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Items: 1 to 20 of 82


Novel genes exhibit distinct patterns of function acquisition and network integration.

Capra JA, Pollard KS, Singh M.

Genome Biol. 2010;11(12):R127. doi: 10.1186/gb-2010-11-12-r127. Epub 2010 Dec 27.


Accurate protein structure annotation through competitive diffusion of enzymatic functions over a network of local evolutionary similarities.

Venner E, Lisewski AM, Erdin S, Ward RM, Amin SR, Lichtarge O.

PLoS One. 2010 Dec 13;5(12):e14286. doi: 10.1371/journal.pone.0014286.


Database resources of the National Center for Biotechnology Information.

Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Federhen S, Feolo M, Fingerman IM, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Lu Z, Madden TL, Madej T, Maglott DR, Marchler-Bauer A, Miller V, Mizrachi I, Ostell J, Panchenko A, Phan L, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Slotta D, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Wang Y, Wilbur WJ, Yaschenko E, Ye J.

Nucleic Acids Res. 2011 Jan;39(Database issue):D38-51. doi: 10.1093/nar/gkq1172. Epub 2010 Nov 21.


Sequence and structure continuity of evolutionary importance improves protein functional site discovery and annotation.

Wilkins AD, Lua R, Erdin S, Ward RM, Lichtarge O.

Protein Sci. 2010 Jul;19(7):1296-311. doi: 10.1002/pro.406.


Dali server: conservation mapping in 3D.

Holm L, Rosenström P.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W545-9. doi: 10.1093/nar/gkq366. Epub 2010 May 10.


Evolution: a guide to perturb protein function and networks.

Lichtarge O, Wilkins A.

Curr Opin Struct Biol. 2010 Jun;20(3):351-9. doi: 10.1016/ Epub 2010 May 3. Review.


Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution.

Omelchenko MV, Galperin MY, Wolf YI, Koonin EV.

Biol Direct. 2010 Apr 30;5:31. doi: 10.1186/1745-6150-5-31.


Evolution-guided discovery and recoding of allosteric pathway specificity determinants in psychoactive bioamine receptors.

Rodriguez GJ, Yao R, Lichtarge O, Wensel TG.

Proc Natl Acad Sci U S A. 2010 Apr 27;107(17):7787-92. doi: 10.1073/pnas.0914877107. Epub 2010 Apr 12. Erratum in: Proc Natl Acad Sci U S A. 2010 May 18;107(20):9476.


Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function.

Almonacid DE, Yera ER, Mitchell JB, Babbitt PC.

PLoS Comput Biol. 2010 Mar 12;6(3):e1000700. doi: 10.1371/journal.pcbi.1000700.


Protein interaction networks--more than mere modules.

Pinkert S, Schultz J, Reichardt J.

PLoS Comput Biol. 2010 Jan 29;6(1):e1000659. doi: 10.1371/journal.pcbi.1000659.


Predicting protein functions by relaxation labelling protein interaction network.

Hu P, Jiang H, Emili A.

BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S64. doi: 10.1186/1471-2105-11-S1-S64.


Evolutionary trace annotation of protein function in the structural proteome.

Erdin S, Ward RM, Venner E, Lichtarge O.

J Mol Biol. 2010 Mar 12;396(5):1451-73. doi: 10.1016/j.jmb.2009.12.037. Epub 2009 Dec 28.


Annotation error in public databases: misannotation of molecular function in enzyme superfamilies.

Schnoes AM, Brown SD, Dodevski I, Babbitt PC.

PLoS Comput Biol. 2009 Dec;5(12):e1000605. doi: 10.1371/journal.pcbi.1000605. Epub 2009 Dec 11.


On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins.

Kahraman A, Morris RJ, Laskowski RA, Favia AD, Thornton JM.

Proteins. 2010 Apr;78(5):1120-36. doi: 10.1002/prot.22633.


The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.

Caspi R, Altman T, Dale JM, Dreher K, Fulcher CA, Gilham F, Kaipa P, Karthikeyan AS, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Paley S, Popescu L, Pujar A, Shearer AG, Zhang P, Karp PD.

Nucleic Acids Res. 2010 Jan;38(Database issue):D473-9. doi: 10.1093/nar/gkp875. Epub 2009 Oct 22.


The Universal Protein Resource (UniProt) in 2010.

UniProt Consortium..

Nucleic Acids Res. 2010 Jan;38(Database issue):D142-8. doi: 10.1093/nar/gkp846. Epub 2009 Oct 20.


How and when should interactome-derived clusters be used to predict functional modules and protein function?

Song J, Singh M.

Bioinformatics. 2009 Dec 1;25(23):3143-50. doi: 10.1093/bioinformatics/btp551. Epub 2009 Sep 21.


Interaction networks: lessons from large-scale studies in yeast.

Cagney G.

Proteomics. 2009 Oct;9(20):4799-811. doi: 10.1002/pmic.200900177. Review.


Comparison of structure-based and threading-based approaches to protein functional annotation.

Brylinski M, Skolnick J.

Proteins. 2010 Jan;78(1):118-34. doi: 10.1002/prot.22566.


FLORA: a novel method to predict protein function from structure in diverse superfamilies.

Redfern OC, Dessailly BH, Dallman TJ, Sillitoe I, Orengo CA.

PLoS Comput Biol. 2009 Aug;5(8):e1000485. doi: 10.1371/journal.pcbi.1000485. Epub 2009 Aug 28.

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