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Papers authored by Sali A

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An atomic model AAA-ATPase/20S core particle sub-complex of the 26S proteasome.

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Förster F, Lasker K, Beck F, Nickell S, Sali A, and Baumeister W

Biochemical and biophysical research communications 388(2):228-33, 2009 Oct 16 - Who cited this? | PubMed ID: 19653995 | Fulltext

Institutional Profile: The University of California Pharmacogenomics Center: at the interface of genomics, biological mechanisms and drug therapy.

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Kroetz DL, Ahituv N, Burchard EG, Guo S, Sali A, and Giacomini KM

Pharmacogenomics 10(10):1569-76, 2009 Oct - Who cited this? | PubMed ID: 19842929 | Fulltext

Alignment of multiple protein structures based on sequence and structure features.

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Madhusudhan MS, Webb BM, Marti-Renom MA, Eswar N, and Sali A

Protein engineering, design & selection : PEDS 22(9):569-74, 2009 Sep - Who cited this? | PubMed ID: 19587024 | Fulltext

Global motions of the nuclear pore complex: insights from elastic network models.

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Lezon TR, Sali A, and Bahar I

PLoS computational biology 5(9):e1000496, 2009 Sep - Who cited this? | PubMed ID: 19730674 | Fulltext

Evidence for a shared nuclear pore complex architecture that is conserved from the last common eukaryotic ancestor.

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DeGrasse JA, DuBois KN, Devos D, Siegel TN, Sali A, Field MC, Rout MP, and Chait BT

Molecular & cellular proteomics : MCP 8(9):2119-30, 2009 Sep - Who cited this? | PubMed ID: 19525551 | Fulltext

Insights into the molecular architecture of the 26S proteasome.

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Nickell S, Beck F, Scheres SH, Korinek A, Förster F, Lasker K, Mihalache O, Sun N, Nagy I, Sali A, Plitzko JM, Carazo JM, Mann M, and Baumeister W

Proceedings of the National Academy of Sciences of the United States of America 106(29):11943-7, 2009 Jul 21 - Who cited this? | PubMed ID: 19581588 | Fulltext

ModLink+: improving fold recognition by using protein-protein interactions.

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Fornes O, Aragues R, Espadaler J, Marti-Renom MA, Sali A, and Oliva B

Bioinformatics (Oxford, England) 25(12):1506-12, 2009 Jun 15 - Who cited this? | PubMed ID: 19357100 | Fulltext

Evolutionary constraints on structural similarity in orthologs and paralogs.

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Peterson ME, Chen F, Saven JG, Roos DS, Babbitt PC, and Sali A

Protein science : a publication of the Protein Society 18(6):1306-15, 2009 Jun - Who cited this? | PubMed ID: 19472362 | Fulltext

Preclinical drug trials in the mdx mouse: Assessment of reliable and sensitive outcome measures.

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Spurney CF, Gordish-Dressman H, Guerron AD, Sali A, Pandey GS, Rawat R, Van Der Meulen JH, Cha HJ, Pistilli EE, Partridge TA, Hoffman EP, and Nagaraju K

Muscle & nerve 39(5):591-602, 2009 May - Who cited this? | PubMed ID: 19260102 | Fulltext

Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly.

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Lasker K, Topf M, Sali A, and Wolfson HJ

Journal of molecular biology 388(1):180-94, 2009 Apr 24 - Who cited this? | PubMed ID: 19233204 | Fulltext

2007 Annual progress report synopsis of the Center for Structures of Membrane Proteins.

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Stroud RM, Choe S, Holton J, Kaback HR, Kwiatkowski W, Minor DL, Riek R, Sali A, Stahlberg H, and Harries W

Journal of structural and functional genomics 10(2):193-208, 2009 Apr - Who cited this? | PubMed ID: 19148774 | Fulltext

A kernel for the Tropical Disease Initiative.

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Ortí L, Carbajo RJ, Pieper U, Eswar N, Maurer SM, Rai AK, Taylor G, Todd MH, Pineda-Lucena A, Sali A, and Marti-Renom MA

Nature biotechnology 27(4):320-1, 2009 Apr - Who cited this? | PubMed ID: 19352362 | Fulltext

Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies.

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Pieper U, Chiang R, Seffernick JJ, Brown SD, Glasner ME, Kelly L, Eswar N, Sauder JM, Bonanno JB, Swaminathan S, Burley SK, Zheng X, Chance MR, Almo SC, Gerlt JA, Raushel FM,

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Journal of structural and functional genomics 10(2):107-25, 2009 Apr - Who cited this? | PubMed ID: 19219566 | Fulltext

Evaluation of the effects of a psychosocial intervention on mood, coping, and quality of life in cancer patients.

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Reavley N, Pallant JF, and Sali A

Integrative cancer therapies 8(1):47-55, 2009 Mar - Who cited this? | PubMed ID: 19147645 | Fulltext

Ratiocinative screen of eukaryotic integral membrane protein expression and solubilization for structure determination.

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Hays FA, Roe-Zurz Z, Li M, Kelly L, Gruswitz F, Sali A, and Stroud RM

Journal of structural and functional genomics 10(1):9-16, 2009 Mar - Who cited this? | PubMed ID: 19031011 | Fulltext

Outcome of a workshop on applications of protein models in biomedical research.

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Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL, Fidelis K, Fiser A, Godzik A, Huang YJ, Humblet C,

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Structure (London, England : 1993) 17(2):151-9, 2009 Feb 13 - Who cited this? | PubMed ID: 19217386 | Fulltext

The structural dynamics of macromolecular processes.

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Russel D, Lasker K, Phillips J, Schneidman-Duhovny D, Velázquez-Muriel JA, and Sali A

Current opinion in cell biology 21(1):97-108, 2009 Feb - Who cited this? | PubMed ID: 19223165 | Fulltext

Selecting optimum eukaryotic integral membrane proteins for structure determination by rapid expression and solubilization screening.

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Li M, Hays FA, Roe-Zurz Z, Vuong L, Kelly L, Ho CM, Robbins RM, Pieper U, O'Connell JD, Miercke LJ, Giacomini KM, Sali A, and Stroud RM

Journal of molecular biology 385(3):820-30, 2009 Jan 23 - Who cited this? | PubMed ID: 19061901 | Fulltext

MODBASE, a database of annotated comparative protein structure models and associated resources.

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Pieper U, Eswar N, Webb BM, Eramian D, Kelly L, Barkan DT, Carter H, Mankoo P, Karchin R, Marti-Renom MA, Davis FP, and Sali A

Nucleic acids research 37(Database issue):D347-54, 2009 Jan - Who cited this? | PubMed ID: 18948282 | Fulltext

A kernel for open source drug discovery in tropical diseases.

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Ortí L, Carbajo RJ, Pieper U, Eswar N, Maurer SM, Rai AK, Taylor G, Todd MH, Pineda-Lucena A, Sali A, and Marti-Renom MA

PLoS neglected tropical diseases 3(4):e418, 2009 - Who cited this? | PubMed ID: 19381286 | Fulltext

Regulatory Elements within the Prodomain of Falcipain-2, a Cysteine Protease of the Malaria Parasite Plasmodium falciparum.

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Pandey KC, Barkan DT, Sali A, and Rosenthal PJ

PLoS ONE 4(5):e5694, 2009 - Who cited this? | PubMed ID: 19479029 | Fulltext

Biodegradation of oxygenated and non-oxygenated imidazolium-based ionic liquids in soil.

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Modelli A, Sali A, Galletti P, and Samorì C

Chemosphere 73(8):1322-7, 2008 Nov - Who cited this? | PubMed ID: 18715611 | Fulltext

How well can the accuracy of comparative protein structure models be predicted?.

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Eramian D, Eswar N, Shen MY, and Sali A

Protein science : a publication of the Protein Society 17(11):1881-93, 2008 Nov - Who cited this? | PubMed ID: 18832340 | Fulltext

Genomic-scale prioritization of drug targets: the TDR Targets database.

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Agüero F, Al-Lazikani B, Aslett M, Berriman M, Buckner FS, Campbell RK, Carmona S, Carruthers IM, Chan AW, Chen F, Crowther GJ, Doyle MA, Hertz-Fowler C, Hopkins AL, McAllister G, Nwaka S,

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Nature reviews. Drug discovery 7(11):900-7, 2008 Nov - Who cited this? | PubMed ID: 18927591 | Fulltext

Effective rescue of dystrophin improves cardiac function in dystrophin-deficient mice by a modified morpholino oligomer.

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Wu B, Moulton HM, Iversen PL, Jiang J, Li J, Li J, Spurney CF, Sali A, Guerron AD, Nagaraju K, Doran T, Lu P, Xiao X, and Lu QL

Proceedings of the National Academy of Sciences of the United States of America, 2008 Sep 19 - Who cited this? | PubMed ID: 18806224 | Fulltext

Global Sequencing of Proteolytic Cleavage Sites in Apoptosis by Specific Labeling of Protein N Termini.

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Mahrus S, Trinidad JC, Barkan DT, Sali A, Burlingame AL, and Wells JA

Cell, 2008 Aug 20 - Who cited this? | PubMed ID: 18722006 | Fulltext

Improved cognitive performance after dietary supplementation with a Pinus radiata bark extract Formulation.

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Pipingas A, Silberstein RB, Vitetta L, Rooy CV, Harris EV, Young JM, Frampton CM, Sali A, and Nastasi J

Phytotherapy research : PTR, 2008 Aug 5 - Who cited this? | PubMed ID: 18683195 | Fulltext

Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies.

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Chiang RA, Sali A, and Babbitt PC

PLoS computational biology 4(8), 2008 Aug - Who cited this? | PubMed ID: 18670595 | Fulltext

Integration of Small-Angle X-Ray Scattering Data into Structural Modeling of Proteins and Their Assemblies.

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Förster F, Webb B, Krukenberg KA, Tsuruta H, Agard DA, and Sali A

Journal of molecular biology, 2008 Jul 31 - Who cited this? | PubMed ID: 18694757 | Fulltext

Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel.

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Serysheva II, Ludtke SJ, Baker ML, Cong Y, Topf M, Eramian D, Sali A, Hamilton SL, and Chiu W

Proceedings of the National Academy of Sciences of the United States of America 105(28):9610-5, 2008 Jul 15 - Who cited this? | PubMed ID: 18621707 | Fulltext

Integrating Diverse Data for Structure Determination of Macromolecular Assemblies.

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Alber F, Förster F, Korkin D, Topf M, and Sali A

Annual review of biochemistry 77:443, 2008 Jul 7 - Who cited this? | PubMed ID: 18318657 | Fulltext

Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT.

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Booth CR, Meyer AS, Cong Y, Topf M, Sali A, Ludtke SJ, Chiu W, and Frydman J

Nature structural & molecular biology, 2008 Jun 8 - Who cited this? | PubMed ID: 18536725 | Fulltext

Alternative therapies for musculoskeletal conditions.

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Vitetta L, Cicuttini F, and Sali A

Best practice & research. Clinical rheumatology 22(3):499-522, 2008 Jun - Who cited this? | PubMed ID: 18519102 | Fulltext

Multiple conformations of E. coli Hsp90 in solution: insights into the conformational dynamics of Hsp90.

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Krukenberg KA, Förster F, Rice LM, Sali A, and Agard DA

Structure (London, England : 1993) 16(5):755-65, 2008 May - Who cited this? | PubMed ID: 18462680 | Fulltext

Structure of the mammalian 80S ribosome at 8.7 A resolution.

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Chandramouli P, Topf M, Ménétret JF, Eswar N, Cannone JJ, Gutell RR, Sali A, and Akey CW

Structure (London, England : 1993) 16(4):535, 2008 Apr - Who cited this? | PubMed ID: 18400176 | Fulltext

Tel2 mediates activation and localization of ATM/Tel1 kinase to a double-strand break.

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Anderson CM, Korkin D, Smith DL, Makovets S, Seidel JJ, Sali A, and Blackburn EH

Genes & development 22(7):854-9, 2008 Apr 1 - Who cited this? | PubMed ID: 18334620 | Fulltext

Protein structure fitting and refinement guided by cryo-EM density.

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Topf M, Lasker K, Webb B, Wolfson H, Chiu W, and Sali A

Structure (London, England : 1993) 16(2):295, 2008 Feb - Who cited this? | PubMed ID: 18275820 | Fulltext

Protein production and purification.

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Structural Genomics Consortium, Gräslund S, Nordlund P, Weigelt J, Bray J, Gileadi O, Knapp S, Oppermann U, Arrowsmith C, Hui R, Ming J, dhe-Paganon S, Park HW, Savchenko A, Yee A, Edwards A,

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Nature methods 5(2):135-46, 2008 Feb - Who cited this? | PubMed ID: 18235434 | Fulltext

Crystallographic conformers of actin in a biologically active bundle of filaments.

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Cong Y, Topf M, Sali A, Matsudaira P, Dougherty M, Chiu W, and Schmid MF

Journal of molecular biology 375(2):331-6, 2008 Jan 11 - Who cited this? | PubMed ID: 18022194 | Fulltext

Prediction of enzyme function by combining sequence similarity and protein interactions.

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Espadaler J, Eswar N, Querol E, Avilés FX, Sali A, Marti-Renom MA, and Oliva B

BMC bioinformatics 9:249, 2008 - Who cited this? | PubMed ID: 18505562 | Fulltext

Protein Structure Modeling with MODELLER.

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Eswar N, Eramian D, Webb B, Shen MY, and Sali A

Methods in molecular biology (Clifton, N.J.) 426:145-59, 2008 - Who cited this? | PubMed ID: 18542861 | Fulltext

Classifying Variants of Undetermined Significance in BRCA2 with Protein Likelihood Ratios.

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Karchin R, Agarwal M, Sali A, Couch F, and Beattie MS

Cancer informatics 6:203-16, 2008 - Who cited this? | PubMed ID: 19043619 | Fulltext

The molecular sociology of the cell.

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Robinson CV, Sali A, and Baumeister W

Nature 450(7172):973, 2007 Dec 13 - Who cited this? | PubMed ID: 18075576 | Fulltext

Host pathogen protein interactions predicted by comparative modeling.

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Davis FP, Barkan DT, Eswar N, McKerrow JH, and Sali A

Protein science : a publication of the Protein Society 16(12):2585-96, 2007 Dec - Who cited this? | PubMed ID: 17965183 | Fulltext

Stereochemical criteria for prediction of the effects of proline mutations on protein stability.

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Bajaj K, Madhusudhan MS, Adkar BV, Chakrabarti P, Ramakrishnan C, Sali A, and Varadarajan R

PLoS computational biology 3(12):e241, 2007 Dec - Who cited this? | PubMed ID: 18069886 | Fulltext

Determining the architectures of macromolecular assemblies.

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Alber F, Dokudovskaya S, Veenhoff LM, Zhang W, Kipper J, Devos D, Suprapto A, Karni-Schmidt O, Williams R, Chait BT, Rout MP, and Sali A

Nature 450(7170):683, 2007 Nov 29 - Who cited this? | PubMed ID: 18046405 | Fulltext

The molecular architecture of the nuclear pore complex.

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Alber F, Dokudovskaya S, Veenhoff LM, Zhang W, Kipper J, Devos D, Suprapto A, Karni-Schmidt O, Williams R, Chait BT, Sali A, and Rout MP

Nature 450(7170):695, 2007 Nov 29 - Who cited this? | PubMed ID: 18046406 | Fulltext

Fold assessment for comparative protein structure modeling.

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Melo F and Sali A

Protein science : a publication of the Protein Society 16(11):2412-26, 2007 Nov - Who cited this? | PubMed ID: 17905832 | Fulltext

Structural genomics.

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Sali A, Lima CD, and Kostic M

Structure (London, England : 1993) 15(11):1341, 2007 Nov - Who cited this? | PubMed ID: 17997955 | Fulltext

Comparative Protein Structure Modeling Using MODELLER.

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Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, and Sali A

Current protocols in protein science / editorial board, John E. Coligan ... [et al.] Chapter 2:Unit2.9, 2007 Nov - Who cited this? | PubMed ID: 18429317 | Fulltext

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