PDB_Amyloid: an extended live amyloid structure list from the PDB.
PDB
amyloid
amyloid‐precursor
human chorionic gonadotropin
thymidylate synthase
web server
Journal
FEBS open bio
ISSN: 2211-5463
Titre abrégé: FEBS Open Bio
Pays: England
ID NLM: 101580716
Informations de publication
Date de publication:
01 2019
01 2019
Historique:
received:
24
05
2018
revised:
21
08
2018
accepted:
03
09
2018
entrez:
18
1
2019
pubmed:
18
1
2019
medline:
18
1
2019
Statut:
epublish
Résumé
The Protein Data Bank (PDB) contains more than 135 000 entries at present. From these, relatively few amyloid structures can be identified, since amyloids are insoluble in water. Therefore, most amyloid structures deposited in the PDB are in the form of solid state NMR data. Based on the geometric analysis of these deposited structures, we have prepared an automatically updated web server, which generates a list of the deposited amyloid structures, and also entries of globular proteins that have amyloid-like substructures of given size and characteristics. We have found that by applying only appropriately selected geometric conditions, it is possible to identify deposited amyloid structures and a number of globular proteins with amyloid-like substructures. We have analyzed these globular proteins and have found proof in the literature that many of them form amyloids more easily than many other globular proteins. Our results relate to the method of Stanković
Identifiants
pubmed: 30652085
doi: 10.1002/2211-5463.12524
pii: FEB412524
pmc: PMC6325586
doi:
Substances chimiques
Amyloid
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
185-190Références
Science. 2009 Jul 17;325(5938):328-32
pubmed: 19541956
Bioinformation. 2007 Dec 30;2(5):216-21
pubmed: 18305831
Nucleic Acids Res. 2000 Jan 1;28(1):235-42
pubmed: 10592235
Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):14126-31
pubmed: 12391326
J Biol Chem. 2010 Jan 29;285(5):3201-10
pubmed: 19955183
Conf Proc IEEE Eng Med Biol Soc. 2006;2006:5755-8
pubmed: 17945915
Proc Natl Acad Sci U S A. 2002 Mar 5;99(5):2754-9
pubmed: 11880627
Int J Bioinform Res Appl. 2010;6(6):594-608
pubmed: 21354965
Cell. 2012 Mar 16;148(6):1188-203
pubmed: 22424229
Neuron. 2009 Dec 24;64(6):783-90
pubmed: 20064386
Nat Chem Biol. 2011 Jul 31;7(9):602-9
pubmed: 21804535
Trends Microbiol. 2012 Feb;20(2):66-73
pubmed: 22197327
Insect Biochem Mol Biol. 2012 Mar;42(3):203-11
pubmed: 22207151
J Mol Biol. 2008 Jul 4;380(2):425-36
pubmed: 18514226
Trends Biochem Sci. 2006 Mar;31(3):150-5
pubmed: 16473510
BMC Bioinformatics. 2008;9 Suppl 1:S11
pubmed: 18315842
Protein Sci. 1996 Aug;5(8):1443-52
pubmed: 8844836
Biochem Biophys Res Commun. 2009 Jun 12;383(4):417-20
pubmed: 19364497
Arch Neurol. 2011 Aug;68(8):1062-4
pubmed: 21482918
Horm Behav. 2008 Jun;54(1):143-52
pubmed: 18413150
J Mol Graph Model. 2007 Mar;25(6):831-6
pubmed: 16971149
J Mol Biol. 2007 Mar 9;366(5):1569-79
pubmed: 17217964
Nature. 2005 Jun 9;435(7043):773-8
pubmed: 15944695
Nat Rev Microbiol. 2005 Apr;3(4):333-41
pubmed: 15806095
Protein Sci. 1996 Feb;5(2):270-7
pubmed: 8745405
Biochem Biophys Res Commun. 2007 Dec 21;364(3):522-7
pubmed: 17959150
Int J Biochem Cell Biol. 2009 Jun;41(6):1261-8
pubmed: 19124085
BMC Bioinformatics. 2008 Jun 10;9:273
pubmed: 18544157
Biophys J. 2007 Nov 1;93(9):3046-57
pubmed: 17675353
J Neuroinflammation. 2012 Jul 02;9:117
pubmed: 22673542
FEBS J. 2010 Mar;277(6):1494-502
pubmed: 20148971
Neurobiol Aging. 2012 Oct;33(10):2247-61
pubmed: 22133278
Radiology. 2014 Oct;273(1):175-84
pubmed: 24865310
Genes Dev. 1994 Jan;8(1):23-32
pubmed: 7507074
Curr Protein Pept Sci. 2008 Jun;9(3):291-309
pubmed: 18537684
Biochim Biophys Acta. 2002 Jan 31;1594(1):1-5
pubmed: 11825603
Protein Sci. 2010 May;19(5):1023-30
pubmed: 20306493
Cell Mol Neurobiol. 2013 Aug;33(6):747-51
pubmed: 23812658
Breast Cancer Res. 2000;2(3):203-10
pubmed: 11250711
Biochim Biophys Acta. 2014 Dec;1844(12):2277-83
pubmed: 25196235
Neurobiol Dis. 2002 Oct;11(1):166-83
pubmed: 12460556
PLoS One. 2014 Dec 09;9(12):e113224
pubmed: 25490095
Lancet. 2008 Jul 19;372(9634):216-23
pubmed: 18640458
Annu Rev Biochem. 2009;78:177-204
pubmed: 19231987