, one-click installation for Netscape and Internet Explorer on PC platforms, and many more improvements!

20 May 99 A new page explains how to link to various NCBI structure group servers

22 Feb 99 Evaluation of the 1995 structure prediction for leptin.

12 Jan 99 A page offering access to numerical evaluation quantities for predictions in the CASP3 Experiment is now available.

11 Nov 98 A page giving access to the non-redundant subset of PDB-chains is now available.

16 Oct 98 Vast neighbors are now being displayed on several pages by default, if the list exceeds 20 hits. The user may change the number of hits displayed per page.

17 Sep 98 Cn3D 2.0 is now distributed separate from network Entrez. Visit Cn3D's home page for instructions on downloading, or go directly to the ftp-site. Cn3D help has been updated.

10 Sep 98 A new option has been added to the visualization of structure superpositions from VAST neighbor pages. By default, the server sends the aligned chains only for multi-chain proteins.

31 Jul 98 Get Cn3D v2.0 Now! A new version of Cn3D is available. Cn3D now displays multiple structure superpositions calculated by VAST. Cn3D now shows both the three-dimensional structures of biopolymers and their sequences, as well as sequence alignments derived from structure superpositions!

13 Jul 98 VAST Search is now available on the NCBI Structure Group pages. Search the MMDB 3D-Structure database with 3D protein coordinates provided by you!

9 Jul 98 A page describing taxonomy assignment to MMDB is available here!

8 Apr 98 Structure neighbors available from the MMDB structure summary pages have been calculated with an improved version of VAST. The VAST structure neighbor pages have been changed too. By default, a non-redundant list of neighbors is reported, but different levels of redundancy can be selected.

10 Feb 98 The NCBI Structure Group Threading Export Package has been updated. Installation help is available online.

5 Nov 97New Structure Summary Format! We have changed the appearance of the MMDB Structure summaries, now including taxonomy information. The NCBI Structure Group WWW-pages have been streamlined too.

20 Oct 97 Links to the NCBI Taxonomy have been added to Structures in MMDB.

11 Aug 97 Cn3D 1.1 is Here. Get it now!. The Cn3D Home Page has also been updated.

6 May 97. CASP-2 Meeting Fold Recognition Evaluation - Updated with new interactive tables and team information.

11 March 97Announcing Cn3D for 68K Macintosh. A CodeWarrior bug kept this out of your hands for nearly 9 months! Download it here on our new Cn3D download area. The Cn3D Home Page has also been updated.

11 Feb 97 The MMDB-Outpost Program
The MMDB database (and soon VAST) can be served by WWW-servers in other locations. We have a special CGI-BIN program wich runs off data stored on your local copy of MMDB as it is on the MMDB ftp site. The MMDB-Outpost will serve up:

• Structure Summary pages with links to NCBI sequence, PubMed/Medline, PDB's 3DB system, and VAST databases.
• MIME-typed ASN.1, PDB, and Kinemage Files, just like WWW-Entrez.
• Optionally the VAST tables, VAST structural alignments in 3D and in text reports.

11 Feb 97 New Structure Summary Format! A new Structure Summary format is introduced here. This is an experimental version available only from the MMDB home page. The server is now faster and more responsive. This will become part of the new WWW-Entrez service, and is what will be served up by new MMDB-Outposts.

30 Jan 97 Structure group Alumni page.

24 Jan 97 MMDB Biostruc ASN.1 data now available at ftp://ncbi.nlm.nih.gov/mmdb/.

24 Jan 97 Mac Helper-App. Installation Bug and Fix. Mac Netscape on some systems (2.0 or 3.0) is mistakenly launching the Entrez configuration program Netentcf instead of standalone Cn3D. Get the Fix

19 Dec 96 CASP-2 Meeting Fold Recognition Evaluation

12 Dec 96 Kinemages in VAST tables are improved - Install MAGE and click here to try: ( K).

14 Nov 96 Standalone Cn3D is Here!