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Papers authored by Adams PD

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Healing and hurting: molecular mechanisms, functions, and pathologies of cellular senescence.

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Adams PD

Molecular cell 36(1):2-14, 2009 Oct 9 - Who cited this? | PubMed ID: 19818705 | Fulltext

electronic Ligand Builder and Optimization Workbench (eLBOW): a tool for ligand coordinate and restraint generation.

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Moriarty NW, Grosse-Kunstleve RW, and Adams PD

Acta crystallographica. Section D, Biological crystallography 65(Pt 10):1074-80, 2009 Oct - Who cited this? | PubMed ID: 19770504 | Fulltext

Recent developments in phasing and structure refinement for macromolecular crystallography.

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Adams PD, Afonine PV, Grosse-Kunstleve RW, Read RJ, Richardson JS, Richardson DC, and Terwilliger TC

Current opinion in structural biology 19(5):566-72, 2009 Oct - Who cited this? | PubMed ID: 19700309 | Fulltext

Averaged kick maps: less noise, more signal...and probably less bias.

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Praaenikar J, Afonine PV, Guncar G, Adams PD, and Turk D

Acta crystallographica. Section D, Biological crystallography 65(Pt 9):921-31, 2009 Sep - Who cited this? | PubMed ID: 19690370 | Fulltext

Structure of endoglucanase Cel9A from the thermoacidophilic Alicyclobacillus acidocaldarius.

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Pereira JH, Sapra R, Volponi JV, Kozina CL, Simmons B, and Adams PD

Acta crystallographica. Section D, Biological crystallography 65(Pt 8):744-50, 2009 Aug - Who cited this? | PubMed ID: 19622857 | Fulltext

Label-free in situ imaging of lignification in the cell wall of low lignin transgenic Populus trichocarpa.

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Schmidt M, Schwartzberg AM, Perera PN, Weber-Bargioni A, Carroll A, Sarkar P, Bosneaga E, Urban JJ, Song J, Balakshin MY, Capanema EA, Auer M, Adams PD, Chiang VL, and Schuck PJ

Planta 230(3):589-97, 2009 Aug - Who cited this? | PubMed ID: 19526248 | Fulltext

Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules.

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Adams PD, Mustyakimov M, Afonine PV, and Langan P

Acta crystallographica. Section D, Biological crystallography 65(Pt 6):567-73, 2009 Jun - Who cited this? | PubMed ID: 19465771 | Fulltext

Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard.

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Terwilliger TC, Adams PD, Read RJ, McCoy AJ, Moriarty NW, Grosse-Kunstleve RW, Afonine PV, Zwart PH, and Hung LW

Acta crystallographica. Section D, Biological crystallography 65(Pt 6):582-601, 2009 Jun - Who cited this? | PubMed ID: 19465773 | Fulltext

Crystallographic model quality at a glance.

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Urzhumtseva L, Afonine PV, Adams PD, and Urzhumtsev A

Acta crystallographica. Section D, Biological crystallography 65(Pt 3):297-300, 2009 Mar - Who cited this? | PubMed ID: 19237753 | Fulltext

Human UBN1 is an ortholog of yeast Hpc2p and has an essential role in the HIRA/ASF1a chromatin-remodeling pathway in senescent cells.

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Banumathy G, Somaiah N, Zhang R, Tang Y, Hoffmann J, Andrake M, Ceulemans H, Schultz D, Marmorstein R, and Adams PD

Molecular and cellular biology 29(3):758-70, 2009 Feb - Who cited this? | PubMed ID: 19029251 | Fulltext

Varicella-zoster virus immediate-early 63 protein interacts with human antisilencing function 1 protein and alters its ability to bind histones h3.1 and h3.3.

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Ambagala AP, Bosma T, Ali MA, Poustovoitov M, Chen JJ, Gershon MD, Adams PD, and Cohen JI

Journal of virology 83(1):200-9, 2009 Jan - Who cited this? | PubMed ID: 18971269 | Fulltext

The protein structure initiative structural genomics knowledgebase.

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Berman HM, Westbrook JD, Gabanyi MJ, Tao W, Shah R, Kouranov A, Schwede T, Arnold K, Kiefer F, Bordoli L, Kopp J, Podvinec M, Adams PD, Carter LG, Minor W, Nair R,

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Nucleic acids research 37(Database issue):D365-8, 2009 Jan - Who cited this? | PubMed ID: 19010965 | Fulltext

Wnt signaling and senescence: A tug of war in early neoplasia?.

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Adams PD and Enders GH

Cancer biology & therapy 7(11), 2008 Nov 7 - Who cited this? | PubMed ID: 18836285 | Fulltext

Aging by epigenetics--a consequence of chromatin damage?.

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Sedivy JM, Banumathy G, and Adams PD

Experimental cell research 314(9):1909, 2008 Jun 10 - Who cited this? | PubMed ID: 18423606 | Fulltext

Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias.

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Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Moriarty NW, Adams PD, Read RJ, Zwart PH, and Hung LW

Acta crystallographica. Section D, Biological crystallography 64(Pt 5):515, 2008 May - Who cited this? | PubMed ID: 18453687 | Fulltext

Protein structures by spallation neutron crystallography.

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Langan P, Fisher Z, Kovalevsky A, Mustyakimov M, Sutcliffe Valone A, Unkefer C, Waltman MJ, Coates L, Adams PD, Afonine PV, Bennett B, Dealwis C, and Schoenborn BP

Journal of synchrotron radiation 15(Pt 3):215-8, 2008 May - Who cited this? | PubMed ID: 18421142 | Fulltext

A method for the prevention of thrombin-induced degradation of recombinant proteins.

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Rajalingam D, Kathir KM, Ananthamurthy K, Adams PD, and Kumar TK

Analytical biochemistry 375(2):361-3, 2008 Apr 15 - Who cited this? | PubMed ID: 18279654 | Fulltext

Identification of cellular proteins that maintain retroviral epigenetic silencing: evidence for an antiviral response.

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Poleshko A, Palagin I, Zhang R, Boimel P, Castagna C, Adams PD, Skalka AM, and Katz RA

Journal of virology 82(5):2313, 2008 Mar - Who cited this? | PubMed ID: 18094192 | Fulltext

Addressing the need for alternative transportation fuels: the Joint BioEnergy Institute.

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Blanch HW, Adams PD, Andrews-Cramer KM, Frommer WB, Simmons BA, and Keasling JD

ACS chemical biology 3(1):17-20, 2008 Jan 18 - Who cited this? | PubMed ID: 18205287 | Fulltext

Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard.

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Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Moriarty NW, Zwart PH, Hung LW, Read RJ, and Adams PD

Acta crystallographica. Section D, Biological crystallography 64(Pt 1):61-9, 2008 Jan - Who cited this? | PubMed ID: 18094468 | Fulltext

Surprises and pitfalls arising from (pseudo)symmetry.

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Zwart PH, Grosse-Kunstleve RW, Lebedev AA, Murshudov GN, and Adams PD

Acta crystallographica. Section D, Biological crystallography 64(Pt 1):99-107, 2008 Jan - Who cited this? | PubMed ID: 18094473 | Fulltext

Automated Structure Solution with the PHENIX Suite.

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Zwart PH, Afonine PV, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, McKee E, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC, and Adams PD

Methods in molecular biology (Clifton, N.J.) 426:419-35, 2008 - Who cited this? | PubMed ID: 18542881 | Fulltext

NMR assignment of Cdc42(T35A), an active Switch I mutant of Cdc42.

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Adams PD and Oswald RE

Biomolecular NMR assignments 1(2):225-7, 2007 Dec - Who cited this? | PubMed ID: 19636871 | Fulltext

On macromolecular refinement at subatomic resolution with interatomic scatterers.

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Afonine PV, Grosse-Kunstleve RW, Adams PD, Lunin VY, and Urzhumtsev A

Acta crystallographica. Section D, Biological crystallography 63(Pt 11):1194-7, 2007 Nov - Who cited this? | PubMed ID: 18007035 | Fulltext

Remodeling of chromatin structure in senescent cells and its potential impact on tumor suppression and aging.

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Adams PD

Gene 397(1-2):84-93, 2007 Aug 1 - Who cited this? | PubMed ID: 17544228 | Fulltext

Remodeling chromatin for senescence.

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Adams PD

Aging cell 6(4):425-7, 2007 Aug - Who cited this? | PubMed ID: 17635419 | Fulltext

Downregulation of Wnt signaling is a trigger for formation of facultative heterochromatin and onset of cell senescence in primary human cells.

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Ye X, Zerlanko B, Kennedy A, Banumathy G, Zhang R, and Adams PD

Molecular cell 27(2):183, 2007 Jul 20 - Who cited this? | PubMed ID: 17643369 | Fulltext

Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models.

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Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Adams PD, Moriarty NW, Zwart P, Read RJ, Turk D, and Hung LW

Acta crystallographica. Section D, Biological crystallography 63(Pt 5):597-610, 2007 May - Who cited this? | PubMed ID: 17452785 | Fulltext

Structure of O67745_AQUAE, a hypothetical protein from Aquifex aeolicus.

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Oganesyan V, Adams PD, Jancarik J, Kim R, and Kim SH

Acta crystallographica. Section F, Structural biology and crystallization communications 63(Pt 5):369-74, 2007 May 1 - Who cited this? | PubMed ID: 17565173 | Fulltext

Definition of pRB- and p53-dependent and -independent steps in HIRA/ASF1a-mediated formation of senescence-associated heterochromatin foci.

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Ye X, Zerlanko B, Zhang R, Somaiah N, Lipinski M, Salomoni P, and Adams PD

Molecular and cellular biology 27(7):2452-65, 2007 Apr - Who cited this? | PubMed ID: 17242198 | Fulltext

Heterochromatin and its relationship to cell senescence and cancer therapy.

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Zhang R and Adams PD

Cell cycle (Georgetown, Tex.) 6(7):784-9, 2007 Apr 1 - Who cited this? | PubMed ID: 17377503 | Fulltext

Molecular dissection of formation of senescence-associated heterochromatin foci.

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Zhang R, Chen W, and Adams PD

Molecular and cellular biology 27(6):2343-58, 2007 Mar - Who cited this? | PubMed ID: 17242207 | Fulltext

HP1 proteins are essential for a dynamic nuclear response that rescues the function of perturbed heterochromatin in primary human cells.

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Zhang R, Liu ST, Chen W, Bonner M, Pehrson J, Yen TJ, and Adams PD

Molecular and cellular biology 27(3):949, 2007 Feb - Who cited this? | PubMed ID: 17101789 | Fulltext

Ligand identification using electron-density map correlations.

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Terwilliger TC, Adams PD, Moriarty NW, and Cohn JD

Acta crystallographica. Section D, Biological crystallography 63(Pt 1):101-7, 2007 Jan - Who cited this? | PubMed ID: 17164532 | Fulltext

SPARX, a new environment for Cryo-EM image processing.

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Hohn M, Tang G, Goodyear G, Baldwin PR, Huang Z, Penczek PA, Yang C, Glaeser RM, Adams PD, and Ludtke SJ

Journal of structural biology 157(1):47-55, 2007 Jan - Who cited this? | PubMed ID: 16931051 | Fulltext

Design and application of a shRNA-based gene replacement retrovirus.

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Zhang R, Adams PD, and Ye X

Methods in molecular biology (Clifton, N.J.) 408:211-21, 2007 - Who cited this? | PubMed ID: 18314585 | Fulltext

Structure of a human ASF1a-HIRA complex and insights into specificity of histone chaperone complex assembly.

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Tang Y, Poustovoitov MV, Zhao K, Garfinkel M, Canutescu A, Dunbrack R, Adams PD, and Marmorstein R

Nature structural & molecular biology 13(10):921-9, 2006 Oct - Who cited this? | PubMed ID: 16980972 | Fulltext

Automated ligand fitting by core-fragment fitting and extension into density.

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Terwilliger TC, Klei H, Adams PD, Moriarty NW, and Cohn JD

Acta crystallographica. Section D, Biological crystallography 62(Pt 8):915-22, 2006 Aug - Who cited this? | PubMed ID: 16855309 | Fulltext

Transcription factors, cAMP-responsive element modulator (CREM) and Tisp40, act in concert in postmeiotic transcriptional regulation.

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Nagamori I, Yomogida K, Adams PD, Sassone-Corsi P, and Nojima H

The Journal of biological chemistry 281(22):15073-81, 2006 Jun 2 - Who cited this? | PubMed ID: 16595651 | Fulltext

Solution structure of an oncogenic mutant of Cdc42Hs.

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Adams PD and Oswald RE

Biochemistry 45(8):2577-83, 2006 Feb 28 - Who cited this? | PubMed ID: 16489751 | Fulltext

Structural basis for double-stranded RNA processing by Dicer.

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Macrae IJ, Zhou K, Li F, Repic A, Brooks AN, Cande WZ, Adams PD, and Doudna JA

Science (New York, N.Y.) 311(5758):195-8, 2006 Jan 13 - Who cited this? | PubMed ID: 16410517 | Fulltext

Crystal structures of an NAD kinase from Archaeoglobus fulgidus in complex with ATP, NAD, or NADP.

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Liu J, Lou Y, Yokota H, Adams PD, Kim R, and Kim SH

Journal of molecular biology 354(2):289-303, 2005 Nov 25 - Who cited this? | PubMed ID: 16242716 | Fulltext

FINDMOL: automated identification of macromolecules in electron-density maps.

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McKee EW, Kanbi LD, Childs KL, Grosse-Kunstleve RW, Adams PD, Sacchettini JC, and Ioerger TR

Acta crystallographica. Section D, Biological crystallography 61(Pt 11):1514-20, 2005 Nov - Who cited this? | PubMed ID: 16239729 | Fulltext

Automated crystallographic ligand building using the medial axis transform of an electron-density isosurface.

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Aishima J, Russel DS, Guibas LJ, Adams PD, and Brunger AT

Acta crystallographica. Section D, Biological crystallography 61(Pt 10):1354-63, 2005 Oct - Who cited this? | PubMed ID: 16204887 | Fulltext

Crystal structure of a bacterial ribonuclease P RNA.

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Kazantsev AV, Krivenko AA, Harrington DJ, Holbrook SR, Adams PD, and Pace NR

Proceedings of the National Academy of Sciences of the United States of America 102(38):13392-7, 2005 Sep 20 - Who cited this? | PubMed ID: 16157868 | Fulltext

Crystal structure of a heat-inducible transcriptional repressor HrcA from Thermotoga maritima: structural insight into DNA binding and dimerization.

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Liu J, Huang C, Shin DH, Yokota H, Jancarik J, Kim JS, Adams PD, Kim R, and Kim SH

Journal of molecular biology 350(5):987-96, 2005 Jul 29 - Who cited this? | PubMed ID: 15979091 | Fulltext

A robust bulk-solvent correction and anisotropic scaling procedure.

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Afonine PV, Grosse-Kunstleve RW, and Adams PD

Acta crystallographica. Section D, Biological crystallography 61(Pt 7):850-5, 2005 Jul - Who cited this? | PubMed ID: 15983406 | Fulltext

Structure of a NAD kinase from Thermotoga maritima at 2.3 A resolution.

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Oganesyan V, Huang C, Adams PD, Jancarik J, Yokota HA, Kim R, and Kim SH

Acta crystallographica. Section F, Structural biology and crystallization communications 61(Pt 7):640-6, 2005 Jul 1 - Who cited this? | PubMed ID: 16511117 | Fulltext

Crystal structure of the "PhoU-like" phosphate uptake regulator from Aquifex aeolicus.

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Oganesyan V, Oganesyan N, Adams PD, Jancarik J, Yokota HA, Kim R, and Kim SH

Journal of bacteriology 187(12):4238-44, 2005 Jun - Who cited this? | PubMed ID: 15937186 | Fulltext

Crystal structure of a PhoU protein homologue: a new class of metalloprotein containing multinuclear iron clusters.

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Liu J, Lou Y, Yokota H, Adams PD, Kim R, and Kim SH

The Journal of biological chemistry 280(16):15960-6, 2005 Apr 22 - Who cited this? | PubMed ID: 15716271 | Fulltext

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