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James Stivers

No longer a member of F1000[ 20-NOV-2003 - 26-JUL-2007 ]
[ Homepage ] [ Evaluations ]
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http://biolchem.bs.jhmi.edu/bcmb/Faculty_person.asp?PersonID=758

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Evaluations

Base-stacking and base-pairing contributions into thermal stability of the DNA double helix.
Yakovchuk P, Protozanova E, Frank-Kamenetskii MD
Nucleic Acids Res 2006 34(2):564-74 [abstract on PubMed] [related articles] [FREE full text]
Selected by | James Stivers
Evaluated 20 Apr 2007

Glycosidase inhibition: an assessment of the binding of 18 putative transition-state mimics.
Gloster TM, Meloncelli P, …, Vasella A, Davies GJ
J Am Chem Soc 2007 Feb 28 129(8):2345-54 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | James Stivers
Evaluated 23 Feb 2007

DNA folding and melting observed in real time redefine the energy landscape.
Ma H, Wan C, Wu A, Zewail AH
Proc Natl Acad Sci U S A 2007 Jan 16 104(3):712-6 [abstract on PubMed] [related articles] [FREE full text]
Selected by | James Stivers
Evaluated 23 Jan 2007

Predicting substrates by docking high-energy intermediates to enzyme structures.
Hermann JC, Ghanem E, …, Irwin JJ, Shoichet BK
J Am Chem Soc 2006 Dec 13 128(49):15882-91 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | James Stivers
Evaluated 13 Dec 2006

Small-molecule activation of procaspase-3 to caspase-3 as a personalized anticancer strategy.
Putt KS, Chen GW, …, Helferich WG, Hergenrother PJ
Nat Chem Biol 2006 Oct 2(10):543-50 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | James Stivers / Robert Copeland
Evaluated 25 Sep 2006

Electric fields at the active site of an enzyme: direct comparison of experiment with theory.
Suydam IT, Snow CD, Pande VS, Boxer SG
Science 2006 Jul 14 313(5784):200-4 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Eddy Arnold / James Stivers
Evaluated 9 Aug 2006

Rapid accessibility of nucleosomal DNA in yeast on a second time scale.
Bucceri A, Kapitza K, Thoma F
EMBO J 2006 Jul 12 25(13):3123-32 [abstract on PubMed] [related articles] [FREE full text]
Selected by | James Stivers / Nick Rhind
Evaluated 26 Jun 2006

Self-catalyzed site-specific depurination of guanine residues within gene sequences.
Amosova O, Coulter R, Fresco JR
Proc Natl Acad Sci U S A 2006 Mar 21 103(12):4392-7 [abstract on PubMed] [related articles] [FREE full text]
Selected by | James Stivers
Evaluated 24 Apr 2006

Structure of a DNA glycosylase searching for lesions.
Banerjee A, Santos WL, Verdine GL
Science 2006 Feb 24 311(5764):1153-7 [abstract on PubMed] [related articles] [FREE full text]
Selected by | James Stivers / Walter Chazin / Barry Stoddard
Evaluated 1 Mar 2006

Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA.
Gowers DM, Wilson GG, Halford SE
Proc Natl Acad Sci U S A 2005 Nov 1 102(44):15883-8 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Tom Misteli / James Stivers
Evaluated 25 Nov 2005

Size-specific ligands for RNA hairpin loops.
Thomas JR, Liu X, Hergenrother PJ
J Am Chem Soc 2005 Sep 14 127(36):12434-5 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | James Stivers
Evaluated 7 Oct 2005

High-throughput assays for promiscuous inhibitors.
Feng BY, Shelat A, …, Guy RK, Shoichet BK
Nat Chem Biol 2005 Aug 1(3):146-8 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | James Stivers / Vincent Rotello
Evaluated 2 Sep 2005

Measuring pK(a) values in protein folding transition state ensembles by NMR spectroscopy.
Tollinger M, Kay LE, Forman-Kay JD
J Am Chem Soc 2005 Jun 29 127(25):8904-5 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | James Stivers
Evaluated 28 Jul 2005

Electrostatic control of aromatic stacking interactions.
Cockroft SL, Hunter CA, …, Perkins J, Urch CJ
J Am Chem Soc 2005 Jun 22 127(24):8594-5 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | James Stivers
Evaluated 23 Jun 2005

Suppression of HIV-1 infection by a small molecule inhibitor of the ATM kinase.
Lau A, Swinbank KM, …, Smith GC, O'Connor MJ
Nat Cell Biol 2005 May 7(5):493-500 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | James Stivers
Evaluated 24 May 2005

Two essential but distinct functions of the mammalian abasic endonuclease.
Izumi T, Brown DB, …, Chen DJ, Mitra S
Proc Natl Acad Sci U S A 2005 Apr 19 102(16):5739-43 [abstract on PubMed] [related articles] [FREE full text]
Selected by | James Stivers
Evaluated 4 May 2005

A genome-wide overexpression screen in yeast for small-molecule target identification.
Luesch H, Wu TY, …, Schultz PG, Supek F
Chem Biol 2005 Jan 12(1):55-63 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | James Stivers
Evaluated 8 Mar 2005

Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution.
Bai Y, Das R, …, Herschlag D, Doniach S
Proc Natl Acad Sci U S A 2005 Jan 25 102(4):1035-40 [abstract on PubMed] [related articles] [FREE full text]
Selected by | James Stivers
Evaluated 7 Feb 2005

Pyridoxal 5'-phosphate inactivates DNA topoisomerase IB by modifying the lysine general acid.
Vermeersch JJ, Christmann-Franck S, …, Mirambeau G, Der Garabedian PA
Nucleic Acids Res 2004 32(18):5649-57 [abstract on PubMed] [related articles] [FREE full text]
Selected by | James Stivers
Evaluated 8 Dec 2004

Engineering subtilisin into a fluoride-triggered processing protease useful for one-step protein purification.
Ruan B, Fisher KE, …, Doroshko V, Bryan PN
Biochemistry 2004 Nov 23 43(46):14539-46 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | James Stivers / Song Tan
Evaluated 5 Nov 2004

In situ click chemistry: enzyme inhibitors made to their own specifications.
Manetsch R, Krasi¿ski A, …, Sharpless KB, Kolb HC
J Am Chem Soc 2004 Oct 13 126(40):12809-18 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | James Stivers
Evaluated 4 Oct 2004

Sir2-independent life span extension by calorie restriction in yeast.
Kaeberlein M, Kirkland KT, Fields S, Kennedy BK
PLoS Biol 2004 Sep 2(9):E296 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Nystrom / James Stivers / Susan Gasser
Evaluated 17 Sep 2004

Simple method for determining nucleobase pK(a) values by indirect labeling and demonstration of a pK(a) of neutrality in dsDNA.
Moody EM, Brown TS, Bevilacqua PC
J Am Chem Soc 2004 Aug 25 126(33):10200-1 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | James Stivers / Donald Burke
Evaluated 17 Aug 2004

Leaving group activation by aromatic stacking: an alternative to general acid catalysis.
Versées W, Loverix S, …, Geerlings P, Steyaert J
J Mol Biol 2004 Apr 16 338(1):1-6 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard / James Stivers / Daniel Herschlag
Evaluated 2 Jul 2004

Directed evolution of protein enzymes using nonhomologous random recombination.
Bittker JA, Le BV, Liu JM, Liu DR
Proc Natl Acad Sci U S A 2004 May 4 101(18):7011-6 [abstract on PubMed] [related articles] [FREE full text]
Selected by | James Stivers / Scott K. Silverman
Evaluated 11 May 2004

Charge development in the transition state for decarboxylations in water: spontaneous and acetone-catalyzed decarboxylation of aminomalonate.
Callahan BP, Wolfenden R
J Am Chem Soc 2004 Apr 14 126(14):4514-5 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | James Stivers
Evaluated 8 Apr 2004

Expanding the substrate repertoire of a DNA polymerase by directed evolution.
Fa M, Radeghieri A, Henry AA, Romesberg FE
J Am Chem Soc 2004 Feb 18 126(6):1748-54 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | James Stivers
Evaluated 8 Mar 2004

Dedifferentiation of lineage-committed cells by a small molecule.
Chen S, Zhang Q, …, Schultz PG, Ding S
J Am Chem Soc 2004 Jan 21 126(2):410-1 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Thomas Kodadek / James Stivers
Evaluated 30 Jan 2004

An oxocarbenium-ion intermediate of a ribozyme reaction indicated by kinetic isotope effects.
Unrau PJ, Bartel DP
Proc Natl Acad Sci U S A 2003 Dec 23 100(26):15393-7 [abstract on PubMed] [related articles] [FREE full text]
Selected by | James Stivers
Evaluated 14 Jan 2004

Role of entropy in increased rates of intramolecular reactions.
Armstrong AA, Amzel LM
J Am Chem Soc 2003 Nov 26 125(47):14596-602 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | James Stivers
Evaluated 15 Dec 2003

Locking the DNA topoisomerase I protein clamp inhibits DNA rotation and induces cell lethality.
Woo MH, Losasso C, …, Benedetti P, Bjornsti MA
Proc Natl Acad Sci U S A 2003 Nov 25 100(24):13767-72 [abstract on PubMed] [related articles] [FREE full text]
Selected by | James Stivers / Matt Redinbo
Evaluated 2 Dec 2003

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