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Results: 1 to 20 of 53

1.

Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks.

Zhao S, Sakai A, Zhang X, Vetting MW, Kumar R, Hillerich B, San Francisco B, Solbiati J, Steves A, Brown S, Akiva E, Barber A, Seidel RD, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP.

Elife. 2014 Jun 30:e03275. doi: 10.7554/eLife.03275. [Epub ahead of print]

PMID:
24980702
[PubMed - as supplied by publisher]
Free PMC Article
2.

Large-scale determination of sequence, structure, and function relationships in cytosolic glutathione transferases across the biosphere.

Mashiyama ST, Malabanan MM, Akiva E, Bhosle R, Branch MC, Hillerich B, Jagessar K, Kim J, Patskovsky Y, Seidel RD, Stead M, Toro R, Vetting MW, Almo SC, Armstrong RN, Babbitt PC.

PLoS Biol. 2014 Apr 22;12(4):e1001843. doi: 10.1371/journal.pbio.1001843. eCollection 2014 Apr.

PMID:
24756107
[PubMed - in process]
Free PMC Article
3.

Evolution of bacterial protein-tyrosine kinases and their relaxed specificity toward substrates.

Shi L, Ji B, Kolar-Znika L, Boskovic A, Jadeau F, Combet C, Grangeasse C, Franjevic D, Talla E, Mijakovic I.

Genome Biol Evol. 2014 Apr;6(4):800-17. doi: 10.1093/gbe/evu056.

PMID:
24728941
[PubMed - in process]
Free PMC Article
4.

Rapid identification of sequences for orphan enzymes to power accurate protein annotation.

Ramkissoon KR, Miller JK, Ojha S, Watson DS, Bomar MG, Galande AK, Shearer AG.

PLoS One. 2013 Dec 30;8(12):e84508. doi: 10.1371/journal.pone.0084508. eCollection 2013.

PMID:
24386392
[PubMed - in process]
Free PMC Article
5.

A pluralistic account of homology: adapting the models to the data.

Haggerty LS, Jachiet PA, Hanage WP, Fitzpatrick DA, Lopez P, O'Connell MJ, Pisani D, Wilkinson M, Bapteste E, McInerney JO.

Mol Biol Evol. 2014 Mar;31(3):501-16. doi: 10.1093/molbev/mst228. Epub 2013 Nov 22.

PMID:
24273322
[PubMed - in process]
Free PMC Article
6.

The Structure-Function Linkage Database.

Akiva E, Brown S, Almonacid DE, Barber AE 2nd, Custer AF, Hicks MA, Huang CC, Lauck F, Mashiyama ST, Meng EC, Mischel D, Morris JH, Ojha S, Schnoes AM, Stryke D, Yunes JM, Ferrin TE, Holliday GL, Babbitt PC.

Nucleic Acids Res. 2014 Jan;42(Database issue):D521-30. doi: 10.1093/nar/gkt1130. Epub 2013 Nov 23.

PMID:
24271399
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

PANADA: protein association network annotation, determination and analysis.

Martin AJ, Walsh I, Domenico TD, Mičetić I, Tosatto SC.

PLoS One. 2013 Nov 12;8(11):e78383. doi: 10.1371/journal.pone.0078383. eCollection 2013.

PMID:
24265686
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

SIMAP--the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage.

Arnold R, Goldenberg F, Mewes HW, Rattei T.

Nucleic Acids Res. 2014 Jan;42(Database issue):D279-84. doi: 10.1093/nar/gkt970. Epub 2013 Oct 27.

PMID:
24165881
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

A network approach to analyzing highly recombinant malaria parasite genes.

Larremore DB, Clauset A, Buckee CO.

PLoS Comput Biol. 2013;9(10):e1003268. doi: 10.1371/journal.pcbi.1003268. Epub 2013 Oct 10.

PMID:
24130474
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Protein similarity networks reveal relationships among sequence, structure, and function within the Cupin superfamily.

Uberto R, Moomaw EW.

PLoS One. 2013 Sep 6;8(9):e74477. doi: 10.1371/journal.pone.0074477. eCollection 2013.

PMID:
24040257
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Consequences of domain insertion on sequence-structure divergence in a superfold.

Pandya C, Brown S, Pieper U, Sali A, Dunaway-Mariano D, Babbitt PC, Xia Y, Allen KN.

Proc Natl Acad Sci U S A. 2013 Sep 3;110(36):E3381-7. doi: 10.1073/pnas.1305519110. Epub 2013 Aug 19.

PMID:
23959887
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

SLC classification: an update.

Schlessinger A, Yee SW, Sali A, Giacomini KM.

Clin Pharmacol Ther. 2013 Jul;94(1):19-23. doi: 10.1038/clpt.2013.73.

PMID:
23778706
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Functional classification of immune regulatory proteins.

Rubinstein R, Ramagopal UA, Nathenson SG, Almo SC, Fiser A.

Structure. 2013 May 7;21(5):766-76. doi: 10.1016/j.str.2013.02.022. Epub 2013 Apr 11.

PMID:
23583034
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Molecular modeling and ligand docking for solute carrier (SLC) transporters.

Schlessinger A, Khuri N, Giacomini KM, Sali A.

Curr Top Med Chem. 2013;13(7):843-56. Review.

PMID:
23578028
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily.

Wallrapp FH, Pan JJ, Ramamoorthy G, Almonacid DE, Hillerich BS, Seidel R, Patskovsky Y, Babbitt PC, Almo SC, Jacobson MP, Poulter CD.

Proc Natl Acad Sci U S A. 2013 Mar 26;110(13):E1196-202. doi: 10.1073/pnas.1300632110. Epub 2013 Mar 14.

PMID:
23493556
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Structural and mechanistic characterization of L-histidinol phosphate phosphatase from the polymerase and histidinol phosphatase family of proteins.

Ghodge SV, Fedorov AA, Fedorov EV, Hillerich B, Seidel R, Almo SC, Raushel FM.

Biochemistry. 2013 Feb 12;52(6):1101-12. doi: 10.1021/bi301496p. Epub 2013 Jan 30.

PMID:
23327428
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Predicting cancer drug mechanisms of action using molecular network signatures.

Pritchard JR, Bruno PM, Hemann MT, Lauffenburger DA.

Mol Biosyst. 2013 Jul;9(7):1604-19. doi: 10.1039/c2mb25459j. Epub 2013 Jan 4.

PMID:
23287973
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Assignment of pterin deaminase activity to an enzyme of unknown function guided by homology modeling and docking.

Fan H, Hitchcock DS, Seidel RD 2nd, Hillerich B, Lin H, Almo SC, Sali A, Shoichet BK, Raushel FM.

J Am Chem Soc. 2013 Jan 16;135(2):795-803. doi: 10.1021/ja309680b. Epub 2013 Jan 2.

PMID:
23256477
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

A global comparison of the human and T. brucei degradomes gives insights about possible parasite drug targets.

Mashiyama ST, Koupparis K, Caffrey CR, McKerrow JH, Babbitt PC.

PLoS Negl Trop Dis. 2012;6(12):e1942. doi: 10.1371/journal.pntd.0001942. Epub 2012 Dec 6.

PMID:
23236535
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Discovery of an L-fucono-1,5-lactonase from cog3618 of the amidohydrolase superfamily.

Hobbs ME, Vetting M, Williams HJ, Narindoshvili T, Kebodeaux DM, Hillerich B, Seidel RD, Almo SC, Raushel FM.

Biochemistry. 2013 Jan 8;52(1):239-53. doi: 10.1021/bi3015554. Epub 2012 Dec 20.

PMID:
23214453
[PubMed - indexed for MEDLINE]
Free PMC Article

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