Version Log

Version  Date     Changes
1.48 24/10/2013    
  • Error in web page: 'Non-existent PDB entry'.
  • Error in XML for assembly list.
  • Some assemblies not displayed correctly.
1.47 21/03/2013    
  • Database search results page navigation.
  • Assembly List page, 'Details' and tooltips.
1.46 12/03/2013    
  • Assembly XML.
1.45 7/03/2013    
  • Remark 350 page formatting.
  • Multiple assembly GET downloads.
1.44 5/03/2013    
  • Cosmetic updates.
1.43 26/02/2013    
  • Cosmetic updates.
1.42 24/02/2013    
  • EBI and PDBe web page update.
1.41 1/01/2013    
  • Download of multiple xml and pdb files.
  • Mis-calculated dG values for uploaded files.
  • Database search.
1.34 3/04/2012    
  • CSS values mis-calculated for uploaded entries.
1.33 16/03/2012    
  • Submission page freezes for viruses
1.32 16/11/2011    
  • Crash (500 internal server error) when entering invalid PDB code.
1.30 3/11/2011    
  • PISA now calculates the assembly etc on the fly for CGI GET requests, when the PDB code is not present in the database but the PDB file exists.
  • Web page links made relative so that hppts requests are handled correctly.
1.29 31/10/2011    
  • PISA query page PDB code out-of-step with internal query code. Analysis of the displayed code is automatically updated when a 4 character code is entered.
1.28 24/10/2011    
  • Fixed 404 error when downloading XML files using 'XML' buttons.
1.27 28/09/2011    
  • e-mail sent to annotators concerning weekly update processing.
1.20 1/3/2011    
  • PISA recompiled as a native 64-bit executable
1.18 30/03/2009    
  • The correspondence between identified oligomeric state and PQS annotation in PDB files (Remark 350) is now reported in "Biomolecule" section of assembly pages.
1.17 06/02/2009    
  • UniProt and SCOP ids are included as options into PISA database searches.
  • The interaction filter is introduced into PISA datbase searches. The filter allows for the selection of PDB entries with specific (e.g. protein-RNA) type of interactions.
  • Fixed a bug that caused PISA interface searches to crash at zero structure similarity level.
1.16 12/01/2009    
  • Source code revised in order to eliminate dependence on the computational platform, which appeared in a limited number of instances. This does not change any previous results.
1.15 12/09/2008    
  • Linking to PISA pages added to URL interface, see here.
1.14 19/09/2007    
  • On request of wwPDB, the format of PDB REMARK 350 changed to include macromolecular complex and software specifications into the output.
1.13 17/08/2007    
  • Adopted changes due to the release of the . PISA will continue to accept old PDB files for processing, however PISA database (pre-calculated results for all PDB entries, used for fast retrieval and searches), is now built using new, remediated, files.
1.12 11/05/2007    
  • Added identification of covalent linkage in interfaces. In assembly analysis, covalently linked interfaces are permanently fixed except cases when it results in infinite-size assemblies.
  • The ligand fixing algorithm is completely revised and rewritten in order to take covalent linkage into account. As a result, ligand fixing is done on a more rigorous basis now, and some minor differences from previous results (e.g. in ligand placements on assemblies) may occur. The assembly-analysis part of PISA is now noticeably faster.
  • Surface and interface atom names are made available for display as an option in interface tables.
1.11 23/04/2007    
  • Added analysis of custom assemblies given As Is by coordinate section in PDB or mmCIF files. This analysis does not use crystal descriptions, therefore it is applicable to NMR structures. The results are found in the "assemblies" section.
  • Minor interface improvements and bug fixes
1.10 06/03/2007    
  • Disulphide bonds are now calculated and taken into account at assembly analysis.
  • A new facility for searching the PISA database has been added to the service. The search options include:
    • by assembly type
    • by free energy of dissociation
    • by assembly's accessible surface area
    • by assembly's buried surface area
    • by percent of buried surface area
    • by presence or absence of salt bridges and disulphide bonds
    • by multimeric state
    • by homomeric/heteromeric assembly type
    • by symmetry number
    • by space group
    • by presence of specific ligands
    • by annotation keywords
  • Fixed a bug in part simulating the crystal structure. The bug caused crash in rare circumstances.
  • Symmetry number calculations revised in algorithmic part in order to improve results where coordinate data are less perfect.
  • Fixed a bug in part generating the visualisation data. The bug, associated with renaming of unnamed chains, caused crash in rare circumstances.
  • Introduced a correction for interfaces that overlap due to imperfectness of coordinate data. Total BSA is now guaranteed not to exceed total ASA on atom level
  • Fixed a bug in chemical-structural equivalencing of NCS mates, had effect on few viral structures.
  • Identification of parallel monomeric units relaxed for non-crystallographically equivalent chains, and tightened for NCS mates. The former is to account for imperfectness of coordinate data, and the latter is to avoid errors in large capsids, like 900-mer 1vb2, where monomeric units may get almost parallel simply because of large number of them.
1.09 11/01/2007    
  • Serial numbers for symmetry operations from International Tables of Crystallography have been dropped, as they appear to be inconsistent through different editions of the Tables. The symetry operations are numbered as used by PDB at RCSB.
  • Assembly output forced for all chains found in ASU. Previously, if e.g. 9 equivalent chains A-I form homohexamers, only one assembly A-F was shown in the resulting tables. Now both A-F and GHIG'H'I' are shown where G'H'I' come from neighbouring ASU.
  • Control over ligand processing has been provided in the Submission Form. This allows to exclude agents used to aid crystallization from the processing. If not excluded, they may lead to artifactually large assemblies by facilitating the macromolecular binding. Cf. details from on-line help.
  • Check enforced for overlapping symmetry mates, when they are supposed to overlap and therefore have fractional occupancy. Previously this occasionally resulted in multiple count of molecular interactions, example 1CYI residue CD 302 (Cd ion).
  • Fixed a job syncronisation bug causing crash before displaying results under certain conditions
  • Fixed a bug in structure search submission when one query structure was an NCS mate, rather than original chain given by PDB entry or coordinate file.
  • Fixed a bug in secondary structure calculations, which have caused crash on a recently deposited structure.
1.08 22/11/2006    
  • PDB/RCSB numbering for symmetry operations has been added. The symmetry ID records now look like S[r]_IJK, where r stands for the PDB/RCSB serial number of the respective symmetry operation.
1.07 20/10/2006    
  • 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.
1.06 05/06/2006    
  • Ligands are now taken into account. This changes oligomeric states in many instances, when ligands are found in interfaces (e.g. 1JL5).
  • Fixed a bug, which sometimes caused incorrect orthogonalisation code for uploaded structures.
  • Chain IDs are now case-sensitive. Note that chain IDs may be case-sensitive in new PDB entries.
  • Identification of structurally similar assemblies now uses a different algorithm, which makes searches for stable assemblies considerably faster.
  • Symmetry operations in output pages are now identified also by their serial numbers in space symmetry group.
1.05 17/02/2006    
  • Protein-DNA/RNA and DNA/RNA-DNA/RNA interactions added to PISA models. PISA includes DNA/RNA-containing complexes now.
  • Remark 350 is written in both orthogonal and fractional coordinates.
  • Generated assemblies are moved such that a maximal number of monomeric units are found in their original orientation.
  • Macromolecular interaction parameters recalibrated, no significant changes for protein complexes.
  • Minor changes of web pages include more visualisation links and direct access to most probable assemblies directly from the submission form.
1.04 14/12/2005    
  • Parameters of chemical-thermodynamical models have been recalibrated. This affects the estimates of dissociation/solvation free energies, entropy etc. No change in oligomeric states has been found in the benchmark entries, however this does not imply that multimeric states of all PDB entries did not change. Change of the dissociation pattern has been noticed in some of the benchmark entries (viruses).
  • A bug in the assembly enumeration procedure has been discovered and fixed. In certain circumstances, this bug caused a premature termination of assembly search in a crystal, so that some of potentially interesting assemblies with around-zero free energies of dissociation were omitted by the search.
  • The graph matching procedure used for identification of equivalent assemblies have been optimized, which has a drastic effect on PISA performance when multimeric state exceeds 20.
  • Structure superposition results and visualisation of superposed structures have been added to the "structure" section of results.
1.03 17/11/2005    
  • Improved identification of chemical-geometrical equivalences in interfaces and monomeric units. This has had an impact on some entries where chemically similar, but crystallographically different chains show noticeable structural differences.
  • Improved identification of casual interfaces, which are most probably experimental artifacts. Some entries, such as 1ir2 are affected.
  • The CPU load is made more even, and a few imperfectnesses in CPU communications cleared up, which results in a faster completion.
1.02 28/10/2005    
  • The interface search facility is enhanced by new search options, limiting target selections to
    • different similarity levels
    • targets with or without multimeric assemblies
    • targets with or with interfaces equivalent to those in the query
    • targets with interfaces equivalent to those in the query, making or making no protein contacts in (target) assemblies
  • On-line documentation updated.
1.01 17/10/2005    
  • Visualisation in is added.
  • Buttons were added for downloading monomeric structures, interfaces and assemblies.
  • Many improvements in the identification of interface and structure equivalences
1.00 05/04/2005     First public release.