title: Interactome3D: adding structural details to protein networks.
abstract: Network-centered approaches are increasingly used to understand the fundamentals of biology. However, the molecular details contained in the interaction networks, often necessary to understand cellular processes, are very limited, and the experimental difficulties surrounding the determination of protein complex structures make computational modeling techniques paramount. Here we present Interactome3D, a resource for the structural annotation and modeling of protein-protein interactions. Through the integration of interaction data from the main pathway repositories, we provide structural details at atomic resolution for over 12,000 protein-protein interactions in eight model organisms. Unlike static databases, Interactome3D also allows biologists to upload newly discovered interactions and pathways in any species, select the best combination of structural templates and build three-dimensional models in a fully automated manner. Finally, we illustrate the value of Interactome3D through the structural annotation of the complement cascade pathway, rationalizing a potential common mechanism of action suggested for several disease-causing mutations.
authors: Joint IRB-BSC Program in Computational Biology, Institute for Research in Biomedicine, Barcelona, Spain.
authors: Roberto
authors: R
authors: Mosca
authors: Arnaud
authors: A
authors: Céol
authors: Patrick
authors: P
authors: Aloy
mesh_terms: D000818:Animals; D003198:Computer Simulation; D030562:Databases, Protein; D006801:Humans; D008954:Models, Biological; D046912:Multiprotein Complexes / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation; D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D046912:Multiprotein Complexes; D011506:Proteins
references: Mol Syst Biol. 2011 Nov 22;7:551
references: 22108793
references: Protein Sci. 2006 Nov;15(11):2507-24
references: 17075131
references: Nucleic Acids Res. 2011 Jan;39(Database issue):D718-23
references: 20965963
references: Cell. 2009 Dec 24;139(7):1255-67
references: 20064372
references: Nature. 2005 Oct 20;437(7062):1173-8
references: 16189514
references: Proc Natl Acad Sci U S A. 2008 Oct 28;105(43):16426-31
references: 18940924
references: PLoS Biol. 2009 Apr 28;7(4):e96
references: 19402753
references: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D449-51
references: 14681454
references: Protein Eng. 2000 Feb;13(2):77-82
references: 10708645
references: Nat Biotechnol. 2012 Jan 15;30(2):159-64
references: 22252508
references: Nucleic Acids Res. 2005 Jan 1;33(Database issue):D262-5
references: 15608192
references: Science. 2006 Dec 22;314(5807):1938-41
references: 17185604
references: Mol Syst Biol. 2007;3:89
references: 17353931
references: Curr Opin Struct Biol. 2011 Apr;21(2):200-8
references: 21320770
references: Bioinformatics. 2010 Sep 15;26(18):2347-8
references: 20656902
references: Bioinformatics. 2005 Feb 1;21(3):410-2
references: 15353450
references: Nat Methods. 2009 Nov;6(11):843-9
references: 19855391
references: BMC Biol. 2007 Oct 09;5:44
references: 17925023
references: J Mol Biol. 1993 Dec 5;234(3):779-815
references: 8254673
references: J Mol Biol. 1987 Aug 5;196(3):641-56
references: 3681970
references: Cell. 2005 Sep 23;122(6):957-68
references: 16169070
references: Nucleic Acids Res. 2000 Jan 1;28(1):235-42
references: 10592235
references: Mol Syst Biol. 2009;5:321
references: 19888216
references: Curr Opin Struct Biol. 2006 Jun;16(3):385-92
references: 16713251
references: Nucleic Acids Res. 2012 Jan;40(Database issue):D109-14
references: 22080510
references: Bioinformatics. 2008 Aug 1;24(15):1743-4
references: 18556668
references: BMC Bioinformatics. 2007 Oct 18;8:401
references: 17945017
references: Nucleic Acids Res. 2009 Jan;37(Database issue):D767-72
references: 18988627
references: Proteomics. 2008 May;8(10):1959-64
references: 18491310
references: Science. 2009 Sep 18;325(5947):1544-9
references: 19762644
references: Nature. 2006 Nov 9;444(7116):217-20
references: 17051150
references: Nat Rev Mol Cell Biol. 2006 Mar;7(3):188-97
references: 16496021
references: Hum Mutat. 2012 Feb;33(2):359-63
references: 22072597
references: Nucleic Acids Res. 2011 Jan;39(Database issue):D235-40
references: 20852260
references: Cell. 2012 May 11;149(4):780-94
references: 22579283
references: J Clin Invest. 2006 Oct;116(10):2817-26
references: 17016562
references: Nucleic Acids Res. 2010 Jan;38(Database issue):D532-9
references: 19897547
references: Nucleic Acids Res. 2003 Jul 1;31(13):3375-80
references: 12824331
references: Bioinformatics. 2003 Jan;19(1):161-2
references: 12499311
references: Nucleic Acids Res. 2012 Jan;40(Database issue):D857-61
references: 22096227
references: Mol Syst Biol. 2008;4:218
references: 18766178
references: J Mol Biol. 2003 Oct 3;332(5):989-98
references: 14499603
references: Nucleic Acids Res. 2012 Jan;40(Database issue):D71-5
references: 22102590
references: Nat Methods. 2009 Jan;6(1):83-90
references: 19060904
references: Science. 2000 Jan 7;287(5450):116-22
references: 10615043
references: Nat Biotechnol. 2011 May;29(5):391-3
references: 21552234
references: PLoS Comput Biol. 2011 Oct;7(10):e1002195
references: 22039361
references: Nucleic Acids Res. 2011 Jan;39(Database issue):D465-74
references: 21097780
references: Nucleic Acids Res. 2012 Jan;40(Database issue):D841-6
references: 22121220
references: PLoS Biol. 2012 Jan;10(1):e1001244
references: 22272186
references: Nature. 2000 Aug 24;406(6798):916-9
references: 10972297
references: Proteins. 2003 Jul 1;52(1):51-67
references: 12784368
references: Bioinformatics. 2005 May 1;21(9):1901-7
references: 15657096
references: Curr Opin Struct Biol. 2012 Jun;22(3):367-77
references: 22575757
references: Nucleic Acids Res. 2012 Jan;40(Database issue):D290-301
references: 22127870
references: Nucleic Acids Res. 2011 Jan;39(Database issue):D698-704
references: 21071413
references: PLoS Comput Biol. 2010 May 20;6(5):e1000789
references: 20502673
references: Database (Oxford). 2011 Jan 12;2011:baq037
references: 21233089
references: Bioinformatics. 2010 Oct 15;26(20):2564-70
references: 20802208
references: Science. 2004 Mar 26;303(5666):2026-9
references: 15044803
references: PLoS Comput Biol. 2009 Aug;5(8):e1000490
references: 19714207
references: Nucleic Acids Res. 2009 Jan;37(Database issue):D619-22
references: 18981052
references: Nat Biotechnol. 2007 Aug;25(8):894-8
references: 17687370
references: Bioinformatics. 2005 May 15;21(10):2541-3
references: 15749693
references: Nat Methods. 2012 Apr;9(4):345-50
references: 22453911
references: Nat Chem Biol. 2008 Nov;4(11):666-73
references: 18936751