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Alan Frankel

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Chemicals & Drugs

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Genes & Molecular Sequences

Amino Acid Sequences

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Protein Binding

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Publications

TOP 3
Iván D'Orso; Tyler B Faust; Gwendolyn M Jang; Alexander W Pastuszak; Elizabeth Quezada; David S Booth; Alan D Frankel
Transition step during assembly of HIV Tat:P-TEFb transcription complexes and transfer to TAR RNA.
Robert L Nakamura; Jemiel Nejim; Lily Chen; Stephen G Landt; Emily Mai; Alan D Frankel
A cell-based method for screening RNA-protein interactions: identification of constitutive transport element-interacting proteins.
Alexander W Pastuszak; marcin joachimiak; Marco Blanchette; Donald C Rio; Steven E Brenner; Alan D Frankel
An SF1 affinity model to identify branch point sequences in human introns.

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All Publications

2012: Iván D'Orso; Tyler B Faust; Gwendolyn M Jang; Alexander W Pastuszak; Elizabeth Quezada; David S Booth; Alan D Frankel
Transition step during assembly of HIV Tat:P-TEFb transcription complexes and transfer to TAR RNA.
Molecular and cellular biology 2012;32(23):4780-93.
2012: Robert L Nakamura; Jemiel Nejim; Lily Chen; Stephen G Landt; Emily Mai; Alan D Frankel
A cell-based method for screening RNA-protein interactions: identification of constitutive transport element-interacting proteins.
PloS one 2012;7(10):e48194.
2011: Alexander W Pastuszak; marcin joachimiak; Marco Blanchette; Donald C Rio; Steven E Brenner; Alan D Frankel
An SF1 affinity model to identify branch point sequences in human introns.
Nucleic acids research 2011;39(6):2344-56.
2011: Marie E Fahey; Alan D Frankel; Stefanie Jäger; Dhiraj Kumar; Cathal Mahon; Lars Pache; Kanury Rao; Alex Shapiro; Melanie J Bennett; Sumit K Chanda; Charles S Craik; Nevan J Krogan
GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data.
BMC bioinformatics 2011;12():298.
2011: Stefanie Jäger; Natali Gulbahce; Peter Cimermancic; Joshua Kane; Nanhai He; Seemay Chou; Iván D'Orso; Jason Fernandes; Gwendolyn Jang; Alan D Frankel; Tom Alber; Qiang Zhou ; Nevan J Krogan
Purification and characterization of HIV-human protein complexes.
Methods (San Diego, Calif.) 2011;53(1):13-9.
2010: Matthew D Daugherty; Bella Liu; Alan D Frankel
Structural basis for cooperative RNA binding and export complex assembly by HIV Rev.
Nature structural & molecular biology 2010;17(11):1337-42.
2010: Matthew D Daugherty; David S Booth; Bhargavi Jayaraman; Yifan Cheng; Alan D Frankel
HIV Rev response element (RRE) directs assembly of the Rev homooligomer into discrete asymmetric complexes.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(28):12481-6.
2010: Iván D'Orso; Alan D Frankel
RNA-mediated displacement of an inhibitory snRNP complex activates transcription elongation.
Nature structural & molecular biology 2010;17(7):815-21.
2009: Iván D'Orso; Alan D Frankel
Tat acetylation modulates assembly of a viral-host RNA-protein transcription complex.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(9):3101-6.
2008: Iván D'Orso; Jocelyn R Grunwell; Robert L Nakamura; Chandreyee Das; Alan D Frankel
Targeting tat inhibitors in the assembly of human immunodeficiency virus type 1 transcription complexes.
Journal of virology 2008;82(19):9492-504.
2008: Matthew D Daugherty; Iván D'Orso; Alan D Frankel
A solution to limited genomic capacity: using adaptable binding surfaces to assemble the functional HIV Rev oligomer on RNA.
Molecular cell 2008;31(6):824-34.
2008: Ali Mokdad; Alan D Frankel
ISFOLD: structure prediction of base pairs in non-helical RNA motifs from isostericity signatures in their sequence alignments.
Journal of biomolecular structure & dynamics 2008;25(5):467-72.
2006: Nicholas L Mills; Matthew D Daugherty; Alan D Frankel; R Kiplin Guy
An alpha-helical peptidomimetic inhibitor of the HIV-1 Rev-RRE interaction.
Journal of the American Chemical Society 2006;128(11):3496-7.
2005: Stephen G Landt; Alejandro Ramirez; Matthew D Daugherty; Alan D Frankel
A simple motif for protein recognition in DNA secondary structures.
Journal of molecular biology 2005;351(5):982-94.
2005: Valerie Calabro; Alan D Frankel
Viral RNA gymnastics.
Nature chemical biology 2005;1(2):67-8.
2005: Valerie Calabro; Matthew D Daugherty; Alan D Frankel
A single intermolecular contact mediates intramolecular stabilization of both RNA and protein.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(19):6849-54.
2005: Stephen G Landt; Alicia R Tipton; Alan D Frankel
Localized influence of 2'-hydroxyl groups and helix geometry on protein recognition in the RNA major groove.
Biochemistry 2005;44(17):6547-58.
2004: Baode Xie; Valerie Calabro; Mark A Wainberg; Alan D Frankel
Selection of TAR RNA-binding chameleon peptides by using a retroviral replication system.
Journal of virology 2004;78(3):1456-63.
2004: Alan C Cheng; Alan D Frankel
Ab initio interaction energies of hydrogen-bonded amino acid side chain[bond]nucleic acid base interactions.
Journal of the American Chemical Society 2004;126(2):434-5.
2004: Chandreyee Das; Stephen P Edgcomb; Ralph Peteranderl; Lily Chen; Alan D Frankel
Evidence for conformational flexibility in the Tat-TAR recognition motif of cyclin T1.
Virology 2004;318(1):306-17.
2003: Chandreyee Das; Alan D Frankel
Sequence and structure space of RNA-binding peptides.
Biopolymers 2003;70(1):80-5.
2003: Alan C Cheng; William W Chen; Cynthia N Fuhrmann; Alan D Frankel
Recognition of nucleic acid bases and base-pairs by hydrogen bonding to amino acid side-chains.
Journal of molecular biology 2003;327(4):781-96.
2003: Bernhard J Walberer; Alan C Cheng; Alan D Frankel
Structural diversity and isomorphism of hydrogen-bonded base interactions in nucleic acids.
Journal of molecular biology 2003;327(4):767-80.
2003: Hadas Peled-Zehavi; Satoru Horiya; Chandreyee Das; Kazuo Harada; Alan D Frankel
Selection of RRE RNA binding peptides using a kanamycin antitermination assay.
RNA (New York, N.Y.) 2003;9(2):252-61.
2003: Baode Xie; Mark A Wainberg; Alan D Frankel
Replication of human immunodeficiency viruses engineered with heterologous Tat-transactivation response element interactions.
Journal of virology 2003;77(3):1984-91.
2001: A C Cheng; Valerie Calabro; Alan D Frankel
Design of RNA-binding proteins and ligands.
Current opinion in structural biology 2001;11(4):478-84.
2001: Hadas Peled-Zehavi; J A Berglund; M Rosbash; Alan D Frankel
Recognition of RNA branch point sequences by the KH domain of splicing factor 1 (mammalian branch point binding protein) in a splicing factor complex.
Molecular and cellular biology 2001;21(15):5232-41.
2001: CM Reyes; Riccardo Nifosì; Alan D Frankel; Peter A Kollman
Molecular dynamics and binding specificity analysis of the bovine immunodeficiency virus BIV Tat-TAR complex.
Biophysical journal 2001;80(6):2833-42.
2001: Q Zhang; K Harada; H S Cho; Alan D Frankel; David E Wemmer
Structural characterization of the complex of the Rev response element RNA with a selected peptide.
Chemistry & biology 2001;8(5):511-20.
2001: D M Campisi; Valerie Calabro; Alan D Frankel
Structure-based design of a dimeric RNA-peptide complex.
The EMBO journal 2001;20(1-2):178-86.
2000: C A Smith; Valerie Calabro; Alan D Frankel
An RNA-binding chameleon.
Molecular cell 2000;6(5):1067-76.
2000: Alan D Frankel
Fitting peptides into the RNA world.
Current opinion in structural biology 2000;10(3):332-40.
2000: S A Robertson; K Harada; Alan D Frankel; David E Wemmer
Structure determination and binding kinetics of a DNA aptamer-argininamide complex.
Biochemistry 2000;39(5):946-54.
2000: Kazuo Harada; Satoru Horiya; H Zehavi; Alan D Frankel
Screening in vivo for RNA-binding peptides from combinatorial libraries.
Nucleic acids symposium series 2000;(44):269-70.
2000: CA Smith; Lily Chen; Alan D Frankel
Using peptides as models of RNA-protein interactions.
Methods in enzymology 2000;318():423-38.
2000: Stephen G Landt; R Tan; Alan D Frankel
Screening RNA-binding libraries using Tat-fusion system in mammalian cells.
Methods in enzymology 2000;318():350-63.
2000: Hadas Peled-Zehavi; CA Smith; Kazuo Harada; Alan D Frankel
Screening RNA-binding libraries by transcriptional antitermination in bacteria.
Methods in enzymology 2000;318():297-308.
1999: Alan D Frankel
If the loop fits...
Nature structural biology 1999;6(12):1081-3.
1999: D J McColl; C D Honchell; Alan D Frankel
Structure-based design of an RNA-binding zinc finger.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(17):9521-6.
1999: Kazuo Harada; S S Martin; Alan D Frankel
In vivo selection of RNA-binding peptides from combinatorial libraries.
Nucleic acids symposium series 1999;(42):213-4.
1999: Kazuo Harada; Alan D Frankel
Screening RNA-binding libraries using a bacterial transcription antitermination assay.
Methods in molecular biology (Clifton, N.J.) 1999;118():177-87.
1998: CA Smith; Shane Crotty; Y Harada; Alan D Frankel
Altering the context of an RNA bulge switches the binding specificities of two viral Tat proteins.
Biochemistry 1998;37(30):10808-14.
1998: R Tan; Alan D Frankel
A novel glutamine-RNA interaction identified by screening libraries in mammalian cells.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(8):4247-52.
1998: Alan D Frankel; C A Smith
Induced folding in RNA-protein recognition: more than a simple molecular handshake.
Cell 1998;92(2):149-51.
1998: Alan D Frankel; J A Young
HIV-1: fifteen proteins and an RNA.
Annual review of biochemistry 1998;67():1-25.
1997: Kazuo Harada; S S Martin; R Tan; Alan D Frankel
Molding a peptide into an RNA site by in vivo peptide evolution.
Proceedings of the National Academy of Sciences of the United States of America 1997;94(22):11887-92.
1997: J Tao; Lily Chen; Alan D Frankel
Dissection of the proposed base triple in human immunodeficiency virus TAR RNA indicates the importance of the Hoogsteen interaction.
Biochemistry 1997;36(12):3491-5.
1996: J L Battiste; H Mao; N S Rao; R Tan; D Ranjith Muhandiram; Lewis E Kay; Alan D Frankel; James R Williamson
Alpha helix-RNA major groove recognition in an HIV-1 rev peptide-RRE RNA complex.
Science (New York, N.Y.) 1996;273(5281):1547-51.
1996: Kazuo Harada; S S Martin; Alan D Frankel
Selection of RNA-binding peptides in vivo.
Nature 1996;380(6570):175-9.
1996: J Tao; Alan D Frankel
Arginine-binding RNAs resembling TAR identified by in vitro selection.
Biochemistry 1996;35(7):2229-38.
1995: K Harada; Alan D Frankel
Identification of two novel arginine binding DNAs.
The EMBO journal 1995;14(23):5798-811.
1995: J L Battiste; R Tan; Alan D Frankel; James R Williamson
Assignment and modeling of the Rev Response Element RNA bound to a Rev peptide using 13C-heteronuclear NMR.
Journal of biomolecular NMR 1995;6(4):375-89.
1995: Joseph D Puglisi; L Chen; S Blanchard; Alan D Frankel
Solution structure of a bovine immunodeficiency virus Tat-TAR peptide-RNA complex.
Science (New York, N.Y.) 1995;270(5239):1200-3.
1995: R Tan; Alan D Frankel
Structural variety of arginine-rich RNA-binding peptides.
Proceedings of the National Academy of Sciences of the United States of America 1995;92(12):5282-6.
1995: L Chen; Alan D Frankel
A peptide interaction in the major groove of RNA resembles protein interactions in the minor groove of DNA.
Proceedings of the National Academy of Sciences of the United States of America 1995;92(11):5077-81.
1995: L L Chen; Alan D Frankel; J L Harder; S Fawell; James Barsoum; B Pepinsky
Increased cellular uptake of the human immunodeficiency virus-1 Tat protein after modification with biotin.
Analytical biochemistry 1995;227(1):168-75.
1995: James R Williamson; J L Battiste; H Mao; Alan D Frankel
Interaction of HIV Rev peptides with the Rev response element RNA.
Nucleic acids symposium series 1995;(33):46-8.
1994: R Tan; Alan D Frankel
Costabilization of peptide and RNA structure in an HIV Rev peptide-RRE complex.
Biochemistry 1994;33(48):14579-85.
1994: J L Battiste; R Tan; Alan D Frankel; James R Williamson
Binding of an HIV Rev peptide to Rev responsive element RNA induces formation of purine-purine base pairs.
Biochemistry 1994;33(10):2741-7.
1994: L Chen; Alan D Frankel
An RNA-binding peptide from bovine immunodeficiency virus Tat protein recognizes an unusual RNA structure.
Biochemistry 1994;33(9):2708-15.
1993: R Tan; L Chen; J A Buettner; D Hudson; Alan D Frankel
RNA recognition by an isolated alpha helix.
Cell 1993;73(5):1031-40.
1993: Joseph D Puglisi; L Chen; Alan D Frankel; James R Williamson
Role of RNA structure in arginine recognition of TAR RNA.
Proceedings of the National Academy of Sciences of the United States of America 1993;90(8):3680-4.
1993: J Tao; Alan D Frankel
Electrostatic interactions modulate the RNA-binding and transactivation specificities of the human immunodeficiency virus and simian immunodeficiency virus Tat proteins.
Proceedings of the National Academy of Sciences of the United States of America 1993;90(4):1571-5.
1992: Alan D Frankel
The importance of being flexible.
Proceedings of the National Academy of Sciences of the United States of America 1992;89(24):11653.
1992: Alan D Frankel
Peptide models of the Tat-TAR protein-RNA interaction.
Protein science : a publication of the Protein Society 1992;1(12):1539-42.
1992: R Tan; Alan D Frankel
Circular dichroism studies suggest that TAR RNA changes conformation upon specific binding of arginine or guanidine.
Biochemistry 1992;31(42):10288-94.
1992: Joseph D Puglisi; R Tan; B J Calnan; Alan D Frankel; James R Williamson
Conformation of the TAR RNA-arginine complex by NMR spectroscopy.
Science (New York, N.Y.) 1992;257(5066):76-80.
1992: Alan D Frankel
Activation of HIV transcription by Tat.
Current opinion in genetics & development 1992;2(2):293-8.
1992: J Tao; Alan D Frankel
Specific binding of arginine to TAR RNA.
Proceedings of the National Academy of Sciences of the United States of America 1992;89(7):2723-6.
1992: J Kjems; B J Calnan; Alan D Frankel; Phillip A Sharp
Specific binding of a basic peptide from HIV-1 Rev.
The EMBO journal 1992;11(3):1119-29.
1991: Alan D Frankel; I W Mattaj; Donald C Rio
RNA-protein interactions.
Cell 1991;67(6):1041-6.
1991: J Kjems; Alan D Frankel; Phillip A Sharp
Specific regulation of mRNA splicing in vitro by a peptide from HIV-1 Rev.
Cell 1991;67(1):169-78.
1991: D A Mann; Alan D Frankel
Endocytosis and targeting of exogenous HIV-1 Tat protein.
The EMBO journal 1991;10(7):1733-9.
1991: Alan D Frankel; Peter S Kim
Modular structure of transcription factors: implications for gene regulation.
Cell 1991;65(5):717-9.
1991: B J Calnan; Bruce Tidor; S Biancalana; D Hudson; Alan D Frankel
Arginine-mediated RNA recognition: the arginine fork.
Science (New York, N.Y.) 1991;252(5009):1167-71.
1991: Mark B Feinberg; David Baltimore; Alan D Frankel
The role of Tat in the human immunodeficiency virus life cycle indicates a primary effect on transcriptional elongation.
Proceedings of the National Academy of Sciences of the United States of America 1991;88(9):4045-9.
1991: B J Calnan; S Biancalana; D Hudson; Alan D Frankel
Analysis of arginine-rich peptides from the HIV Tat protein reveals unusual features of RNA-protein recognition.
Genes & development 1991;5(2):201-10.
1990: Robert Marciniak; B J Calnan; Alan D Frankel; Phillip A Sharp
HIV-1 Tat protein trans-activates transcription in vitro.
Cell 1990;63(4):791-802.
1990: T J Daly; J R Rusche; T E Maione; Alan D Frankel
Circular dichroism studies of the HIV-1 Rev protein and its specific RNA binding site.
Biochemistry 1990;29(42):9791-5.
1989: Raphael P Viscidi; K Mayur; Howard M Lederman; Alan D Frankel
Inhibition of antigen-induced lymphocyte proliferation by Tat protein from HIV-1.
Science (New York, N.Y.) 1989;246(4937):1606-8.
1989: Alan D Frankel; S Biancalana; D Hudson
Activity of synthetic peptides from the Tat protein of human immunodeficiency virus type 1.
Proceedings of the National Academy of Sciences of the United States of America 1989;86(19):7397-401.
1988: Alan D Frankel; Carl O Pabo
Cellular uptake of the tat protein from human immunodeficiency virus.
Cell 1988;55(6):1189-93.
1988: R S Stearman; Alan D Frankel; Ernesto Freire; B S Liu; Carl O Pabo
Combining thermostable mutations increases the stability of lambda repressor.
Biochemistry 1988;27(19):7571-4.
1988: Alan D Frankel; L Chen; Robert J Cotter; Carl O Pabo
Dimerization of the tat protein from human immunodeficiency virus: a cysteine-rich peptide mimics the normal metal-linked dimer interface.
Proceedings of the National Academy of Sciences of the United States of America 1988;85(17):6297-300.
1988: Alan D Frankel; Carl O Pabo
Fingering too many proteins.
Cell 1988;53(5):675.
1988: J C Houtz; Alan D Frankel
Hemisphericity and problem-solving ability.
Perceptual and motor skills 1988;66(3):771-4.
1988: Alan D Frankel; D S Bredt; Carl O Pabo
Tat protein from human immunodeficiency virus forms a metal-linked dimer.
Science (New York, N.Y.) 1988;240(4848):70-3.
1987: Alan D Frankel; Jeremy Berg; C O Pabo
Metal-dependent folding of a single zinc finger from transcription factor IIIA.
Proceedings of the National Academy of Sciences of the United States of America 1987;84(14):4841-5.
1985: Alan D Frankel; G K Ackers; Hamilton O Smith
Measurement of DNA-protein equilibria using gel chromatography: application to the HinfI restriction endonuclease.
Biochemistry 1985;24(12):3049-54.
1983: Carl O Pabo; S R Jordan; Alan D Frankel
Systematic analysis of possible hydrogen bonds between amino acid side chains and B-form DNA.
Journal of biomolecular structure & dynamics 1983;1(4):1039-49.
1981: Alan D Frankel; Hamilton O Smith
Restriction and modification enzymes detect no allosteric changes in DNA with bound lac repressor or RNA polymerase.
Journal of molecular biology 1981;146(4):611-9.
1980: Alan D Frankel; R F Jones
Changes in enzyme activity during differentiation in Chlamydomonas reinhardtii.
Biochimica et biophysica acta 1980;630(2):157-64.
1980: Alan D Frankel; B K Duncan; P E Hartman
Nitrous acid damage to duplex deoxyribonucleic acid: distinction between deamination of cytosine residues and a novel mutational lesion.
Journal of bacteriology 1980;142(1):335-8.