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Progress towards mapping the universe of protein folds
Alastair Grant, David Lee, Christine Orengo
Genome Biol. 2004; 5(5): 107. Published online 2004 April 29.
PMCID:
PMC416458
Abstract Full Text PDF–196K

Is Cited by the Following 18 Articles in this Archive:

Insights into the Fold Organization of TIM Barrel from Interaction Energy Based Structure Networks
M. S. Vijayabaskar, Saraswathi Vishveshwara
PLoS Comput Biol. 2012 May; 8(5): e1002505. Published online 2012 May 17. doi: 10.1371/journal.pcbi.1002505
PMCID:
PMC3355060
Abstract Full Text PDF–1.8M Supplementary Material
Relative Packing Groups in Template-Based Structure Prediction: Cooperative Effects of True Positive Constraints
Ryan Day, Xiaotao Qu, Rosemarie Swanson, Zach Bohannan, Robert Bliss, Jerry Tsai
J Comput Biol. 2011 January; 18(1): 17–26. doi: 10.1089/cmb.2010.0078
PMCID:
PMC3123881
Abstract Full Text PDF–346K
An improved hybrid global optimization method for protein tertiary structure prediction
Scott R. McAllister, Christodoulos A. Floudas
Comput Optim Appl. Author manuscript; available in PMC 2010 March 30.
Published in final edited form as: Comput Optim Appl. 2010 March 1; 45(2): 377–413. doi: 10.1007/s10589-009-9277-y
PMCID:
PMC2847311
Abstract Full Text PDF–2.5M Supplementary Material
De novo backbone scaffolds for protein design
James T MacDonald, Katarzyna Maksimiak, Michael I Sadowski, William R Taylor
Proteins. 2010 April; 78(5): 1311–1325. Published online 2009 November 5. doi: 10.1002/prot.22651
PMCID:
PMC2841848
Abstract Full Text PDF–1.1M Supplementary Material
Exploration of Uncharted Regions of the Protein Universe
Lukasz Jaroszewski, Zhanwen Li, S. Sri Krishna, Constantina Bakolitsa, John Wooley, Ashley M. Deacon, Ian A. Wilson, Adam Godzik
PLoS Biol. 2009 September; 7(9): e1000205. Published online 2009 September 29. doi: 10.1371/journal.pbio.1000205
PMCID:
PMC2744874
Abstract Full Text PDF–884K Supplementary Material
The CATH Hierarchy Revisited—Structural Divergence in Domain Superfamilies and the Continuity of Fold Space
Alison Cuff, Oliver C. Redfern, Lesley Greene, Ian Sillitoe, Tony Lewis, Mark Dibley, Adam Reid, Frances Pearl, Tim Dallman, Annabel Todd, Richard Garratt, Janet Thornton, Christine Orengo
Structure. 2009 August 12; 17(8-8): 1051–1062. doi: 10.1016/j.str.2009.06.015
PMCID:
PMC2741583
Abstract Full Text Supplementary Material
Universal partitioning of the hierarchical fold network of 50-residue segments in proteins
Jun-ichi Ito, Yuki Sonobe, Kazuyoshi Ikeda, Kentaro Tomii, Junichi Higo
BMC Struct Biol. 2009; 9: 34. Published online 2009 May 20. doi: 10.1186/1472-6807-9-34
PMCID:
PMC2693521
Abstract Full Text PDF–2.1M Supplementary Material
Reduced amino acid alphabets exhibit an improved sensitivity and selectivity in fold assignment
Eric L. Peterson, Jané Kondev, Julie A. Theriot, Rob Phillips
Bioinformatics. 2009 June 1; 25(11): 1356–1362. Published online 2009 April 7. doi: 10.1093/bioinformatics/btp164
PMCID:
PMC2732308
Abstract Full Text PDF–194K Supplementary Material
Structural genomics is the largest contributor of novel structural leverage
Rajesh Nair, Jinfeng Liu, Ta-Tsen Soong, Thomas B. Acton, John K. Everett, Andrei Kouranov, Andras Fiser, Adam Godzik, Lukasz Jaroszewski, Christine Orengo, Gaetano T. Montelione, Burkhard Rost
J Struct Funct Genomics. 2009 April; 10(2): 181–191. Published online 2009 February 5. doi: 10.1007/s10969-008-9055-6
PMCID:
PMC2705706
Abstract Full Text PDF–489K
Novel protein folds and their nonsequential structural analogs
Aysam Guerler, Ernst-Walter Knapp
Protein Sci. 2008 August; 17(8): 1374–1382. doi: 10.1110/ps.035469.108
PMCID:
PMC2492825
Abstract Full Text PDF–446K
CATHEDRAL: A Fast and Effective Algorithm to Predict Folds and Domain Boundaries from Multidomain Protein Structures
Oliver C Redfern, Andrew Harrison, Tim Dallman, Frances M. G Pearl, Christine A Orengo
PLoS Comput Biol. 2007 November; 3(11): e232. Published online 2007 November 30. doi: 10.1371/journal.pcbi.0030232
PMCID:
PMC2098860
Abstract Full Text PDF–931K Supplementary Material
Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world
Minglei Wang, Liudmila S. Yafremava, Derek Caetano-Anollés, Jay E. Mittenthal, Gustavo Caetano-Anollés
Genome Res. 2007 November; 17(11): 1572–1585. doi: 10.1101/gr.6454307
PMCID:
PMC2045140
Abstract Full Text PDF–953K
Structural genomics: keeping up with expanding knowledge of the protein universe
Marek Grabowski, Andrzej Joachimiak, Zbyszek Otwinowski, Wladek Minor
Curr Opin Struct Biol. Author manuscript; available in PMC 2010 June 15.
Published in final edited form as: Curr Opin Struct Biol. 2007 June; 17(3): 347–353. Published online 2007 June 22. doi: 10.1016/j.sbi.2007.06.003
PMCID:
PMC2885969
Abstract Full Text PDF–1.3M
Growth of novel protein structural data
Michael Levitt
Proc Natl Acad Sci U S A. 2007 February 27; 104(9): 3183–3188. Published online 2007 February 20. doi: 10.1073/pnas.0611678104
PMCID:
PMC1802002
Abstract Full Text PDF–1.7M Supplementary Material
Conserved thermodynamic contributions of backbone hydrogen bonds in a protein fold
Min Wang, Thomas E. Wales, Michael C. Fitzgerald
Proc Natl Acad Sci U S A. 2006 February 21; 103(8): 2600–2604. Published online 2006 February 10. doi: 10.1073/pnas.0508121103
PMCID:
PMC1413781
Abstract Full Text PDF–316K Supplementary Material
Exploiting protein structure data to explore the evolution of protein function and biological complexity
Russell L Marsden, Juan A.G Ranea, Antonio Sillero, Oliver Redfern, Corin Yeats, Michael Maibaum, David Lee, Sarah Addou, Gabrielle A Reeves, Timothy J Dallman, Christine A Orengo
Philos Trans R Soc Lond B Biol Sci. 2006 March 29; 361(1467): 425–440. Published online 2006 February 1. doi: 10.1098/rstb.2005.1801
PMCID:
PMC1609337
Abstract Full Text PDF–755K
Evolutionary Plasticity of Protein Families: Coupling Between Sequence and Structure Variation
Anna R. Panchenko, Yuri I. Wolf, Larisa A. Panchenko, Thomas Madej
Proteins. Author manuscript; available in PMC 2007 August 8.
Published in final edited form as: Proteins. 2005 November 15; 61(3): 535–544. doi: 10.1002/prot.20644
PMCID:
PMC1941674
Abstract Full Text PDF–810K
A functional hierarchical organization of the protein sequence space
Noam Kaplan, Moriah Friedlich, Menachem Fromer, Michal Linial
BMC Bioinformatics. 2004; 5: 196. Published online 2004 December 14. doi: 10.1186/1471-2105-5-196
PMCID:
PMC544566
Abstract Full Text PDF–427K
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