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A gold standard set of mechanistically diverse enzyme superfamilies
Shoshana D Brown, John A Gerlt, Jennifer L Seffernick, Patricia C Babbitt
Genome Biol. 2006; 7(1): R8. Published online 2006 January 31. doi: 10.1186/gb-2006-7-1-r8
PMCID:
PMC1431709
Abstract Full Text PDF–434K Supplementary Material

Is Cited by the Following 14 Articles in this Archive:

Exploring the Evolution of Novel Enzyme Functions within Structurally Defined Protein Superfamilies
Nicholas Furnham, Ian Sillitoe, Gemma L. Holliday, Alison L. Cuff, Roman A. Laskowski, Christine A. Orengo, Janet M. Thornton
PLoS Comput Biol. 2012 March; 8(3): e1002403. Published online 2012 March 1. doi: 10.1371/journal.pcbi.1002403
PMCID:
PMC3291543
Abstract Full Text PDF–1.5M Supplementary Material
Cutoff Scanning Matrix (CSM): structural classification and function prediction by protein inter-residue distance patterns
Douglas EV Pires, Raquel C de Melo-Minardi, Marcos A dos Santos, Carlos H da Silveira, Marcelo M Santoro, Wagner Meira, Jr.
BMC Genomics. 2011; 12(Suppl 4): S12. Published online 2011 December 22. doi: 10.1186/1471-2164-12-S4-S12
PMCID:
PMC3287581
Abstract Full Text PDF–1.5M Supplementary Material
The Enzyme Function Initiative
John A. Gerlt, Karen N. Allen, Steven C. Almo, Richard N. Armstrong, Patricia C. Babbitt, John E. Cronan, Debra Dunaway-Mariano, Heidi J. Imker, Matthew P. Jacobson, Wladek Minor, C. Dale Poulter, Frank M. Raushel, Andrej Sali, Brian K. Shoichet, Jonathan V. Sweedler
Biochemistry. Author manuscript; available in PMC 2012 November 22.
Published in final edited form as: Biochemistry. 2011 November 22; 50(46): 9950–9962. Published online 2011 October 26. doi: 10.1021/bi201312u
PMCID:
PMC3238057
Free in PMC on 2012/11/22
FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies
Nicholas Furnham, Ian Sillitoe, Gemma L. Holliday, Alison L. Cuff, Syed A. Rahman, Roman A. Laskowski, Christine A. Orengo, Janet M. Thornton
Nucleic Acids Res. 2012 January; 40(D1): D776–D782. Published online 2011 October 17. doi: 10.1093/nar/gkr852
PMCID:
PMC3245072
Abstract Full Text PDF–5.7M
Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution
Leonard Apeltsin, John H. Morris, Patricia C. Babbitt, Thomas E. Ferrin
Bioinformatics. 2011 February 1; 27(3): 326–333. Published online 2010 November 29. doi: 10.1093/bioinformatics/btq655
PMCID:
PMC3031030
Abstract Full Text PDF–694K Supplementary Material
GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains
David A. Lee, Robert Rentzsch, Christine Orengo
Nucleic Acids Res. 2010 January; 38(3): 720–737. Published online 2010 January. doi: 10.1093/nar/gkp1049
PMCID:
PMC2817468
Abstract Full Text PDF–931K
Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies
Alexandra M. Schnoes, Shoshana D. Brown, Igor Dodevski, Patricia C. Babbitt
PLoS Comput Biol. 2009 December; 5(12): e1000605. Published online 2009 December 11. doi: 10.1371/journal.pcbi.1000605
PMCID:
PMC2781113
Abstract Full Text PDF–1.3M Supplementary Material
Improving classification in protein structure databases using text mining
Antonis Koussounadis, Oliver C Redfern, David T Jones
BMC Bioinformatics. 2009; 10: 129. Published online 2009 May 5. doi: 10.1186/1471-2105-10-129
PMCID:
PMC2688513
Abstract Full Text PDF–710K
Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies
Ursula Pieper, Ranyee Chiang, Jennifer J. Seffernick, Shoshana D. Brown, Margaret E. Glasner, Libusha Kelly, Narayanan Eswar, J. Michael Sauder, Jeffrey B. Bonanno, Subramanyam Swaminathan, Stephen K. Burley, Xiaojing Zheng, Mark R. Chance, Steven C. Almo, John A. Gerlt, Frank M. Raushel, Matthew P. Jacobson, Patricia C. Babbitt, Andrej Sali
J Struct Funct Genomics. 2009 April; 10(2): 107–125. Published online 2009 February 14. doi: 10.1007/s10969-008-9056-5
PMCID:
PMC2693957
Abstract Full Text PDF–716K Supplementary Material
Towards structured output prediction of enzyme function
Katja Astikainen, Liisa Holm, Esa Pitkänen, Sandor Szedmak, Juho Rousu
BMC Proc. 2008; 2(Suppl 4): S2. Published online 2008 December 17.
PMCID:
PMC2654971
Abstract Full Text PDF–342K
MotifCluster: an interactive online tool for clustering and visualizing sequences using shared motifs
Micah Hamady, Jeremy Widmann, Shelley D Copley, Rob Knight
Genome Biol. 2008; 9(8): R128. Published online 2008 August 15. doi: 10.1186/gb-2008-9-8-r128
PMCID:
PMC2575518
Abstract Full Text PDF–3.4M
Characterization and prediction of residues determining protein functional specificity
John A. Capra, Mona Singh
Bioinformatics. 2008 July 1; 24(13): 1473–1480. Published online 2008 May 1. doi: 10.1093/bioinformatics/btn214
PMCID:
PMC2718669
Abstract Full Text PDF–222K Supplementary Material
High precision multi-genome scale reannotation of enzyme function by EFICAz
Adrian K Arakaki, Weidong Tian, Jeffrey Skolnick
BMC Genomics. 2006; 7: 315. Published online 2006 December 13. doi: 10.1186/1471-2164-7-315
PMCID:
PMC1764738
Abstract Full Text PDF–464K Supplementary Material
Functional Classification Using Phylogenomic Inference
Duncan Brown, Kimmen Sjölander
PLoS Comput Biol. 2006 June; 2(6): e77. Published online 2006 June 30. doi: 10.1371/journal.pcbi.0020077
PMCID:
PMC1484587
Full Text PDF–184K
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