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Andrej Sali
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26
Eswar, Narayanan
22
Marti-Renom, Marc
19
Pieper, Ursula
18
Madhusudhan, Mallur
18
Fiser, András
11
Blundell, Tom
10
Stevens, Richard
10
Topf, Maya
9
Krilis, Steven
9
Davis, Fred
8
Burley, Stephen
8
Alber, Frank
8
Kelly, Libusha
7
Ilyin, Valentin
7
Chiu, Wah
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All Publications
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2009: Madhusudhan M S; Webb Benjamin M; Marti-Renom Marc A; Eswar Narayanan; Sali Andrej
Alignment of multiple protein structures based on sequence and structure features.
Protein engineering, design & selection : PEDS 2009;22(9):569-74.
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2009: Pieper Ursula; Chiang Ranyee; Seffernick Jennifer J; Brown Shoshana D; Glasner Margaret E; Kelly Libusha; Eswar Narayanan; Sauder J Michael; Bonanno Jeffrey B; Swaminathan Subramanyam; Burley Stephen K; Zheng Xiaojing; Chance Mark R; Almo Steven C; Gerlt John A; Raushel Frank M; Jacobson Matthew P; Babbitt Patricia C; Sali Andrej
Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies.
Journal of structural and functional genomics 2009;10(2):107-25.
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2009: Li Min; Hays Franklin A; Roe-Zurz Zygy; Vuong Linda; Kelly Libusha; Ho Chi-Min; Robbins Renée M; Pieper Ursula; O'Connell Joseph D; Miercke Larry J W; Giacomini Kathleen M; Sali Andrej; Stroud Robert M
Selecting optimum eukaryotic integral membrane proteins for structure determination by rapid expression and solubilization screening.
Journal of molecular biology 2009;385(3):820-30.
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2008: Agüero Fernán; Al-Lazikani Bissan; Aslett Martin; Berriman Matthew; Buckner Frederick S; Campbell Robert K; Carmona Santiago; Carruthers Ian M; Chan A W Edith; Chen Feng; Crowther Gregory J; Doyle Maria A; Hertz-Fowler Christiane; Hopkins Andrew L; McAllister Gregg; Nwaka Solomon; Overington John P; Pain Arnab; Paolini Gaia V; Pieper Ursula; Ralph Stuart A; Riechers Aaron; Roos David S; Sali Andrej; Shanmugam Dhanasekaran; Suzuki Takashi; Van Voorhis Wesley C; Verlinde Christophe L M J
Genomic-scale prioritization of drug targets: the TDR Targets database.
Nature reviews. Drug discovery 2008;7(11):900-7.
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2008: Eramian David; Eswar Narayanan; Shen Min-Yi; Sali Andrej
How well can the accuracy of comparative protein structure models be predicted?
Protein science : a publication of the Protein Society 2008;17(11):1881-93.
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2008: Förster Friedrich; Webb Benjamin; Krukenberg Kristin A; Tsuruta Hiro; Agard David A; Sali Andrej
Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies.
Journal of molecular biology 2008;382(4):1089-106.
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2008: Mahrus Sami; Trinidad Jonathan C; Barkan David T; Sali Andrej; Burlingame Alma L; Wells James A
Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini.
Cell 2008;134(5):866-76.
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2008: Serysheva Irina I; Ludtke Steven J; Baker Matthew L; Cong Yao; Topf Maya; Eramian David; Sali Andrej; Hamilton Susan L; Chiu Wah
Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(28):9610-5.
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2008: Booth Christopher R; Meyer Anne S; Cong Yao; Topf Maya; Sali Andrej; Ludtke Steven J; Chiu Wah; Frydman Judith
Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT.
Nature structural & molecular biology 2008;15(7):746-53.
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2008: Krukenberg Kristin A; Förster Friedrich; Rice Luke M; Sali Andrej; Agard David A
Multiple conformations of E. coli Hsp90 in solution: insights into the conformational dynamics of Hsp90.
Structure (London, England : 1993) 2008;16(5):755-65.
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2008: Chandramouli Preethi; Topf Maya; Ménétret Jean-François; Eswar Narayanan; Cannone Jamie J; Gutell Robin R; Sali Andrej; Akey Christopher W
Structure of the mammalian 80S ribosome at 8.7 A resolution.
Structure (London, England : 1993) 2008;16(4):535-48.
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2008: Anderson Carol M; Korkin Dmitry; Smith Dana L; Makovets Svetlana; Seidel Jeffrey J; Sali Andrej; Blackburn Elizabeth H
Tel2 mediates activation and localization of ATM/Tel1 kinase to a double-strand break.
Genes & development 2008;22(7):854-9.
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2008: Topf Maya; Lasker Keren; Webb Ben; Wolfson Haim; Chiu Wah; Sali Andrej
Protein structure fitting and refinement guided by cryo-EM density.
Structure (London, England : 1993) 2008;16(2):295-307.
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2008: Cong Yao; Topf Maya; Sali Andrej; Matsudaira Paul; Dougherty Matthew; Chiu Wah; Schmid Michael F
Crystallographic conformers of actin in a biologically active bundle of filaments.
Journal of molecular biology 2008;375(2):331-6.
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2008: Chiang Ranyee A; Sali Andrej; Babbitt Patricia C
Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies.
PLoS computational biology 2008;4(8):e1000142.
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2008: Eswar Narayanan; Eramian David; Webb Ben; Shen Min-Yi; Sali Andrej
Protein structure modeling with MODELLER.
Methods in molecular biology (Clifton, N.J.) 2008;426():145-59.
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2008: Espadaler Jordi; Eswar Narayanan; Querol Enrique; Avilés Francesc X; Sali Andrej; Marti-Renom Marc A; Oliva Baldomero
Prediction of enzyme function by combining sequence similarity and protein interactions.
BMC bioinformatics 2008;9():249.
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2008: Alber Frank; Förster Friedrich; Korkin Dmitry; Topf Maya; Sali Andrej
Integrating diverse data for structure determination of macromolecular assemblies.
Annual review of biochemistry 2008;77():443-77.
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2007: Robinson Carol V; Sali Andrej; Baumeister Wolfgang
The molecular sociology of the cell.
Nature 2007;450(7172):973-82.
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2007: Bajaj Kanika; Madhusudhan M S; Adkar Bharat V; Chakrabarti Purbani; Ramakrishnan C; Sali Andrej; Varadarajan Raghavan
Stereochemical criteria for prediction of the effects of proline mutations on protein stability.
PLoS computational biology 2007;3(12):e241.
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2007: Davis Fred P; Barkan David T; Eswar Narayanan; McKerrow James H; Sali Andrej
Host pathogen protein interactions predicted by comparative modeling.
Protein science : a publication of the Protein Society 2007;16(12):2585-96.
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2007: Eswar Narayanan; Webb Ben; Marti-Renom Marc A; Madhusudhan M S; Eramian David; Shen Min-Yi; Pieper Ursula; Sali Andrej
Comparative protein structure modeling using MODELLER.
Current protocols in protein science / editorial board, John E. Coligan ... [et al.] 2007;Chapter 2():Unit 2.9.
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2007: Alber Frank; Dokudovskaya Svetlana; Veenhoff Liesbeth M; Zhang Wenzhu; Kipper Julia; Devos Damien; Suprapto Adisetyantari; Karni-Schmidt Orit; Williams Rosemary; Chait Brian T; Sali Andrej; Rout Michael P
The molecular architecture of the nuclear pore complex.
Nature 2007;450(7170):695-701.
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2007: Alber Frank; Dokudovskaya Svetlana; Veenhoff Liesbeth M; Zhang Wenzhu; Kipper Julia; Devos Damien; Suprapto Adisetyantari; Karni-Schmidt Orit; Williams Rosemary; Chait Brian T; Rout Michael P; Sali Andrej
Determining the architectures of macromolecular assemblies.
Nature 2007;450(7170):683-94.
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2007: Sali Andrej; Lima Christopher D; Kostic Milka
Structural genomics.
Structure (London, England : 1993) 2007;15(11):1341.
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2007: Melo Francisco; Sali Andrej
Fold assessment for comparative protein structure modeling.
Protein science : a publication of the Protein Society 2007;16(11):2412-26.
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2007: Almo Steven C; Bonanno Jeffrey B; Sauder J Michael; Emtage Spencer; Dilorenzo Teresa P; Malashkevich Vladimir; Wasserman Steven R; Swaminathan S; Eswaramoorthy Subramaniam; Agarwal Rakhi; Kumaran Desigan; Madegowda Mahendra; Ragumani Sugadev; Patskovsky Yury; Alvarado Johnjeff; Ramagopal Udupi A; Faber-Barata Joana; Chance Mark R; Sali Andrej; Fiser Andras; Zhang Zhong-yin; Lawrence David S; Burley Stephen K
Structural genomics of protein phosphatases.
Journal of structural and functional genomics 2007;8(2-3):121-40.
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2007: Aragues Ramon; Sali Andrej; Bonet Jaume; Marti-Renom Marc A; Oliva Baldo
Characterization of protein hubs by inferring interacting motifs from protein interactions.
PLoS computational biology 2007;3(9):1761-71.
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2007: Feyfant Eric; Sali Andrej; Fiser András
Modeling mutations in protein structures.
Protein science : a publication of the Protein Society 2007;16(9):2030-41.
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2007: Marti-Renom Marc A; Pieper Ursula; Madhusudhan M S; Rossi Andrea; Eswar Narayanan; Davis Fred P; Al-Shahrour Fátima; Dopazo Joaquín; Sali Andrej
DBAli tools: mining the protein structure space.
Nucleic acids research 2007;35(Web Server issue):W393-7.
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2007: Wang Stephanie X; Pandey Kailash C; Scharfstein Julio; Whisstock James; Huang Rick K; Jacobelli Jordan; Fletterick Robert J; Rosenthal Philip J; Abrahamson Magnus; Brinen Linda S; Rossi Andrea; Sali Andrej; McKerrow James H
The structure of chagasin in complex with a cysteine protease clarifies the binding mode and evolution of an inhibitor family.
Structure (London, England : 1993) 2007;15(5):535-43.
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2007: Soranzo Nicole; Kelly Libusha; Martinian Lillian; Burley Mari-Wyn; Thom Maria; Sali Andrej; Kroetz Deanna L; Goldstein David B; Sisodiya Sanjay M
Lack of support for a role for RLIP76 (RALBP1) in response to treatment or predisposition to epilepsy.
Epilepsia 2007;48(4):674-83.
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2007: Winn Virginia D; Haimov-Kochman Ronit; Paquet Agnes C; Yang Y Jean; Madhusudhan M S; Gormley Matthew; Feng Kui-Tzu V; Bernlohr David A; McDonagh Susan; Pereira Lenore; Sali Andrej; Fisher Susan J
Gene expression profiling of the human maternal-fetal interface reveals dramatic changes between midgestation and term.
Endocrinology 2007;148(3):1059-79.
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2007: Carvalho Marcelo A; Marsillac Sylvia M; Karchin Rachel; Manoukian Siranoush; Grist Scott; Swaby Ramona F; Urmenyi Turan P; Rondinelli Edson; Silva Rosane; Gayol Luis; Baumbach Lisa; Sutphen Rebecca; Pickard-Brzosowicz Jennifer L; Nathanson Katherine L; Sali Andrej; Goldgar David; Couch Fergus J; Radice Paolo; Monteiro Alvaro N A
Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis.
Cancer research 2007;67(4):1494-501.
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2007: Karchin Rachel; Monteiro Alvaro N A; Tavtigian Sean V; Carvalho Marcelo A; Sali Andrej
Functional impact of missense variants in BRCA1 predicted by supervised learning.
PLoS computational biology 2007;3(2):e26.
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2007: Kelly Libusha; Karchin Rachel; Sali Andrej
Protein interactions and disease phenotypes in the ABC transporter superfamily.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2007;():51-63.
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2007: Marti-Renom Marc A; Rossi Andrea; Al-Shahrour Fátima; Davis Fred P; Pieper Ursula; Dopazo Joaquín; Sali Andrej
The AnnoLite and AnnoLyze programs for comparative annotation of protein structures.
BMC bioinformatics 2007;8 Suppl 4():S4.
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2006: Korkin Dmitry; Davis Fred P; Alber Frank; Luong Tinh; Shen Min-Yi; Lucic Vladan; Kennedy Mary B; Sali Andrej
Structural modeling of protein interactions by analogy: application to PSD-95.
PLoS computational biology 2006;2(11):e153.
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2006: Shen Min-Yi; Sali Andrej
Statistical potential for assessment and prediction of protein structures.
Protein science : a publication of the Protein Society 2006;15(11):2507-24.
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2006: Colubri Andrés; Jha Abhishek K; Shen Min-Yi; Sali Andrej; Berry R Stephen; Sosnick Tobin R; Freed Karl F
Minimalist representations and the importance of nearest neighbor effects in protein folding simulations.
Journal of molecular biology 2006;363(4):835-57.
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2006: Eswar Narayanan; Webb Ben; Marti-Renom Marc A; Madhusudhan M S; Eramian David; Shen Min-Yi; Pieper Ursula; Sali Andrej
Comparative protein structure modeling using Modeller.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 2006;Chapter 5():Unit 5.6.
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2006: Rossi Andrea; Marti-Renom Marc A; Sali Andrej
Localization of binding sites in protein structures by optimization of a composite scoring function.
Protein science : a publication of the Protein Society 2006;15(10):2366-80.
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2006: Berman Helen M; Burley Stephen K; Chiu Wah; Sali Andrej; Adzhubei Alexei; Bourne Philip E; Bryant Stephen H; Dunbrack Roland L; Fidelis Krzysztof; Frank Joachim; Godzik Adam; Henrick Kim; Joachimiak Andrzej; Heymann Bernard; Jones David; Markley John L; Moult John; Montelione Gaetano T; Orengo Christine; Rossmann Michael G; Rost Burkhard; Saibil Helen; Schwede Torsten; Standley Daron M; Westbrook John D
Outcome of a workshop on archiving structural models of biological macromolecules.
Structure (London, England : 1993) 2006;14(8):1211-7.
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2006: Eramian David; Shen Min-yi; Devos Damien; Melo Francisco; Sali Andrej; Marti-Renom Marc A
A composite score for predicting errors in protein structure models.
Protein science : a publication of the Protein Society 2006;15(7):1653-66.
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2006: Dokudovskaya Svetlana; Williams Rosemary; Devos Damien; Sali Andrej; Chait Brian T; Rout Michael P
Protease accessibility laddering: a proteomic tool for probing protein structure.
Structure (London, England : 1993) 2006;14(4):653-60.
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2006: Topf Maya; Baker Matthew L; Marti-Renom Marc A; Chiu Wah; Sali Andrej
Refinement of protein structures by iterative comparative modeling and CryoEM density fitting.
Journal of molecular biology 2006;357(5):1655-68.
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2006: Nguyen Tan D; Gow Jason M; Chinn Leslie W; Kelly Libusha; Jeong Hotcherl; Huang Conrad C; Stryke Doug; Kawamoto Michiko; Johns Susan J; Carlson Elaine; Taylor Travis; Ferrin Thomas E; Sali Andrej; Giacomini Kathleen M; Kroetz Deanna L
PharmGKB submission update: IV. PMT submissions of genetic variations in ATP-Binding cassette transporters to the PharmGKB network.
Pharmacological reviews 2006;58(1):1-2.
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2006: Madhusudhan M S; Marti-Renom Marc A; Sanchez Roberto; Sali Andrej
Variable gap penalty for protein sequence-structure alignment.
Protein engineering, design & selection : PEDS 2006;19(3):129-33.
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2006: Devos Damien; Dokudovskaya Svetlana; Williams Rosemary; Alber Frank; Eswar Narayanan; Chait Brian T; Rout Michael P; Sali Andrej
Simple fold composition and modular architecture of the nuclear pore complex.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(7):2172-7.
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2006: Pieper Ursula; Eswar Narayanan; Davis Fred P; Braberg Hannes; Madhusudhan M S; Rossi Andrea; Marti-Renom Marc; Karchin Rachel; Webb Ben M; Eramian David; Shen Min-Yi; Kelly Libusha; Melo Francisco; Sali Andrej
MODBASE: a database of annotated comparative protein structure models and associated resources.
Nucleic acids research 2006;34(Database issue):D291-5.
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2006: Davis Fred P; Braberg Hannes; Shen Min-Yi; Pieper Ursula; Sali Andrej; Madhusudhan M S
Protein complex compositions predicted by structural similarity.
Nucleic acids research 2006;34(10):2943-52.
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2005: McMahon Stephen A; Miller Jason L; Lawton Jeffrey A; Kerkow Donald E; Hodes Asher; Marti-Renom Marc A; Doulatov Sergei; Narayanan Eswar; Sali Andrej; Miller Jeff F; Ghosh Partho
The C-type lectin fold as an evolutionary solution for massive sequence variation.
Nature structural & molecular biology 2005;12(10):886-92.
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2005: Topf Maya; Sali Andrej
Combining electron microscopy and comparative protein structure modeling.
Current opinion in structural biology 2005;15(5):578-85.
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2005: Korkin Dmitry; Davis Fred P; Sali Andrej
Localization of protein-binding sites within families of proteins.
Protein science : a publication of the Protein Society 2005;14(9):2350-60.
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2005: Dvorák Jan; Delcroix Melaine; Rossi Andrea; Vopálenský Václav; Pospísek Martin; Sedinová Miroslava; Mikes Libor; Sajid Mohammed; Sali Andrej; McKerrow James H; Horák Petr; Caffrey Conor R
Multiple cathepsin B isoforms in schistosomula of Trichobilharzia regenti: identification, characterisation and putative role in migration and nutrition.
International journal for parasitology 2005;35(8):895-910.
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2005: Karchin Rachel; Diekhans Mark; Kelly Libusha; Thomas Daryl J; Pieper Ursula; Eswar Narayanan; Haussler David; Sali Andrej
LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources.
Bioinformatics (Oxford, England) 2005;21(12):2814-20.
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2005: Espadaler Jordi; Aragüés Ramón; Eswar Narayanan; Marti-Renom Marc A; Querol Enrique; Avilés Francesc X; Sali Andrej; Oliva Baldomero
Detecting remotely related proteins by their interactions and sequence similarity.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(20):7151-6.
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2005: Yasuda Shinsuke; Morokawa Nasa; Wong G William; Rossi Andrea; Madhusudhan Mallur S; Sali Andrej; Askew Yuko S; Adachi Roberto; Silverman Gary A; Krilis Steven A; Stevens Richard L
Urokinase-type plasminogen activator is a preferred substrate of the human epithelium serine protease tryptase epsilon/PRSS22.
Blood 2005;105(10):3893-901.
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2005: Davis Fred P; Sali Andrej
PIBASE: a comprehensive database of structurally defined protein interfaces.
Bioinformatics (Oxford, England) 2005;21(9):1901-7.
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2005: Alber Frank; Kim Michael F; Sali Andrej
Structural characterization of assemblies from overall shape and subcomplex compositions.
Structure (London, England : 1993) 2005;13(3):435-45.
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2005: Topf Maya; Baker Matthew L; John Bino; Chiu Wah; Sali Andrej
Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy.
Journal of structural biology 2005;149(2):191-203.
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2005: Bonanno Jeffrey B; Almo Steven C; Bresnick Anne; Chance Mark R; Fiser Andras; Swaminathan S; Jiang J; Studier F William; Shapiro Lawrence; Lima Christopher D; Gaasterland Theresa M; Sali Andrej; Bain Kevin; Feil Ingeborg; Gao Xia; Lorimer Don; Ramos Aurora; Sauder J Michael; Wasserman Steven R; Emtage Spencer; D'Amico Kevin L; Burley Stephen K
New York-Structural GenomiX Research Consortium (NYSGXRC): a large scale center for the protein structure initiative.
Journal of structural and functional genomics 2005;6(2-3):225-32.
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2005: Karchin R; Kelly L; Sali A
Improving functional annotation of non-synonomous SNPs with information theory.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2005;():397-408.
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2004: Maurer Stephen M; Rai Arti; Sali Andrej
Finding cures for tropical diseases: is open source an answer?
PLoS medicine 2004;1(3):e56.
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2004: Devos Damien; Dokudovskaya Svetlana; Alber Frank; Williams Rosemary; Chait Brian T; Sali Andrej; Rout Michael P
Components of coated vesicles and nuclear pore complexes share a common molecular architecture.
PLoS biology 2004;2(12):e380.
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2004: Chance Mark R; Fiser Andras; Sali Andrej; Pieper Ursula; Eswar Narayanan; Xu Guiping; Fajardo J Eduardo; Radhakannan Thirumuruhan; Marinkovic Nebojsa
High-throughput computational and experimental techniques in structural genomics.
Genome research 2004;14(10B):2145-54.
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2004: Russell Robert B; Alber Frank; Aloy Patrick; Davis Fred P; Korkin Dmitry; Pichaud Matthieu; Topf Maya; Sali Andrej
A structural perspective on protein-protein interactions.
Current opinion in structural biology 2004;14(3):313-24.
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2004: Mirkovic Nebojsa; Marti-Renom Marc A; Weber Barbara L; Sali Andrej; Monteiro Alvaro N A
Structure-based assessment of missense mutations in human BRCA1: implications for breast and ovarian cancer predisposition.
Cancer research 2004;64(11):3790-7.
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2004: Rossi Andrea; Deveraux Quinn; Turk Boris; Sali Andrej
Comprehensive search for cysteine cathepsins in the human genome.
Biological chemistry 2004;385(5):363-72.
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2004: Marti-Renom Marc A; Madhusudhan M S; Sali Andrej
Alignment of protein sequences by their profiles.
Protein science : a publication of the Protein Society 2004;13(4):1071-87.
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2004: John Bino; Sali Andrej
Detection of homologous proteins by an intermediate sequence search.
Protein science : a publication of the Protein Society 2004;13(1):54-62.
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2004: Pieper Ursula; Eswar Narayanan; Braberg Hannes; Madhusudhan M S; Davis Fred P; Stuart Ashley C; Mirkovic Nebojsa; Rossi Andrea; Marti-Renom Marc A; Fiser Andras; Webb Ben; Greenblatt Daniel; Huang Conrad C; Ferrin Thomas E; Sali Andrej
MODBASE, a database of annotated comparative protein structure models, and associated resources.
Nucleic acids research 2004;32(Database issue):D217-22.
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2003: Fiser András; Sali Andrej
ModLoop: automated modeling of loops in protein structures.
Bioinformatics (Oxford, England) 2003;19(18):2500-1.
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2003: Sali Andrej
NIH workshop on structural proteomics of biological complexes.
Structure (London, England : 1993) 2003;11(9):1043-7.
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2003: John Bino; Sali Andrej
Comparative protein structure modeling by iterative alignment, model building and model assessment.
Nucleic acids research 2003;31(14):3982-92.
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2003: Eswar Narayanan; John Bino; Mirkovic Nebojsa; Fiser Andras; Ilyin Valentin A; Pieper Ursula; Stuart Ashley C; Marti-Renom Marc A; Madhusudhan M S; Yerkovich Bozidar; Sali Andrej
Tools for comparative protein structure modeling and analysis.
Nucleic acids research 2003;31(13):3375-80.
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2003: Koh Ingrid Y Y; Eyrich Volker A; Marti-Renom Marc A; Przybylski Dariusz; Madhusudhan Mallur S; Eswar Narayanan; Graña Osvaldo; Pazos Florencio; Valencia Alfonso; Sali Andrej; Rost Burkhard
EVA: Evaluation of protein structure prediction servers.
Nucleic acids research 2003;31(13):3311-5.
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2003: Gao Haixiao; Sengupta Jayati; Valle Mikel; Korostelev Andrei; Eswar Narayanan; Stagg Scott M; Van Roey Patrick; Agrawal Rajendra K; Harvey Stephen C; Sali Andrej; Chapman Michael S; Frank Joachim
Study of the structural dynamics of the E coli 70S ribosome using real-space refinement.
Cell 2003;113(6):789-801.
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2003: Lee Susie A; Shen Ellen L; Fiser Andras; Sali Andrej; Guo Su
The zebrafish forkhead transcription factor Foxi1 specifies epibranchial placode-derived sensory neurons.
Development (Cambridge, England) 2003;130(12):2669-79.
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2003: Sali Andrej; Glaeser Robert; Earnest Thomas; Baumeister Wolfgang
From words to literature in structural proteomics.
Nature 2003;422(6928):216-25.
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2003: Ilyin Valentin A; Pieper Ursula; Stuart Ashley C; Marti-Renom Marc A; McMahan Linda; Sali Andrej
ModView, visualization of multiple protein sequences and structures.
Bioinformatics (Oxford, England) 2003;19(1):165-6.
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2003: Fiser András; Sali Andrej
Modeller: generation and refinement of homology-based protein structure models.
Methods in enzymology 2003;374():461-91.
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2002: Iverson G Michael; Reddel Stephen; Victoria Edward J; Cockerill Keith A; Wang Ying-Xia; Marti-Renom Marc A; Sali Andrej; Marquis David M; Krilis Steven A; Linnik Matthew D
Use of single point mutations in domain I of beta 2-glycoprotein I to determine fine antigenic specificity of antiphospholipid autoantibodies.
Journal of immunology (Baltimore, Md. : 1950) 2002;169(12):7097-103.
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2002: Yang Yi; Li Lixin; Wong Guang W; Krilis Steven A; Madhusudhan M S; Sali Andrej; Stevens Richard L
RasGRP4, a new mast cell-restricted Ras guanine nucleotide-releasing protein with calcium- and diacylglycerol-binding motifs. Identification of defective variants of this signaling protein in asthma, mastocytosis, and mast cell leukemia patients and demonstration of the importance of RasGRP4 in mast cell development and function.
The Journal of biological chemistry 2002;277(28):25756-74.
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2002: Fiser András; Feig Michael; Brooks Charles L; Sali Andrej
Evolution and physics in comparative protein structure modeling.
Accounts of chemical research 2002;35(6):413-21.
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2002: Vernal Javier; Fiser András; Sali Andrej; Müller Miklós; Cazzulo Juan José; Nowicki Cristina
Probing the specificity of a trypanosomal aromatic alpha-hydroxy acid dehydrogenase by site-directed mutagenesis.
Biochemical and biophysical research communications 2002;293(1):633-9.
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2002: Chance Mark R; Bresnick Anne R; Burley Stephen K; Jiang Jian-Sheng; Lima Christopher D; Sali Andrej; Almo Steven C; Bonanno Jeffrey B; Buglino John A; Boulton Simon; Chen Hua; Eswar Narayanan; He Guoshun; Huang Raymond; Ilyin Valentin; McMahan Linda; Pieper Ursula; Ray Soumya; Vidal Marc; Wang Li Kai
Structural genomics: a pipeline for providing structures for the biologist.
Protein science : a publication of the Protein Society 2002;11(4):723-38.
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2002: Marti-Renom Marc A; Madhusudhan M S; Fiser András; Rost Burkhard; Sali Andrej
Reliability of assessment of protein structure prediction methods.
Structure (London, England : 1993) 2002;10(3):435-40.
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2002: Melo Francisco; Sánchez Roberto; Sali Andrej
Statistical potentials for fold assessment.
Protein science : a publication of the Protein Society 2002;11(2):430-48.
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2002: Stuart Ashley C; Ilyin Valentin A; Sali Andrej
LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures.
Bioinformatics (Oxford, England) 2002;18(1):200-1.
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2002: Pieper Ursula; Eswar Narayanan; Stuart Ashley C; Ilyin Valentin A; Sali Andrej
MODBASE, a database of annotated comparative protein structure models.
Nucleic acids research 2002;30(1):255-9.
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2001: Eyrich V A; Martí-Renom M A; Przybylski D; Madhusudhan M S; Fiser A; Pazos F; Valencia A; Sali A; Rost B
EVA: continuous automatic evaluation of protein structure prediction servers.
Bioinformatics (Oxford, England) 2001;17(12):1242-3.
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2001: Wong G W; Yasuda S; Madhusudhan M S; Li L; Yang Y; Krilis S A; Sali A; Stevens R L
Human tryptase epsilon (PRSS22), a new member of the chromosome 16p13.3 family of human serine proteases expressed in airway epithelial cells.
The Journal of biological chemistry 2001;276(52):49169-82.
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2001: Spahn C M; Beckmann R; Eswar N; Penczek P A; Sali A; Blobel G; Frank J
Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions.
Cell 2001;107(3):373-86.
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2001: Beckmann R; Spahn C M; Eswar N; Helmers J; Penczek P A; Sali A; Frank J; Blobel G
Architecture of the protein-conducting channel associated with the translating 80S ribosome.
Cell 2001;107(3):361-72.
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2001: Bonanno J B; Edo C; Eswar N; Pieper U; Romanowski M J; Ilyin V; Gerchman S E; Kycia H; Studier F W; Sali A; Burley S K
Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(23):12896-901.
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2001: Baker D; Sali A
Protein structure prediction and structural genomics.
Science (New York, N.Y.) 2001;294(5540):93-6.
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2001: Martí-Renom M A; Ilyin V A; Sali A
DBAli: a database of protein structure alignments.
Bioinformatics (Oxford, England) 2001;17(8):746-7.
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2001: Sali A
Target practice.
Nature structural biology 2001;8(6):482-4.
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2001: Wong G W; Li L; Madhusudhan M S; Krilis S A; Gurish M F; Rothenberg M E; Sali A; Stevens R L
Tryptase 4, a new member of the chromosome 17 family of mouse serine proteases.
The Journal of biological chemistry 2001;276(23):20648-58.
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2001: Barrientos L G; Campos-Olivas R; Louis J M; Fiser A; Sali A; Gronenborn A M
1H, 13C, 15N resonance assignments and fold verification of a circular permuted variant of the potent HIV-inactivating protein cyanovirin-N.
Journal of biomolecular NMR 2001;19(3):289-90.
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2001: Gopal S; Schroeder M; Pieper U; Sczyrba A; Aytekin-Kurban G; Bekiranov S; Fajardo J E; Eswar N; Sanchez R; Sali A; Gaasterland T
Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome.
Nature genetics 2001;27(3):337-40.
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2000: Groft C M; Beckmann R; Sali A; Burley S K
Crystal structures of ribosome anti-association factor IF6.
Nature structural biology 2000;7(12):1156-64.
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2000: Sánchez R; Pieper U; Melo F; Eswar N; Martí-Renom M A; Madhusudhan M S; Mirkovic N; Sali A
Protein structure modeling for structural genomics.
Nature structural biology 2000;7 Suppl():986-90.
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2000: Liedtke W; Choe Y; Martí-Renom M A; Bell A M; Denis C S; Sali A; Hudspeth A J; Friedman J M; Heller S
Vanilloid receptor-related osmotically activated channel (VR-OAC), a candidate vertebrate osmoreceptor.
Cell 2000;103(3):525-35.
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2000: Fiser A; Do R K; Sali A
Modeling of loops in protein structures.
Protein science : a publication of the Protein Society 2000;9(9):1753-73.
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2000: Wu G; McArthur A G; Fiser A; Sali A; Sogin M L; Mllerm M
Core histones of the amitochondriate protist, Giardia lamblia.
Molecular biology and evolution 2000;17(8):1156-63.
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2000: Dinner A R; Sali A; Smith L J; Dobson C M; Karplus M
Understanding protein folding via free-energy surfaces from theory and experiment.
Trends in biochemical sciences 2000;25(7):331-9.
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2000: Jin S; Martinek S; Joo W S; Wortman J R; Mirkovic N; Sali A; Yandell M D; Pavletich N P; Young M W; Levine A J
Identification and characterization of a p53 homologue in Drosophila melanogaster.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(13):7301-6.
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2000: Huang C; Morales G; Vagi A; Chanasyk K; Ferrazzi M; Burklow C; Qiu W T; Feyfant E; Sali A; Stevens R L
Formation of enzymatically active, homotypic, and heterotypic tetramers of mouse mast cell tryptases. Dependence on a conserved Trp-rich domain on the surface.
The Journal of biological chemistry 2000;275(1):351-8.
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2000: Sánchez R; Pieper U; Mirkovic N; de Bakker P I; Wittenstein E; Sali A
MODBASE, a database of annotated comparative protein structure models.
Nucleic acids research 2000;28(1):250-3.
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2000: Sánchez R; Sali A
Comparative protein structure modeling. Introduction and practical examples with modeller.
Methods in molecular biology (Clifton, N.J.) 2000;143():97-129.
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2000: Martí-Renom M A; Stuart A C; Fiser A; Sánchez R; Melo F; Sali A
Comparative protein structure modeling of genes and genomes.
Annual review of biophysics and biomolecular structure 2000;29():291-325.
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1999: Sánchez R; Sali A
ModBase: a database of comparative protein structure models.
Bioinformatics (Oxford, England) 1999;15(12):1060-1.
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1999: Sali A; Kuriyan J
Challenges at the frontiers of structural biology.
Trends in cell biology 1999;9(12):M20-4.
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1999: Sali A
Functional links between proteins.
Nature 1999;402(6757):23, 25-6.
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1999: Wong G W; Tang Y; Feyfant E; Sali A; Li L; Li Y; Huang C; Friend D S; Krilis S A; Stevens R L
Identification of a new member of the tryptase family of mouse and human mast cell proteases which possesses a novel COOH-terminal hydrophobic extension.
The Journal of biological chemistry 1999;274(43):30784-93.
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1999: Burley S K; Almo S C; Bonanno J B; Capel M; Chance M R; Gaasterland T; Lin D; Sali A; Studier F W; Swaminathan S
Structural genomics: beyond the human genome project.
Nature genetics 1999;23(2):151-7.
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1999: Nagata T; Gupta V; Sorce D; Kim W Y; Sali A; Chait B T; Shigesada K; Ito Y; Werner M H
Immunoglobulin motif DNA recognition and heterodimerization of the PEBP2/CBF Runt domain.
Nature structural biology 1999;6(7):615-9.
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1999: Miwa J M; Ibanez-Tallon I; Crabtree G W; Sánchez R; Sali A; Role L W; Heintz N
lynx1, an endogenous toxin-like modulator of nicotinic acetylcholine receptors in the mammalian CNS.
Neuron 1999;23(1):105-14.
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1999: Wu G; Fiser A; ter Kuile B; Sali A; Müller M
Convergent evolution of Trichomonas vaginalis lactate dehydrogenase from malate dehydrogenase.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(11):6285-90.
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1998: Sali A
100,000 protein structures for the biologist.
Nature structural biology 1998;5(12):1029-32.
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1998: Sánchez R; Sali A
Large-scale protein structure modeling of the Saccharomyces cerevisiae genome.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(23):13597-602.
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1998: Wolf E; Vassilev A; Makino Y; Sali A; Nakatani Y; Burley S K
Crystal structure of a GCN5-related N-acetyltransferase: Serratia marcescens aminoglycoside 3-N-acetyltransferase.
Cell 1998;94(4):439-49.
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1998: Huang C; Sali A; Stevens R L
Regulation and function of mast cell proteases in inflammation.
Journal of clinical immunology 1998;18(3):169-83.
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1998: Kandiah D A; Sali A; Sheng Y; Victoria E J; Marquis D M; Coutts S M; Krilis S A
Current insights into the "antiphospholipid" syndrome: clinical, immunological, and molecular aspects.
Advances in immunology 1998;70():507-63.
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1997: Huang C; Wong G W; Ghildyal N; Gurish M F; Sali A; Matsumoto R; Qiu W T; Stevens R L
The tryptase, mouse mast cell protease 7, exhibits anticoagulant activity in vivo and in vitro due to its ability to degrade fibrinogen in the presence of the diverse array of protease inhibitors in plasma.
The Journal of biological chemistry 1997;272(50):31885-93.
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1997: Hunt J E; Friend D S; Gurish M F; Feyfant E; Sali A; Huang C; Ghildyal N; Stechschulte S; Austen K F; Stevens R L
Mouse mast cell protease 9, a novel member of the chromosome 14 family of serine proteases that is selectively expressed in uterine mast cells.
The Journal of biological chemistry 1997;272(46):29158-66.
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1997: Guenther B; Onrust R; Sali A; O'Donnell M; Kuriyan J
Crystal structure of the delta' subunit of the clamp-loader complex of E. coli DNA polymerase III.
Cell 1997;91(3):335-45.
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1997: Russel M; Linderoth N A; Sali A
Filamentous phage assembly: variation on a protein export theme.
Gene 1997;192(1):23-32.
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1997: Sheng Y; Krilis S A; Sali A
Site-directed mutagenesis of recombinant human beta 2-glycoprotein I. Effect of phospholipid binding and anticardiolipin antibody activity.
Annals of the New York Academy of Sciences 1997;815():331-3.
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1997: Sánchez R; Sali A
Advances in comparative protein-structure modelling.
Current opinion in structural biology 1997;7(2):206-14.
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1997: Koulich D; Orlova M; Malhotra A; Sali A; Darst S A; Borukhov S
Domain organization of Escherichia coli transcript cleavage factors GreA and GreB.
The Journal of biological chemistry 1997;272(11):7201-10.
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1997: Sánchez R; Sali A
Evaluation of comparative protein structure modeling by MODELLER-3.
Proteins 1997;Suppl 1():50-8.
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1996: Sheng Y; Sali A; Herzog H; Lahnstein J; Krilis S A
Site-directed mutagenesis of recombinant human beta 2-glycoprotein I identifies a cluster of lysine residues that are critical for phospholipid binding and anti-cardiolipin antibody activity.
Journal of immunology (Baltimore, Md. : 1950) 1996;157(8):3744-51.
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1996: Xu L Z; Sánchez R; Sali A; Heintz N
Ligand specificity of brain lipid-binding protein.
The Journal of biological chemistry 1996;271(40):24711-9.
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1996: Ghildyal N; Friend D S; Stevens R L; Austen K F; Huang C; Penrose J F; Sali A; Gurish M F
Fate of two mast cell tryptases in V3 mastocytosis and normal BALB/c mice undergoing passive systemic anaphylaxis: prolonged retention of exocytosed mMCP-6 in connective tissues, and rapid accumulation of enzymatically active mMCP-7 in the blood.
The Journal of experimental medicine 1996;184(3):1061-73.
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1996: Dinner A R; Sali A; Karplus M
The folding mechanism of larger model proteins: role of native structure.
Proceedings of the National Academy of Sciences of the United States of America 1996;93(16):8356-61.
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1996: Wu S; de Lencastre H; Sali A; Tomasz A
A phosphoglucomutase-like gene essential for the optimal expression of methicillin resistance in Staphylococcus aureus: molecular cloning and DNA sequencing.
Microbial drug resistance (Larchmont, N.Y.) 1996;2(2):277-86.
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1995: Sali A; Potterton L; Yuan F; van Vlijmen H; Karplus M
Evaluation of comparative protein modeling by MODELLER.
Proteins 1995;23(3):318-26.
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1995: Sali A
Comparative protein modeling by satisfaction of spatial restraints.
Molecular medicine today 1995;1(6):270-7.
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1995: Matsumoto R; Sali A; Ghildyal N; Karplus M; Stevens R L
Packaging of proteases and proteoglycans in the granules of mast cells and other hematopoietic cells. A cluster of histidines on mouse mast cell protease 7 regulates its binding to heparin serglycin proteoglycans.
The Journal of biological chemistry 1995;270(33):19524-31.
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1995: Sali A
Modeling mutations and homologous proteins.
Current opinion in biotechnology 1995;6(4):437-51.
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1995: Karplus M; Sali A
Theoretical studies of protein folding and unfolding.
Current opinion in structural biology 1995;5(1):58-73.
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1995: Wu X; Knudsen B; Feller S M; Zheng J; Sali A; Cowburn D; Hanafusa H; Kuriyan J
Structural basis for the specific interaction of lysine-containing proline-rich peptides with the N-terminal SH3 domain of c-Crk.
Structure (London, England : 1993) 1995;3(2):215-26.
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1994: Sali A; Overington J P
Derivation of rules for comparative protein modeling from a database of protein structure alignments.
Protein science : a publication of the Protein Society 1994;3(9):1582-96.
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1994: Sali A; Shakhnovich E; Karplus M
How does a protein fold?
Nature 1994;369(6477):248-51.
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1994: Sali A; Shakhnovich E; Karplus M
Kinetics of protein folding. A lattice model study of the requirements for folding to the native state.
Journal of molecular biology 1994;235(5):1614-36.
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1993: Sali A; Blundell T L
Comparative protein modelling by satisfaction of spatial restraints.
Journal of molecular biology 1993;234(3):779-815.
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1993: Overington J P; Zhu Z Y; Sali A; Johnson M S; Sowdhamini R; Louie G V; Blundell T L
Molecular recognition in protein families: a database of aligned three-dimensional structures of related proteins.
Biochemical Society transactions 1993;21 ( Pt 3)(3):597-604.
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1993: Sali A; Matsumoto R; McNeil H P; Karplus M; Stevens R L
Three-dimensional models of four mouse mast cell chymases. Identification of proteoglycan binding regions and protease-specific antigenic epitopes.
The Journal of biological chemistry 1993;268(12):9023-34.
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1992: Veerapandian B; Cooper J B; Sali A; Blundell T L; Rosati R L; Dominy B W; Damon D B; Hoover D J
Direct observation by X-ray analysis of the tetrahedral "intermediate" of aspartic proteinases.
Protein science : a publication of the Protein Society 1992;1(3):322-8.
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1992: Sali A; Veerapandian B; Cooper J B; Moss D S; Hofmann T; Blundell T L
Domain flexibility in aspartic proteinases.
Proteins 1992;12(2):158-70.
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1992: Overington J; Donnelly D; Johnson M S; Sali A; Blundell T L
Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds.
Protein science : a publication of the Protein Society 1992;1(2):216-26.
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1992: Zhu Z Y; Sali A; Blundell T L
A variable gap penalty function and feature weights for protein 3-D structure comparisons.
Protein engineering 1992;5(1):43-51.
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1991: Blundell T L; Cooper J B; Sali A; Zhu Z Y
Comparisons of the sequences, 3-D structures and mechanisms of pepsin-like and retroviral aspartic proteinases.
Advances in experimental medicine and biology 1991;306():443-53.
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1990: Veerapandian B; Cooper J B; Sali A; Blundell T L
X-ray analyses of aspartic proteinases. III Three-dimensional structure of endothiapepsin complexed with a transition-state isostere inhibitor of renin at 1.6 A resolution.
Journal of molecular biology 1990;216(4):1017-29.
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1990: Overington J; Johnson M S; Sali A; Blundell T L
Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction.
Proceedings. Biological sciences / The Royal Society 1990;241(1301):132-45.
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1990: Sali A; Overington J P; Johnson M S; Blundell T L
From comparisons of protein sequences and structures to protein modelling and design.
Trends in biochemical sciences 1990;15(6):235-40.
-
1990: Sali A; Blundell T L
Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming.
Journal of molecular biology 1990;212(2):403-28.
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1990: Johnson M S; Sali A; Blundell T L
Phylogenetic relationships from three-dimensional protein structures.
Methods in enzymology 1990;183():670-90.
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1989: Sali A; Veerapandian B; Cooper J B; Foundling S I; Hoover D J; Blundell T L
High-resolution X-ray diffraction study of the complex between endothiapepsin and an oligopeptide inhibitor: the analysis of the inhibitor binding and description of the rigid body shift in the enzyme.
The EMBO journal 1989;8(8):2179-88.
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1987: Sali A; Turk V
Prediction of the secondary structures of stefins and cystatins, the low-molecular mass protein inhibitors of cysteine proteinases.
Biological chemistry Hoppe-Seyler 1987;368(5):493-9.
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