title: Dynameomics: a comprehensive database of protein dynamics.
abstract: The dynamic behavior of proteins is important for an understanding of their function and folding. We have performed molecular dynamics simulations of the native state and unfolding pathways of over 2000 protein/peptide systems (approximately 11,000 independent simulations) representing the majority of folds in globular proteins. These data are stored and organized using an innovative database approach, which can be mined to obtain both general and specific information about the dynamics and folding/unfolding of proteins, relevant subsets thereof, and individual proteins. Here we describe the project in general terms and the type of information contained in the database. Then we provide examples of mining the database for information relevant to protein folding, structure building, the effect of single-nucleotide polymorphisms, and drug design. The native state simulation data and corresponding analyses for the 100 most populated metafolds, together with related resources, are publicly accessible through http://www.dynameomics.org.
authors.affiliation: Department of Bioengineering, University of Washington, Seattle, WA 98195-5013, USA.
authors.forename: Marc W
authors.initials: MW
authors.lastname: van der Kamp
authors.forename: R Dustin
authors.initials: RD
authors.lastname: Schaeffer
authors.forename: Amanda L
authors.initials: AL
authors.lastname: Jonsson
authors.forename: Alexander D
authors.initials: AD
authors.lastname: Scouras
authors.forename: Andrew M
authors.initials: AM
authors.lastname: Simms
authors.forename: Rudesh D
authors.initials: RD
authors.lastname: Toofanny
authors.forename: Noah C
authors.initials: NC
authors.lastname: Benson
authors.forename: Peter C
authors.initials: PC
authors.lastname: Anderson
authors.forename: Eric D
authors.initials: ED
authors.lastname: Merkley
authors.forename: Steven
authors.initials: S
authors.lastname: Rysavy
authors.forename: Dennis
authors.initials: D
authors.lastname: Bromley
authors.forename: David A C
authors.initials: DA
authors.lastname: Beck
authors.forename: Valerie
authors.initials: V
authors.lastname: Daggett
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D006801:Humans; D008958:Models, Molecular; D008968:Molecular Conformation; D020641:Polymorphism, Single Nucleotide; D011489:Protein Denaturation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics / Q000379:methods
chemical_list: D011506:Proteins
references.citation: J Mol Graph. 1996 Feb;14(1):33-8, 27-8
references.pmid: 8744570
references.citation: Proc Natl Acad Sci U S A. 2008 Jul 29;105(30):10360-5
references.pmid: 18650397
references.citation: Protein Sci. 2008 Dec;17(12):2038-50
references.pmid: 18796694
references.citation: Nat Rev Mol Cell Biol. 2003 Jun;4(6):497-502
references.pmid: 12778129
references.citation: Nat Struct Biol. 1995 Jul;2(7):596-603
references.pmid: 7664128
references.citation: Biochemistry. 2008 Jan 22;47(3):893-901
references.pmid: 18154359
references.citation: Nat Struct Mol Biol. 2009 Mar;16(3):318-24
references.pmid: 19252485
references.citation: J Mol Biol. 1995 Apr 7;247(4):536-40
references.pmid: 7723011
references.citation: Biophys J. 2009 Dec 2;97(11):2958-66
references.pmid: 19948125
references.citation: J R Soc Interface. 2008 Dec 6;5 Suppl 3:S173-90
references.pmid: 18611844
references.citation: Proc Natl Acad Sci U S A. 1998 Jul 21;95(15):8473-8
references.pmid: 9671702
references.citation: Chem Rev. 2006 May;106(5):1898-916
references.pmid: 16683760
references.citation: Bioinformatics. 2004 Jan 22;20(2):276-8
references.pmid: 14734322
references.citation: Chem Rev. 2006 May;106(5):1877-97
references.pmid: 16683759
references.citation: Proteins. 2008 May 1;71(2):655-69
references.pmid: 17975840
references.citation: Protein Sci. 1997 Aug;6(8):1661-81
references.pmid: 9260279
references.citation: Science. 2009 Apr 10;324(5924):198-203
references.pmid: 19359576
references.citation: Science. 2009 Apr 10;324(5924):203-7
references.pmid: 19359577
references.citation: Structure. 2009 Jul 15;17(7):919-29
references.pmid: 19604472
references.citation: Biochemistry. 1998 Aug 11;37(32):11182-92
references.pmid: 9698364
references.citation: Biophys J. 2010 Jun 2;98(11):2671-81
references.pmid: 20513412
references.citation: Hum Mutat. 2001 Apr;17(4):263-70
references.pmid: 11295823
references.citation: Protein Sci. 2003 Oct;12(10):2150-60
references.pmid: 14500873
references.citation: Nucleic Acids Res. 2000 Jan 1;28(1):235-42
references.pmid: 10592235
references.citation: Protein Sci. 1997 Dec;6(12):2589-605
references.pmid: 9416608
references.citation: Curr Opin Struct Biol. 2002 Aug;12(4):431-40
references.pmid: 12163064
references.citation: Adv Protein Chem. 2002;62:163-240
references.pmid: 12418104
references.citation: J Am Chem Soc. 2009 Dec 9;131(48):17647-54
references.pmid: 19950993
references.citation: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D189-92
references.pmid: 14681391
references.citation: J Mol Biol. 2005 Oct 21;353(2):459-73
references.pmid: 16169011
references.citation: Proc Natl Acad Sci U S A. 2008 Aug 26;105(34):12259-64
references.pmid: 18713857
references.citation: J Am Chem Soc. 2009 Jul 15;131(27):9506-15
references.pmid: 19537786
references.citation: Biophys J. 2007 Nov 15;93(10):3382-91
references.pmid: 17978165
references.citation: Microbiol Mol Biol Rev. 2001 Mar;65(1):1-43
references.pmid: 11238984
references.citation: J Mol Biol. 1998 May 1;278(2):439-56
references.pmid: 9571063
references.citation: J Mol Biol. 2008 Jun 13;379(4):803-14
references.pmid: 18482735
references.citation: Biopolymers. 2005;80(2-3):179-85
references.pmid: 15700296
references.citation: Nat Struct Biol. 2002 Sep;9(9):646-52
references.pmid: 12198485
references.citation: Nature. 2003 Feb 20;421(6925):863-7
references.pmid: 12594518
references.citation: Biochemistry. 2008 Sep 9;47(36):9380-93
references.pmid: 18707128
references.citation: Biophys J. 2009 Sep 16;97(6):1709-18
references.pmid: 19751676
references.citation: J Am Chem Soc. 2004 Jun 30;126(25):7734-5
references.pmid: 15212494
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D310-4
references.pmid: 18996897
references.citation: Proc Natl Acad Sci U S A. 2007 Feb 20;104(8):2661-6
references.pmid: 17307875
references.citation: Proc Natl Acad Sci U S A. 2007 Jan 16;104(3):796-801
references.pmid: 17215349
references.citation: Proc Natl Acad Sci U S A. 1994 Oct 25;91(22):10430-4
references.pmid: 7937969
references.citation: Nat Struct Biol. 2001 Nov;8(11):953-7
references.pmid: 11685241
references.citation: J Mol Biol. 1996 Mar 29;257(2):412-29
references.pmid: 8609633
references.citation: J Mol Biol. 1999 Jul 2;290(1):283-304
references.pmid: 10388573
references.citation: Biochemistry. 2008 Jul 8;47(27):7079-89
references.pmid: 18553935
references.citation: Structure. 2009 Mar 11;17(3):386-94
references.pmid: 19278653
references.citation: Protein Eng Des Sel. 2009 Dec;22(12):713-21
references.pmid: 19801578
references.citation: Curr Opin Struct Biol. 2008 Feb;18(1):4-9
references.pmid: 18242977
references.citation: Acc Chem Res. 2002 Jun;35(6):422-9
references.pmid: 12069627
references.citation: J Mol Biol. 2007 Feb 16;366(2):677-86
references.pmid: 17174331
references.citation: Protein Eng Des Sel. 2008 Jun;21(6):369-77
references.pmid: 18411223
references.citation: Annu Rev Biochem. 2006;75:333-66
references.pmid: 16756495
references.citation: Methods. 2004 Sep;34(1):112-20
references.pmid: 15283920
references.citation: Structure. 2009 Jan 14;17(1):88-95
references.pmid: 19141285
references.citation: Protein Eng Des Sel. 2008 Jun;21(6):379-86
references.pmid: 18411222
references.citation: Biochemistry. 2005 Jan 18;44(2):609-16
references.pmid: 15641786
references.citation: Science. 2009 Apr 10;324(5924):213-5
references.pmid: 19359579
references.citation: J Mol Biol. 2008 Jun 27;380(1):120-30
references.pmid: 18486144
references.citation: Proc Natl Acad Sci U S A. 2005 May 10;102(19):6679-85
references.pmid: 15870208
references.citation: Proc Natl Acad Sci U S A. 2000 Mar 28;97(7):3166-70
references.pmid: 10716696
references.citation: Nat Struct Biol. 2002 Mar;9(3):209-16
references.pmid: 11875516
references.citation: Structure. 2009 Mar 11;17(3):319-20
references.pmid: 19278644
references.citation: Biopolymers. 1968;6(12):1767-70
references.pmid: 5704346
references.citation: Cell. 2002 Feb 22;108(4):573-82
references.pmid: 11909527
references.citation: Protein Eng Des Sel. 2008 Jun;21(6):353-68
references.pmid: 18411224
references.citation: Biochemistry. 2006 Feb 21;45(7):2178-88
references.pmid: 16475806
references.citation: J Comput Biol. 2003;10(3-4):617-34
references.pmid: 12935348
references.citation: Biochemistry. 2009 Jul 14;48(27):6450-60
references.pmid: 19435324
references.citation: Biochemistry. 2005 Jul 19;44(28):9691-702
references.pmid: 16008354