3DFlu: database of sequence and structural variability of the influenza hemagglutinin at population scale.
The influenza virus type A (IVA) is an important pathogen which is able to cause annual epidemics and even pandemics. This fact is the consequence of the antigenic shifts and drifts capabilities of IVA, caused by the high mutation rate and the reassortment capabilities of the virus. The hemagglutinin (HA) protein constitutes the main IVA antigen and has a crucial role in the infection mechanism, being responsible for the recognition of host-specific sialic acid derivatives. Despite the relative abundance of HA sequence and serological studies, comparative structure-based analysis of HA are less investigated. The 3DFlu database contains well annotated HA representatives: 1192 models and 263 crystallographic structures. The relations between these proteins are defined using different metrics and are visualized as a network in the provided web interface. Moreover structural and sequence comparison of the proteins can be explored. Metadata information (e.g. protein identifier, IVA strain, year and location of infection) can enhance the exploration of the presented data. With our database researchers gain a useful tool for the exploration of high quality HA models, viewing and comparing changes in the HA viral subtypes at several information levels (sequence, structure, ESP). The complete and integrated view of those relations might be useful to determine the efficiency of transmission, pathogenicity and for the investigation of evolutionary tendencies of the influenza virus.Database URL: http://nucleus3d.cent.uw.edu.pl/influenza.
Centre of New Technologies, University of Warsaw, Warsaw, Poland Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland.
Giovanni
G
Mazzocco
Centre of New Technologies, University of Warsaw, Warsaw, Poland Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, Warsaw, Poland.
Michal
M
Lazniewski
Centre of New Technologies, University of Warsaw, Warsaw, Poland.
Piotr
P
Migdał
Centre of New Technologies, University of Warsaw, Warsaw, Poland.
Teresa
T
Szczepińska
Interdisciplinary Centre for Mathematical and Computational Modeling, University of Warsaw, Warsaw, Poland.
Jan P
JP
Radomski
Centre of New Technologies, University of Warsaw, Warsaw, Poland Faculty of Pharmacy, Medical University of Warsaw, Warsaw, Poland d.plewczynski@cent.uw.edu.pl.
Dariusz
D
Plewczynski
D030562:Databases, Protein; D019143:Evolution, Molecular; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000737:chemistry / Q000235:genetics; D006801:Humans; D009980:Influenza A virus / Q000737:chemistry / Q000235:genetics; D000071253:Metadata; D008958:Models, Molecular; D000072417:Protein Domains; D020539:Sequence Analysis, Protein / Q000379:methods*
D019267:Hemagglutinin Glycoproteins, Influenza Virus
Nucleic Acids Res. 1999 Jan 1;27(1):368-9
9847231
J Virol. 2008 Jan;82(2):596-601
17942553
Einstein (Sao Paulo). 2012 Jul-Sep;10(3):391-3
23386026
Nat Med. 2002 Sep;8(9):950-4
12195436
Nucleic Acids Res. 2000 Jan 1;28(1):235-42
10592235
Cell Host Microbe. 2015 Mar 11;17(3):377-84
25766296
Acta Crystallogr D Biol Crystallogr. 2010 Jan;66(Pt 1):12-21
20057044
Nature. 2014 Jul 24;511(7510):475-7
24870229
Amino Acids. 2012 Aug;43(2):583-94
21993537
Database (Oxford). 2010 Jul 06;2010:baq004
20624713
Nucleic Acids Res. 2015 Jan;43(Database issue):D364-8
25352545
Virol J. 2013 Jun 06;10:179
23742717
Virology. 2005 Apr 10;334(2):276-83
15780877
Protein Cell. 2010 Apr;1(4):342-54
21203946
Comput Sci Discov. 2012 Jul 26;5(1):null
22905037
Proc Jpn Acad Ser B Phys Biol Sci. 2012;88(6):226-49
22728439
Nucleic Acids Res. 2007 Jan;35(Database issue):D376-80
17065465
J Mol Biol. 2004 Jul 2;340(2):385-95
15201059
J Mol Biol. 1990 Oct 5;215(3):403-10
2231712
Bioinformatics. 2003 Feb 12;19(3):427-8
12584134
Nucleic Acids Res. 2005 Apr 22;33(7):2302-9
15849316
Methods Enzymol. 2003;374:461-91
14696385
Bioinformatics. 2011 Jun 1;27(11):1575-7
21471012
Influenza Other Respir Viruses. 2012 Nov;6(6):404-16
22260278
Science. 2006 Apr 21;312(5772):404-10
16543414
EMBO J. 2002 Mar 1;21(5):865-75
11867515
Lancet Infect Dis. 2012 Sep;12(9):687-95
22738893
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W510-4
19429685