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Relibase+ Release Notes
June 2006
Supported Platforms and System Requirements
Introduction
Relibase+ Version 2.1 is a full release of Relibase+ which includes new features, modifications and bug fixes.
If you require more information about these or any other matters relating to Relibase+, please contact CCDC User Support at:
12 Union Road
Cambridge
CB2 1EZ
UKTel. +44 1223 336022
Email support@ccdc.cam.ac.ukDatabase Statistics
In June 2006, Relibase+ contained 33,371 protein entries, 192,554 ligands and 67,671 chains.
A list of all PDB entries which have been excluded from Relibase+, with associated reasons are available in:
$RELIBASE_ROOT/etc/Refused_PDB_entries.listSupported Platforms and System Requirements
Server
The Relibase+ server installation is supported on the following systems:
Note: As we add support for newer versions of Linux, support for older versions may have to be withdrawn.
The total disk space required is approximately 23.5 Gb (1.2 Gb software and 22 Gb data). At least 512 Mb physical RAM and 512 Mb swap space are also highly recommended.
Client
The Relibase+ client installation is supported on the following platforms:
Note: As we add support for newer versions of Linux, support for older versions may have to be withdrawn.
The client installation requires approximately 20Mb (Windows) and up to 50 Mb on UNIX platforms.
Note: Relibase+ cannot be supported on Netscape 4.x browsers in this release. Please refer to the Relibase+ Installation Notes for further client technical information.
Please contact support@ccdc.cam.ac.uk if you have any problems with either the server or the client side installation.
New Features
- An embedded visualiser, AstexViewer (http://www.astex-therapeutics.com/AstexViewer/) is now available on ligand, protein and similar binding site search results pages.
- It is now possible to export ligand hitlists from the Hitlists page as ligand or complex multi-mol2 files.
- For keyword and SMILES searches, the database(s) to be searched may be selected from a pull-down list. The default behaviour is to search all loaded databases.
- Hitlists can now be saved post-search for protein, ligand, similar ligand and similar binding site results pages using the Save in Hitlist button.
- Sequence search results can be stored on the server and retrieved via the Stored Results page.
- Protein chain sequences can be displayed using the Show Sequence hyperlinks at the bottom of Protein Information pages.
- Stored cavity search results can be accessed via a link from the Stored Results window.
- Cavity hitlists can be saved on the Relibase+ server post-search (on the search results page), or when viewing a stored cavity search result set.
- When performing a binding site superposition it is now possible to keep the reference ligand position (though the option to centre on the origin is still available).
- Exact connectivity matching is available for SMILES searches.
- New sketcher options for variable atom, variable bond and variable molecule type have been added.
- Atom constraints are available in the sketcher: the number of bonded heavy atoms, number of connections to carbon and the number of hydrogen atoms on carbon atoms can be specified.
- Smallest ring size constraints can be added to atoms or bonds in the sketcher.
- Occupancy and temperature factor constraints can be defined for sketched protein and ligand atoms.
- Constraints that include vectors and planes can be defined in 3D substructure searches.
- A filter allowing the exclusion of DNA-containing structures has been added for 2D/3D searches.
- A basic database statistics page is available by following the Database Statistics link from the Help page.
Modifications
- The general usability of the sketcher has been further improved.
- The Set PDB Mirror button has been removed from the protein display page, and the PDB Mirror button renamed PDB Website since the RCSB has discontinued maintenance of PDB mirror sites.
- X-Ray and NMR structure filter checkboxes have been added to the SMILES search page.
- The Tanimoto threshold value can now be user-defined in the similar ligands search results page.
- Ligand PDB code searches (formerly Ligand 3-Letter code) can now be used to search for individual residues and allow searches for one (e.g. F) and two-character (e.g. Ca) residue codes.
- The Superpositions page has been renamed Stored Results and contains results of other saved searches (i.e. similar sequence and cavity similarity searches as well as similar binding site superpositions).
- The search options text Lowest Resolution (Å) and Highest Resolution (Å) is now used consistently throughout.
- Centroids that span more than one substructure can be defined in the sketcher.
- Cavity similarity searches may now use a protein or ligand hitlist as a search subset; the conversion to cavity hitlist is performed automatically.
- Ligand, ligand model and protein identifiers have been added to the property lines of molfile (SDfile) output.
- Hydrogens on amino acid templates are now defined as constraints rather than being included explicitly.
Bug Fixes
- A bug that caused binding site superposition searches to occasionally fail, if the query returned particular numbers of hits, has been fixed.
- A bug that prevented protein or ligand results pages from being displayed where data in the summary table were missing has been fixed.
- The Overwrite Existing Hitlist checkboxes on search pages are now always enabled.
- Substructure searches failed for naphthalene fragments where both naphthalene rings are fused to a third ring, if the bonds are defined as single/double rather than aromatic in the naphthalene rings. This has been fixed.
- Duplicate atoms could be written when displaying ligands or proteins causing poor performance of Reliview: this has been fixed.
- Cavity similarity search results can now correctly be ranked in both directions for each sorting criterion.
- Entire binding site superposition option is now disabled correctly in the sketcher if no ligands are defined in the substructure search.
- A Waterbase data processing bug, which caused invalid XML output for entries with multiple water models, has been fixed.
- A Cavbase data processing problem has been fixed. This caused processing to terminate after an error rather than continuing to process remaining entries.
- PDB header files are now generated correctly for in-house entries.
- Deuterium is now handled correctly during data processing if it is present in the input PDB file.
- A bug that caused ring detection to fail for certain ligands during data processing has been fixed.
- A data processing bug that prevented more than 8 connections being stored for an atom, e.g. for ferrocenes has been fixed.
- A bug which caused redundant permutations to be saved in superposition mol2 files when doing a 3D search in the sketcher has been fixed.
Relibase+ Mailing List
A Relibase+ Mailing List has been created to keep users up-to-date with news of the latest software and data releases, in addition to general Relibase+ news. Interested parties may sign up to this mailing list at the following page on the CCDC website: http://www.ccdc.cam.ac.uk/products/life_sciences/relibase/user_mailing_list.
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Cambridge Crystallographic Data Centre Web: http://www.ccdc.cam.ac.uk Support Email: support@ccdc.cam.ac.uk Support Phone: +44 1223 336022 |