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Fred Dyda
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), United States of America

Faculty Member: Structural Biology > Experimental Biophysical Methods [ since 3 October 2002 ]
[ Homepage ] [ Evaluations ]
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http://intramural.niddk.nih.gov/research/faculty.asp?People_ID=1577

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Evaluations

A magic triangle for experimental phasing of macromolecules.
Beck T, Krasauskas A, Gruene T, Sheldrick GM
Acta Crystallogr D Biol Crystallogr 2008 Nov 64(Pt 11):1179-82 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Fred Dyda
Evaluated 4 Dec 2008

Mechanisms of human immunodeficiency virus type 1 concerted integration related to strand transfer inhibition and drug resistance.
Zahm JA, Bera S, …, Hazuda D, Grandgenett DP
Antimicrob Agents Chemother 2008 Sep 52(9):3358-68 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Fred Dyda
Evaluated 24 Sep 2008

Tetrameric structure of a serine integrase catalytic domain.
Yuan P, Gupta K, Van Duyne GD
Structure 2008 Aug 6 16(8):1275-86 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Fred Dyda
Evaluated 19 Sep 2008

Macromolecular structure solution by charge flipping.
Dumas C, van der Lee A
Acta Crystallogr D Biol Crystallogr 2008 Aug 64(Pt 8):864-73 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Fred Dyda
Evaluated 6 Aug 2008

Architecture of a serine recombinase-DNA regulatory complex.
Mouw KW, Rowland SJ, …, Stark WM, Rice PA
Mol Cell 2008 Apr 25 30(2):145-55 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Fred Dyda
Evaluated 16 May 2008

Complete in vitro reconstitution of adeno-associated virus DNA replication requires the minichromosome maintenance complex proteins.
Nash K, Chen W, Muzyczka N
J Virol 2008 Feb 82(3):1458-64 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Fred Dyda
Evaluated 25 Mar 2008

Why phase errors affect the electron function more than amplitude errors.
Lattman E, Derosier D
Acta Crystallogr A 2008 Mar 64(Pt 2):341-4 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Fred Dyda
Evaluated 25 Mar 2008

The charge flipping algorithm.
Oszlányi G, Süto A
Acta Crystallogr A 2008 Jan 1 64(Pt 1):123-134 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Fred Dyda
Evaluated 22 Jan 2008

Structure determination of the O-methyltransferase NovP using the 'free lunch algorithm' as implemented in SHELXE.
Usón I, Stevenson CE, Lawson DM, Sheldrick GM
Acta Crystallogr D Biol Crystallogr 2007 Oct 63(Pt 10):1069-74 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Fred Dyda
Evaluated 16 Nov 2007

Crystal structure of the human beta2 adrenergic G-protein-coupled receptor.
Rasmussen SG, Choi HJ, …, Weis WI, Kobilka BK
Nature 2007 Nov 15 450(7168):383-7 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Leonardo Pardo / Fred Dyda / Carmen Dessauer / Arthur Christopoulos / Patricia C. Weber / Ian Hall / Marc Caron / Stephan Nussberger
Evaluated 16 Nov 2007

Phosphorylation regulates integration of the yeast Ty5 retrotransposon into heterochromatin.
Dai J, Xie W, …, Gao J, Voytas DF
Mol Cell 2007 Jul 20 27(2):289-99 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Fred Dyda
Evaluated 21 Sep 2007

LEDGF/p75 functions downstream from preintegration complex formation to effect gene-specific HIV-1 integration.
Shun MC, Raghavendra NK, …, Cherepanov P, Engelman A
Genes Dev 2007 Jul 15 21(14):1767-78 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Fred Dyda
Evaluated 20 Sep 2007

FASTDXL: a generalized screen to trap disulfide-stabilized complexes for use in structural studies.
Corn JE, Berger JM
Structure 2007 Jul 15(7):773-80 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Fred Dyda
Evaluated 2 Aug 2007

A novel strategy for the crystallization of proteins: X-ray diffraction validation.
Larson SB, Day JS, Cudney R, McPherson A
Acta Crystallogr D Biol Crystallogr 2007 Mar 63(Pt 3):310-8 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Fred Dyda
Evaluated 29 Mar 2007

Hyperquenching for protein cryocrystallography.
Warkentin M, Berejnov V, Husseini NS, Thorne RE
J Appl Cryst 2006 39:805-811 [full text]
Selected by | Fred Dyda
Evaluated 6 Feb 2007

What can be done with a good crystal and an accurate beamline?
Wang J, Dauter M, Dauter Z
Acta Crystallogr D Biol Crystallogr 2006 Dec 62(Pt 12):1475-83 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Fred Dyda
Evaluated 4 Dec 2006

Viewing single lambda site-specific recombination events from start to finish.
Mumm JP, Landy A, Gelles J
EMBO J 2006 Oct 4 25(19):4586-95 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Fred Dyda
Evaluated 20 Nov 2006

Kinking occurs during molecular dynamics simulations of small DNA minicircles.
Lankas F, Lavery R, Maddocks JH
Structure 2006 Oct 14(10):1527-34 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Fred Dyda
Evaluated 9 Nov 2006

Considerations for the refinement of low-resolution crystal structures.
DeLaBarre B, Brunger AT
Acta Crystallogr D Biol Crystallogr 2006 Aug 62(Pt 8):923-32 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Fred Dyda
Evaluated 7 Aug 2006

Genomic instability due to V(D)J recombination-associated transposition.
Reddy YV, Perkins EJ, Ramsden DA
Genes Dev 2006 Jun 15 20(12):1575-82 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Pierre Ferrier / Fred Dyda
Evaluated 31 Jul 2006

Structural basis for broad DNA-specificity in integron recombination.
MacDonald D, Demarre G, …, Mazel D, Gopaul DN
Nature 2006 Apr 27 440(7088):1157-62 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Fred Dyda
Evaluated 25 May 2006

Optimal description of a protein structure in terms of multiple groups undergoing TLS motion.
Painter J, Merritt EA
Acta Crystallogr D Biol Crystallogr 2006 Apr 62(Pt 4):439-50 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Fred Dyda
Evaluated 20 Apr 2006

Molecular dynamics simulations of the complete satellite tobacco mosaic virus.
Freddolino PL, Arkhipov AS, …, McPherson A, Schulten K
Structure 2006 Mar 14(3):437-49 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Fred Dyda
Evaluated 20 Mar 2006

UV laser-excited fluorescence as a tool for the visualization of protein crystals mounted in loops.
Vernede X, Lavault B, …, Cipriani F, Bourgeois D
Acta Crystallogr D Biol Crystallogr 2006 Mar 62(Pt 3):253-61 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Fred Dyda
Evaluated 20 Mar 2006

Integron cassette insertion: a recombination process involving a folded single strand substrate.
Bouvier M, Demarre G, Mazel D
EMBO J 2005 Dec 21 24(24):4356-67 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Fred Dyda
Evaluated 10 Feb 2006

The Structural Biology Center 19ID undulator beamline: facility specifications and protein crystallographic results.
Rosenbaum G, Alkire RW, …, Westbrook E, Joachimiak A
J Synchrotron Radiat 2006 Jan 13(Pt 1):30-45 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Fred Dyda
Evaluated 31 Jan 2006

Structural basis for the recognition between HIV-1 integrase and transcriptional coactivator p75.
Cherepanov P, Ambrosio AL, …, Ellenberger T, Engelman A
Proc Natl Acad Sci U S A 2005 Nov 29 102(48):17308-13 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Fred Dyda
Evaluated 4 Jan 2006

High-resolution neutron protein crystallography with radically small crystal volumes: application of perdeuteration to human aldose reductase.
Hazemann I, Dauvergne MT, …, Myles DA, Podjarny A
Acta Crystallogr D Biol Crystallogr 2005 Oct 61(Pt 10):1413-7 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Fred Dyda
Evaluated 20 Oct 2005

Rev1 employs a novel mechanism of DNA synthesis using a protein template.
Nair DT, Johnson RE, …, Prakash S, Aggarwal AK
Science 2005 Sep 30 309(5744):2219-22 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Fred Dyda / Larry McLaughlin / Martin Egli / Lucio Comai / Barry Stoddard
Evaluated 11 Oct 2005

The single-stranded genome of phage CTX is the form used for integration into the genome of Vibrio cholerae.
Val ME, Bouvier M, …, Mazel D, Barre FX
Mol Cell 2005 Aug 19 19(4):559-66 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Fred Dyda
Evaluated 13 Sep 2005

Structure of a synaptic gammadelta resolvase tetramer covalently linked to two cleaved DNAs.
Li W, Kamtekar S, …, Grindley ND, Steitz TA
Science 2005 Aug 19 309(5738):1210-5 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Fred Dyda
Evaluated 30 Aug 2005

A structural basis for allosteric control of DNA recombination by lambda integrase.
Biswas T, Aihara H, …, Landy A, Ellenberger T
Nature 2005 Jun 23 435(7045):1059-66 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Walter Chazin / Fred Dyda
Evaluated 25 Jul 2005

Two-wavelength MAD phasing and radiation damage: a case study.
González A, von Delft F, Liddington RC, Bakolitsa C
J Synchrotron Radiat 2005 May 12(Pt 3):285-91 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Fred Dyda
Evaluated 1 Jun 2005

3D reconstruction of the Mu transposase and the Type 1 transpososome: a structural framework for Mu DNA transposition.
Yuan JF, Beniac DR, Chaconas G, Ottensmeyer FP
Genes Dev 2005 Apr 1 19(7):840-52 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Fred Dyda
Evaluated 14 Apr 2005

X-ray absorption, refraction and resonant scattering tensors in selenated protein crystals: implications for data collection strategies in macromolecular crystallography.
Evans G, Bricogne S.C., Roversi P, Schiltz M
J App Crystallog 2005 38:168-182 [order article]
Selected by | Fred Dyda
Evaluated 23 Feb 2005

Protein biophysical properties that correlate with crystallization success in Thermotoga maritima: maximum clustering strategy for structural genomics.
Canaves JM, Page R, Wilson IA, Stevens RC
J Mol Biol 2004 Dec 3 344(4):977-91 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Michael Sundstrom / Fred Dyda / Xiayang Qiu
Evaluated 15 Dec 2004

Structural insights into the catalytic mechanism of phosphate ester hydrolysis by dUTPase.
Barabás O, Pongrácz V, …, Wilmanns M, Vértessy BG
J Biol Chem 2004 Oct 8 279(41):42907-15 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Fred Dyda
Evaluated 1 Nov 2004

The site-specific incorporation of p-iodo-L-phenylalanine into proteins for structure determination.
Xie J, Wang L, …, Spraggon G, Schultz PG
Nat Biotechnol 2004 Oct 22(10):1297-301 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Fred Dyda / David Waugh / Makoto Komiyama / Mark Nelson
Evaluated 1 Nov 2004

Architecture of the hin synaptic complex during recombination: the recombinase subunits translocate with the DNA strands.
Dhar G, Sanders ER, Johnson RC
Cell 2004 Oct 1 119(1):33-45 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Fred Dyda
Evaluated 22 Oct 2004

X-ray absorption by macromolecular crystals: the effects of wavelength and crystal composition on absorbed dose.
Murray JW, Garman EF, Ravelli RBG
J Appl Crystallogr 2004 37:513-522 [order article]
Selected by | Fred Dyda
Evaluated 16 Sep 2004

Liquid-chromatography-coupled SAXS for accurate sizing of aggregating proteins.
Mathew E, Mirza A, Menhart N
J Synchrotron Radiat 2004 Jul 1 11(Pt 4):314-8 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Fred Dyda
Evaluated 27 Jul 2004

Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography.
DePristo MA, de Bakker PI, Blundell TL
Structure 2004 May 12(5):831-8 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Matthew Jacobson / Fred Dyda / E. Neil G. Marsh / Douglas Freymann
Evaluated 8 Jun 2004

RAG proteins shepherd double-strand breaks to a specific pathway, suppressing error-prone repair, but RAG nicking initiates homologous recombination.
Lee GS, Neiditch MB, Salus SS, Roth DB
Cell 2004 Apr 16 117(2):171-84 [abstract on PubMed] [related articles] [order article]
Selected by | Fred Dyda
Evaluated 17 May 2004

Structural basis for the mechanism and regulation of Sir2 enzymes.
Avalos JL, Boeke JD, Wolberger C
Mol Cell 2004 Mar 12 13(5):639-48 [abstract on PubMed] [related articles] [order article]
Selected by | Fred Dyda / Sylvie Doublie
Evaluated 30 Mar 2004

Ab initio structure solution by charge flipping.
Oszlányi G, Süto A
Acta Crystallogr A 2004 Mar 60(Pt 2):134-41 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Fred Dyda
Evaluated 17 Mar 2004

The role of solvent transport in cryo-annealing of macromolecular crystals.
Juers DH, Matthews BW
Acta Crystallogr D Biol Crystallogr 2004 Mar 60(Pt 3):412-21 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Fred Dyda
Evaluated 12 Mar 2004

The crystal structure of the bifunctional primase-helicase of bacteriophage T7.
Toth EA, Li Y, …, Cheng Y, Ellenberger T
Mol Cell 2003 Nov 12(5):1113-23 [abstract on PubMed] [related articles] [order article]
Selected by | Matt Redinbo / Fred Dyda
Evaluated 17 Dec 2003

Structural insights into single-stranded DNA binding and cleavage by F factor TraI.
Datta S, Larkin C, Schildbach JF
Structure 2003 Nov 11(11):1369-79 [abstract on PubMed] [related articles] [order article]
Selected by | Fred Dyda
Evaluated 10 Dec 2003

Pound-wise but penny-foolish: How well do micromolecules fare in macromolecular refinement?
Kleywegt GJ, Henrick K, Dodson EJ, van Aalten DM
Structure 2003 Sep 11(9):1051-9 [abstract on PubMed] [related articles] [order article]
Selected by | Fred Dyda
Evaluated 24 Oct 2003

The dimeric versus monomeric status of 14-3-3zeta is controlled by phosphorylation of Ser58 at the dimer interface.
Woodcock JM, Murphy J, …, Berndt MC, Lopez AF
J Biol Chem 2003 Sep 19 278(38):36323-7 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Fred Dyda
Evaluated 30 Sep 2003

A conformational switch controls the DNA cleavage activity of lambda integrase.
Aihara H, Kwon HJ, …, Landy A, Ellenberger T
Mol Cell 2003 Jul 12(1):187-98 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Fred Dyda
Evaluated 14 Aug 2003

Multiparametric scaling of diffraction intensities.
Otwinowski Z, Borek D, Majewski W, Minor W
Acta Crystallogr A 2003 May 59(Pt 3):228-34 [abstract on PubMed] [related articles] [order article]
Selected by | Fred Dyda
Evaluated 29 Jul 2003

How does radiation damage in protein crystals depend on X-ray dose?
Sliz P, Harrison SC, Rosenbaum G
Structure 2003 Jan 11(1):13-9 [abstract on PubMed] [related articles] [order article]
Selected by | Michael Eck / Fred Dyda
Evaluated 15 May 2003

Sheldrick's 1.2 A rule and beyond.
Morris RJ, Bricogne G
Acta Crystallogr D Biol Crystallogr 2003 Mar 59(Pt 3):615-7 [abstract on PubMed] [related articles] [order article]
Selected by | Fred Dyda
Evaluated 18 Mar 2003

Cellular mobile genetic elements in the regulatory region of the pneumotropic mouse polyomavirus genome: structure and function in viral gene expression and DNA replication.
Zhang S, Magnusson G
J Virol 2003 Mar 77(6):3477-86 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Fred Dyda
Evaluated 17 Mar 2003

A general method to quantify quasi-equivalence in icosahedral viruses.
Damodaran KV, Reddy VS, Johnson JE, Brooks CL
J Mol Biol 2002 Dec 6 324(4):723-37 [abstract on PubMed] [related articles] [order article]
Selected by | Fred Dyda
Evaluated 14 Jan 2003

Structure of the single-strand annealing domain of human RAD52 protein.
Singleton MR, Wentzell LM, …, West SC, Wigley DB
Proc Natl Acad Sci U S A 2002 Oct 15 99(21):13492-7 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Fred Dyda
Evaluated 8 Jan 2003

Crystal structure of the RuvA-RuvB complex: a structural basis for the Holliday junction migrating motor machinery.
Yamada K, Miyata T, …, Mayanagi K, Morikawa K
Mol Cell 2002 Sep 10(3):671-81 [abstract on PubMed] [related articles] [order article]
Selected by | Fred Dyda
Evaluated 20 Nov 2002

Structure and catalytic mechanism of a SET domain protein methyltransferase.
Trievel RC, Beach BM, …, Houtz RL, Hurley JH
Cell 2002 Oct 4 111(1):91-103 [abstract on PubMed] [related articles] [order article]
Selected by | Fred Dyda
Evaluated 12 Nov 2002

Ab initio determination of a crystal structure by means of the Schrödinger equation.
Bethanis K, Tzamalis P, Hountas A, Tsoucaris G
Acta Crystallogr A 2002 May 58(Pt 3):265-9 [abstract on PubMed] [related articles] [order article]
Selected by | Fred Dyda
Evaluated 29 Oct 2002

The Rad50 zinc-hook is a structure joining Mre11 complexes in DNA recombination and repair.
Hopfner KP, Craig L, …, Petrini JH, Tainer JA
Nature 2002 Aug 1 418(6897):562-6 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Stephen Jackson / Fred Dyda
Evaluated 29 Oct 2002

Substructure solution with SHELXD.
Schneider TR, Sheldrick GM
Acta Crystallogr D Biol Crystallogr 2002 Oct 58(Pt 10 Pt 2):1772-9 [abstract on PubMed] [related articles] [order article]
Selected by | Fred Dyda
Evaluated 29 Oct 2002

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