FireDB & firestar news

16 Nov2020 PDB scanning: 440480 chains; 33124 molecular compounds. Also, we add the data from M-CSA
28 Jan2020 PDB scanning: 404153 chains; 30594 molecular compounds
01 Jun2016 PDB scanning: 284647 chains; 22110 molecular compounds
03 Oct2014 PDB scanning: 259893 chains; 18782 molecular compounds
28 Aug2014 PDB scanning: 257507 chains; 18622 molecular compounds
15 Aug2014 PDB scanning: 256313 chains; 18566 molecular compounds
22 Aug2013 PDB scanning: 224691 chains; 16661 molecular compounds
20 Aug2013 New ligand info web page with external references and pharmacological annotations
02 Apr2013 PDB scanning: 211306 chains; 15872 molecular compounds
16 Jan2013 PDB scanning: 206000 chains; 15524 molecular compounds
14 Jan2013 Happy New Year from firestar' staff. After CASP experiment results came out and an internal evaluation, we decided to move back to HHsearch.
08 Oct2012 PDB scanning: 200278 chains; 15040 molecular compounds
06 Jul2012 PDB scanning: 194903 chains; 14509 molecular compounds
29 May2012 PDB scanning: 192374 chains; 14337 molecular compounds
22 Feb2012 Coverage and mean SQUARE's score are now calculated from initial alignments in firestar. (for more info, see also HERE)
22 Feb2012 Collapsing of the sites for summary results now is guided by biological relevance in firestar.
21 Feb2012 Information from metal binding sites with no biological relevance is now filtered out in firestar.
16 Feb2012 13 more COGNATE compounds identified
27 Jan2012 PDB scanning: 183852 chains; 13536 molecular compounds
18 Nov2011 PDB scanning: 178160 chains; 13374 molecular compounds
17 Nov2011 A minor bug fixed in FireDB update program.
13 Nov2011 Some minor bugs have been fixed for the batch mode of firestar. New parameters are now available.
10 Nov2011 HHblits has been integrated in substitution of HHsearch in firestar.
02 Nov2011 New Predicted Site Reliability score available in the firestar results page.
25 Oct2011 Bug fixed in the 3D model generation option.
19 Oct2011 Cognate / Possible Cognate lists update based on annotation data. For more details see firestar help page.
03 Oct2011 New Per-residue Frequency score for each catalytic site predicted is now available in the summary results page
27Sep2011 PDB scanning: 175611 chains; 13159 molecular compounds
15Aug2011 PDB scanning: 173993 chains; 13014 molecular compounds
08Jul 2011 3D model generation option in summary results' page of firestar added
11May2011New filter rules for some metal ligands added in firestar
18Mar2011HIGHLIGHT option in summary results' page of firestar added
07Dec2010Integration of HHsearch in firestar
24Nov2010PDB scanning: 158103 chains; 11869 molecular compounds
20Sep2010Classification of functional residues in FireDB in terms of biological relevance
27Aug2010PDB scanning: 152629 chains; 11512 molecular compounds
10Apr2010Automatic and high throughput modes made available
26Feb2010PDB scanning: 144260 chains; 10908 molecular compounds
26Feb2010Two classes of binding sites defined: metal binding sites and non-metal.
04Dec2009PDB scanning: 142125 chains; 10537 molecular compounds
05Aug2009PDB scanning: 134743 chains; 10099 molecular compounds
29Sep2008PDB scanning: 115103 chains; 9098 molecular compounds
14Jul2008PDB scanning: 111328 chains; 8785 molecular compounds
20May2008PDB scanning: 108381 chains; 8686 molecular compounds
08Apr2008PDB scanning: 106642 chains; 8531 molecular compounds
28Feb2008Non biologically relevant sites are filtered out in firestar prediction display
28Feb2008PDB scanning: 104926 chains; 8326 molecular compounds
08Jan2008FireDB is updated with the new PDB (remediated) version
08Jan2008PDB scanning: 102479 chains; 8153 molecular compounds
04Oct2007PDB scanning: 93560 chains; 7921 molecular compounds
25Jun2007PDB scanning: 89924 chains; 7705 molecular compounds
17Apr2007PDB scanning: 88551 chains; 7493 molecular compounds
23Feb2007Protein ligand contact criteria has changed: Van der Waals radii is taken into account. New cutoffs are 0.5, 1.0 and 1.5 Angstroms plus the sum of Van der Waals radii of atoms involved in the contact.
23Feb2007PDB scanning: 86261 chains; 7339 molecular compounds
08Jan2007PDB scanning: 84219 chains; 7239 molecular compounds
21Dec2006PDB scanning: 83794 chains; 7223 molecular compounds
14Nov2006PDB scanning: 81994 chains; 7103 molecular compounds
11Oct2006PDB scanning: 80500 chains; 7029 molecular compounds


[1] FireDB--a database of functionally important residues from proteins of known structure. Lopez G, Valencia A and Tress ML.
Nucleic Acids Research, Volume 35, Issue suppl_1, 1 January 2007, Pages D219-D223;

Technical support:
Scientific support:, Gonzalo Lopez