Caffrey DR - Search Results

1

PFRED: A computational platform for siRNA and antisense oligonucleotides design.

Sciabola S, Xi H, Cruz D, Cao Q, Lawrence C, Zhang T, Rotstein S, Hughes JD, Caffrey DR, Stanton RV. Sciabola S, et al. Among authors: caffrey dr. PLoS One. 2021 Jan 22;16(1):e0238753. doi: 10.1371/journal.pone.0238753. eCollection 2021. PLoS One. 2021. PMID: 33481821 Free PMC article.

2

siRNA off-target effects can be reduced at concentrations that match their individual potency.

Caffrey DR, Zhao J, Song Z, Schaffer ME, Haney SA, Subramanian RR, Seymour AB, Hughes JD. Caffrey DR, et al. PLoS One. 2011;6(7):e21503. doi: 10.1371/journal.pone.0021503. Epub 2011 Jul 5. PLoS One. 2011. PMID: 21750714 Free PMC article.

3

Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?

Caffrey DR, Somaroo S, Hughes JD, Mintseris J, Huang ES. Caffrey DR, et al. Protein Sci. 2004 Jan;13(1):190-202. doi: 10.1110/ps.03323604. Protein Sci. 2004. PMID: 14691234 Free PMC article.

4

Structure-based maximal affinity model predicts small-molecule druggability.

Cheng AC, Coleman RG, Smyth KT, Cao Q, Soulard P, Caffrey DR, Salzberg AC, Huang ES. Cheng AC, et al. Among authors: caffrey dr. Nat Biotechnol. 2007 Jan;25(1):71-5. doi: 10.1038/nbt1273. Nat Biotechnol. 2007. PMID: 17211405

5

The domain structure and distribution of Alu elements in long noncoding RNAs and mRNAs.

Kim EZ, Wespiser AR, Caffrey DR. Kim EZ, et al. Among authors: caffrey dr. RNA. 2016 Feb;22(2):254-64. doi: 10.1261/rna.048280.114. Epub 2015 Dec 10. RNA. 2016. PMID: 26654912 Free PMC article.

6

PFAAT version 2.0: a tool for editing, annotating, and analyzing multiple sequence alignments.

Caffrey DR, Dana PH, Mathur V, Ocano M, Hong EJ, Wang YE, Somaroo S, Caffrey BE, Potluri S, Huang ES. Caffrey DR, et al. Among authors: caffrey be. BMC Bioinformatics. 2007 Oct 11;8:381. doi: 10.1186/1471-2105-8-381. BMC Bioinformatics. 2007. PMID: 17931421 Free PMC article.

7

Cutting Edge: A Natural Antisense Transcript, AS-IL1α, Controls Inducible Transcription of the Proinflammatory Cytokine IL-1α.

Chan J, Atianand M, Jiang Z, Carpenter S, Aiello D, Elling R, Fitzgerald KA, Caffrey DR. Chan J, et al. Among authors: caffrey dr. J Immunol. 2015 Aug 15;195(4):1359-63. doi: 10.4049/jimmunol.1500264. Epub 2015 Jul 15. J Immunol. 2015. PMID: 26179904 Free PMC article.

8

A method to predict residues conferring functional differences between related proteins: application to MAP kinase pathways.

Caffrey DR, O'Neill LA, Shields DC. Caffrey DR, et al. Protein Sci. 2000 Apr;9(4):655-70. doi: 10.1110/ps.9.4.655. Protein Sci. 2000. PMID: 10794408 Free PMC article.

9

Evolution of specific protein-protein interaction sites following gene duplication.

Aiello D, Caffrey DR. Aiello D, et al. Among authors: caffrey dr. J Mol Biol. 2012 Oct 19;423(2):257-72. doi: 10.1016/j.jmb.2012.06.039. Epub 2012 Jul 9. J Mol Biol. 2012. PMID: 22789570

10

Prediction of specificity-determining residues for small-molecule kinase inhibitors.

Caffrey DR, Lunney EA, Moshinsky DJ. Caffrey DR, et al. BMC Bioinformatics. 2008 Nov 25;9:491. doi: 10.1186/1471-2105-9-491. BMC Bioinformatics. 2008. PMID: 19032760 Free PMC article.

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