Version Log

PDBeFold version Date     Changes
2.58 08/04/2014    
  • 'Select domain' function, Help text links, narrow warning/help text pane and 'Arrange by SCOP familyi' fixed.
2.56 12/11/2013    
  • Check all button on match results.
2.55 26/3/2013    
  • Multiple alignment results JMol options.
2.54 22/2/2013    
  • Winter Update.
  • Fix the View link on 'Submission Page'
2.51 2/4/2012    
  • Problem with one or or more processes not completing, when specifying low persentage match.
  • Results page headers are now help links.
  • Fixes for Google Chrome.
2.50 14/12/2011    
  • Problem with one or two CPUs slow to complete fixed.
  • PDB codes in match list are links.
2.49 15/11/2011    
  • Exclusions list added to weeekly perocessing capability.
2.47 14/11/2011    
  • Web page links made relative so that hppts requests are handled correctly.
2.47 12/11/2011    
  • RMSD values correctly displayed for multi-alignments. (Some values were zero).
  • Alignment number displayed (Alignment i of n) in alignment details page.
2.46 26/10/2011    
  • Fixed cut-and-paste problems in HTML pages.
2.42 5/7/2011    
  • Summer make over. 64bit native code and data files.
2.36 13/03/2009    
  • Fixed a bug preventing Jmol applet from starting in certain MS Windows setups.
2.35 02/10/2008    
  • A major revision of PDBeFold database structure due to the increased size of PDB archive. No changes in results and functionality with the except for recent PDB entries now appearing in database searches
2.34 07/08/2007    
  • A facility to reject unfair-use users has been added.
2.33 08/12/2006    
  • New checkbox "enforce sequence identity" is added to the Submission Form when both query and target are given by single structures (PDB/SCOP entries or coordinate files). The checkbox is unchecked by default, which corresponds to the way PDBeFold used to work in earlier versions. When the checkbox is checked, PDBeFold tries to calculate initial superposition from sequence alignment, rather than from matching secondary structure graphs. This option should be used when a sequence-identical alignment is required, even if it results in a lower geometric score. A typical example is the calculation of transformation matrix between identical chains in ASU, not related by crystal symmetry (NCS matrix).
2.32 30/10/2006    
  • New checkbox "superpose whole entries" is added to the result pages. When it is unchecked, only selected parts of entries (chain, range, domain) are superposed and visualised/downloaded. When the checkbox is checked, PDBeFold applies superposition matrices to the whole entries or coordinate files and sends them for visualisation or download.
  • Data sent to rasmol/jmol are now uniquely named, which overcomes cache problems caused by custom browser and proxy settings
  • Wait pages are renamed at every reload, also for forcing browsers and proxy servers to obtain the page afresh.
2.31 05/05/2006    
  • C-alpha alignment added as an option to XML output in off-line mode.
  • Fixed yet another bug in multiple alignment module, which caused crash under certain conditions.
  • Fixed bug which caused occasional crashes in XML output of C-alpha alignment.
2.30 24/04/2006    
  • Chain IDs in capital and small letters are now differentiated (i.e. chain "A" is different of "a"). Example: 1s5l.
2.29 06/04/2006    
  • Fixed few bugs which caused PDBeFold to crash when downloading results (XML and sequences) at certain conditions.
2.28 31/03/2006    
  • A bug causing termination of computational jobs in Multiple Alignment has been identified and fixed. Due to this bug, PDBeFold was showing never ending calculations for some rare type of input data.
2.27 15/02/2006    
2.26 07/10/2005    
  • Visualisation in Jmol added.
  • Original residue sequence numbers and insertion codes are now preserved in coordinate data sent for visualisation in both Jmol and Rasmol. Wherever the opposite is written in documentation should be ignored now. The chain ID may differ in the visualisation scripts, where originally duplicated. Atom serial numbers are used for selection and they do differ from original.
2.24 08/06/2005    
  • Fixed bug in parsing lists of PDB and SCOP entries in Submission Form for multiple alignment.
2.23 08/04/2005    
  • Fixed a bug, which in rare instances prevented PDBeFold from loading the results of multiple alignments, so that session looked like never finishing calculations
  • File parser was slightly modified such as to accept some roque formats like Windows text UTF-8
  • Session ID changed to encrypted form
2.22 07/02/2005    
  • PDBeFold may work with gzipped or compressed PDB archives. This affects only details of local installations and makes no difference to user interface or results.
2.21 20/01/2005    
  • PDBeFold accepts compressed (*.Z) files for upload, those may be coordinate files, tarballs, code lists etc. Any file to be uploaded to PDBeFold may be gzipped (*.gz) or compressed for faster transmission.
2.20 11/01/2005    
  • Introduced a new option of uploading a list of PDB or SCOP codes for Multiple Alignment.
  • Improved diagnostics on inacceptable structures in Multiple Alignment submissions.
2.19 01/12/2004    
  • The sharing mechanism of accessing the PDBeFold log file has been improved, which should prevent log crashes at multiple simultaneous access in busy environments. The fix has no effect on PDBeFold's calculation results.
2.18 02/11/2004    
  • Fixed bug that caused a permanent PDBeFold misconfiguration in mixed-platform setups (e.g. Sun+Linux) under certain circumstances
2.17 05/10/2004    
  • Fixed bug that prevented submission of structures for multiple alignment from the list of (pairwise) results after resorting the latter.
  • Fixed bug that caused the output of incorrect sample of xml input file used by off-line (command-prompt) PDBeFold. This also affects the copy of input data in the output xml files.
  • Fixed bug that prevented PDBeFold from taking entries without sidechains but with complete mainchain.
  • XML tag <3DAlignment>, which was in violation of XML naming conventions, changed for <StructAlignment>. The tag was used in PDBeFold's output XML (downloadable) files for pairwise structure alignment.
2.16 13/09/2004    
  • Prevented occasional server failures due to NFS delays at opening files/directories.
  • Improved server's diagnostics in case of submitting non-aminoacid chains or chains made of only backbone C-alphas.
  • Fixed a bug blocking submission of SCOP matches for Multiple Alignment from the result list.
2.15 02/09/2004    
  • PDBeFold PDB parser is softened to allow for minor violations of PDB specifications in coordinate files like disagreement in atom names between ATOM and ANISOU etc. records.
2.14 27/08/2004    
  • Fixed bug in displaying the results of multiple alignment, which caused indefinite looping in certain circumstances
  • Fixed bug in generating Rasmol scripts for individual structures in multiple alignment result page, which caused PDBeFold to crash erratically on pushing the "view" buttons.
  • Algorithm of multiple 3D alignment improved in part concerning the analysis of multiple atom contacts for candidate mappings. In many instances, this results now in longer alignments with higher Q-score.
2.13 19/08/2004    
  • PDBeFold database of precompiled structures is aggressively optimized, which resulted in 30-50% gain in space and access time. PDBeFold should server queries in general faster now, with most effect seen for setups on the edge of hardware requirements.
2.12 28/07/2004    
  • Fixed bug, which, in the case of a residue range selection from query/target structures, caused sending the whole structure in the PDBeFold rasmol scripts instead of sending only the selected part.
  • Enhanced security of PDBeFold CGI web pages.
  • Fixed bug making specification of PDB and SCOP codes in PDBeFold URL queries case-sensitive.
  • Introduced suggestion of SSE similarity thresholds in case when querying an archive does not yield non-identical matches.
2.11 29/06/2004    
  • Number of matches obtainable for each pair of structures with option "Best Matches Only" switched off is now limited such as to avoid enormous number of alternatives in some cases (because of which PDBeFold could hang for a long time).
2.10 19/06/2004    
  • Fixed bug in reading mmCIF coordinate files because of which Ca atoms were not recognized under certain conditions.
  • Added facilities for working with multiple alignments through the URL link and off-line, see linking PDBeFold).
2.09 04/06/2004    
  • Fixed bug in generating the Rasmol scripts, because of which the colouring of superposed structures might be incorrect in rare instances.
  • Fixed bug causing occasional misinterpretation of calcium and Ca atoms in PDBeFold database under certain conditions.
2.08 17/05/2004    
  • Fixed bug, due to which the correspondence between SCOP domains and PDB entries was being established on the level of entries, rather than chains. Now different chains of a PDB entry are, if that should be so, put in correspondence with different SCOP domains.
  • Fixed bug, due to which the secondary structure assignment in the output table of Ca was wrong or missing for SCOP domains starting not from the begining of a chain.
2.07 12/04/2004    
  • Algorithm of multiple alignment in 3D tuned up as to perform better in situations when common secondary structure motif contains only a few (1-3) SSEs.
2.06 06/04/2004    
  • The search in PDB and SCOP archive may be narrowed by uploading the list of PDB or SCOP entries which should be taken as target structures.
  • Sub-structures may be formed by selecting a range of residues (in addition to chain and domain selections).
  • On-line documentation (help) updated.
2.05 28/03/2004    
  • Added incremental procedure of updating the PDBeFold's precompiled archives.
  • Fixed bug in the calculation of P-values, which caused an appearance of infinite P-values in rare instances.
  • When connectivity check is turned off and Ca-alignment results in parts of chains being misconnected, the match is selected by italic in the list of results.
  • When a structure is matched against PDB or SCOP archives, the results may be arranged into groups by SCOP families. The sorting order is preserved within the groups and between the groups, based on the sorting score of the group's leading hit. The list of results may be paged up and down by SCOP groups, and brought to a SCOP group directly. See new control elements following the list of results.
  • Fixed bug in the module decoding query string (when PDBeFold is linked as http://url/ssmserver?query_string, see linking PDBeFold).
  • When PDBeFold is linked through a URL, local files may be specified as query/target structures (cf. linking PDBeFold).
2.04 27/02/2004    
  • Added submission of tarballs of structures for Multiple Alignment.
  • Fixed bug in the representation of multiple alignment of secondary structure elements.
2.03 17/02/2004    
  • Added selection of matches. Selected matches may be specified for downloading target sequences and alignments, brought on top of the results and submitted for multiple alignment.
2.02 06/01/2004    
  • Added XML and plain text output of results of multiple alignment.
  • Removed bug which excluded chains without SSEs in case when many-chain structures were compared as a whole rather then chain-by-chain.
  • Improved synchronization of PDBeFold's parallel computational jobs such as to minimize the effect of file system caching on CPU clusters. The results should now load faster and should not get lost due to PDBeFold desynchronization.
  • On-line Help updated as to cover the multiple alignement.
2.01 12/12/2003    
  • PDBeFold is extended for multiple 3D alignment. More than 2 structures may be aligned simultaneously, the results are scored in respect to coordinate consensus and each aligned structure. Both SSE and Ca alignments are given in the output. The pairwise/multiple alignments are chosen on the very top of the PDBeFold Submission Form.
  • Linking the results to PDBe Atlas Pages is added.
1.39 16/07/2003    
  • A bug is removed, which caused premature end of parsing PDB files containing duplicate sequence numbers, empty lines and syntactical errors in non-coordinate section, in data uploaded as a file set tarball.
1.38 30/06/2003    
  • A bug is removed, which prevented PDBeFold from properly selecting chains with numerical identifiers, when those are specified in the Submission Form.
1.37 24/06/2003    
  • PDBeFold parser is further modified to properly read PDB/mmCIF files coming from different platforms and therefore having different line terminators. As practice shows, in many instances uploaded PDB-like files have empty lines, which is against PDB syntax; such lines are now silently ignored.
1.36 13/05/2003    
  • Result pages for individual matches now display secondary structure alignment in terms of strings composed of "H" for helices and "S" for strands, so that match topology may be seen immediately.
  • Result pages for individual matches now display a direct reference to SCOP families where available.
1.35 02/05/2003    
  • SCOP domain may be specified as a query structure and as a single target structure. Both SCOP domain name and sunid may be used for identifying the structure.
  • Fixed bug which caused spliting SCOP domains consisting of more then 1 chain, if matching individual chains is set on.
1.34 24/04/2003    
  • A bug, which enforced ordering of SSEs found in different chains, is removed. This affected matches of structures or domains consisting of more than one protein chains.
  • In structure-to-structure regime, selection of chains or domains is now allowed also for the target structure.
  • Internal threshold value are slightly adjusted according to experience accumulated. This does not invalidate any previous results, however new hits may emerge in some cases.
1.33 10/04/2003    
  • Coordinate files with <CR> line terminators (Windows standard), as well as <LF><CR> (MS DOS) are now acceptable.
1.32 27/03/2003    
  • Q-score is added to the PDBeFold output.
  • Q-score is made default sort subject (instead of RMSD).
  • Sequence identity is reported in result pages and in downloaded files.
  • Aligned sequences may be download in FASTA format.
  • PDBeFold on-line help updated in order to reflect last changes.
1.31 18/02/2003    
  • 3D Ca alignment algorithm is modified to better handle the situations when only one SSE has been matched (extremely low structural similarity).
1.30 11/02/2003    
  • Tune-up of parameters controlling the 3D Ca alignment for improving the ratio of alignment length to RMSD.
  • Modified convergence conditions for 3D Ca alignment iterations. No change in results was noticed, however PDBeFold is 20% to 30% faster.
1.29 03/02/2003    
  • Advanced algorithm for 3D Ca alignment, which includes a modified target function. You might see a slight change in the results for remote structural neighbours, which should be seen in longer alignments and/or lower RMSDs.
  • Changed the mechanism of PDBeFold session expiration. Now the session expires after 4 hours since the last access to its results. If the results were not accessed immediately after the calculations (e.g. if the wait (progress) page was bookmarked and browser switched to another site or page), the session expires in 48 hours after the calculations have actually finished.
  • Results for individual matches, including the 3D Ca alignments, may now be downloaded from the result page in either XML or plain text format.
1.28 07/01/2003    
  • PDBeFold uploads the query and target structures into separate session sub-directories, which eliminates a possibility of file name conflict with PDBeFold own files.
  • PDBeFold accepts lists of pairs for multiple pairwise matching of structures uploaded in a file set tarball (a special query option is added).
1.27 02/01/2003    
  • PDBeFold accepts gzipped coordinate (PDB and mmCIF) files
  • PDBeFold accepts file sets as a target (a special target option is added).
1.26 18/12/2002    
  • The transformation matrix now superposes the target structure over the query (it was the other way round before)
  • PDBeFold version is added into output XML file
  • WWW linking is added, so that PDBeFold queries may be launched from any web site