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Andrej Sali

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TOP 3
Libusha Kelly; Hisayo Fukushima; Rachel Karchin; Jason M Gow; Leslie W Chinn; Ursula Pieper; Mark Segal; Deanna L Kroetz; Andrej Sali
Functional hot spots in human ATP-binding cassette transporter nucleotide binding domains.
David T Barkan; Daniel R Hostetter; Sami Mahrus; Ursula Pieper; James A Wells; Charles S Craik; Andrej Sali
Prediction of protease substrates using sequence and structure features.
Dina Schneidman-Duhovny; Michal Hammel; Andrej Sali
FoXS: a web server for rapid computation and fitting of SAXS profiles.

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All Publications

2010: Libusha Kelly; Hisayo Fukushima; Rachel Karchin; Jason M Gow; Leslie W Chinn; Ursula Pieper; Mark Segal; Deanna L Kroetz; Andrej Sali
Functional hot spots in human ATP-binding cassette transporter nucleotide binding domains.
Protein science : a publication of the Protein Society 2010;19(11):2110-21.
2010: David T Barkan; Daniel R Hostetter; Sami Mahrus; Ursula Pieper; James A Wells; Charles S Craik; Andrej Sali
Prediction of protease substrates using sequence and structure features.
Bioinformatics (Oxford, England) 2010;26(14):1714-22.
2010: Dina Schneidman-Duhovny; Michal Hammel; Andrej Sali
FoXS: a web server for rapid computation and fitting of SAXS profiles.
Nucleic acids research 2010;38(Web Server issue):W540-4.
2009: Libusha Kelly; Ursula Pieper; Narayanan Eswar; Franklin A Hays; Min Li; Zygy Roe-Zurz; Deanna L Kroetz; Kathleen M Giacomini; Robert M Stroud; Andrej Sali
A survey of integral alpha-helical membrane proteins.
Journal of structural and functional genomics 2009;10(4):269-80.
2009: Mallur S Madhusudhan; Benjamin M Webb; maricus MR; Narayanan Eswar; Andrej Sali
Alignment of multiple protein structures based on sequence and structure features.
Protein engineering, design & selection : PEDS 2009;22(9):569-74.
2009: Ursula Pieper; Ranyee Chiang; Jennifer J Seffernick; Shoshana D Brown; Margaret E Glasner; Libusha Kelly; Narayanan Eswar; J Michael Sauder; Jeffrey B Bonanno; Subramanyam Swaminathan; Stephen K Burley; Xiaojing Zheng; Mark R Chance; Steven C Almo; John Alan Gerlt; Frank M Raushel; Matthew P Jacobson; Patricia C Babbitt; Andrej Sali
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.
2009: Min Li; Franklin A Hays; Zygy Roe-Zurz; Linda Vuong; Libusha Kelly; Chi-Min Ho; Renée M Robbins; Ursula Pieper; Joseph D O'Connell; Larry J W Miercke; Kathleen M Giacomini; Andrej Sali; Robert M Stroud
Selecting optimum eukaryotic integral membrane proteins for structure determination by rapid expression and solubilization screening.
Journal of molecular biology 2009;385(3):820-30.
2008: Fernán Agüero; Bissan Al-Lazikani; Martin Aslett; Matthew Berriman; Frederick S Buckner; Robert K Campbell; Santiago Carmona; Ian M Carruthers; A W Edith Chan; Feng Chen; Gregory J Crowther; Maria A Doyle; Christiane Hertz-Fowler; Andrew L Hopkins; Gregg McAllister; Solomon Nwaka; John Overington; Arnab Pain; Gaia V Paolini; Ursula Pieper; Stuart A Ralph; Aaron Riechers; David S Roos; Andrej Sali; Dhanasekaran Shanmugam; Takashi Suzuki; Wesley C Van Voorhis; Christophe Verlinde
Genomic-scale prioritization of drug targets: the TDR Targets database.
Nature reviews. Drug discovery 2008;7(11):900-7.
2008: David Eramian; Narayanan Eswar; Min-Yi Shen; Andrej Sali
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.
2008: Friedrich Förster; Benjamin Webb; Kristin A Krukenberg; Hiro Tsuruta; David A Agard; Andrej Sali
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.
2008: Sami Mahrus; Jonathan C Trinidad; David T Barkan; Andrej Sali; Alma L Burlingame; James A Wells
Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini.
Cell 2008;134(5):866-76.
2008: Irina I Serysheva; Steven J Ludtke; Matthew Baker; Yao Cong; Maya Topf; David Eramian; Andrej Sali; Susan Hamilton; Wah Chiu
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.
2008: Christopher Booth; Anne S. Meyer; Yao Cong; Maya Topf; Andrej Sali; Steven J Ludtke; Wah Chiu; Judith Frydman
Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT.
Nature structural & molecular biology 2008;15(7):746-53.
2008: Kristin A Krukenberg; Friedrich Förster; Luke M Rice; Andrej Sali; David A Agard
Multiple conformations of E. coli Hsp90 in solution: insights into the conformational dynamics of Hsp90.
Structure (London, England : 1993) 2008;16(5):755-65.
2008: Preethi Chandramouli; Maya Topf; Jean-François Ménétret; Narayanan Eswar; Jamie J Cannone; Robin R Gutell; Andrej Sali; Christopher W Akey
Structure of the mammalian 80S ribosome at 8.7 A resolution.
Structure (London, England : 1993) 2008;16(4):535-48.
2008: Carol M Anderson; Dmitry Korkin; Dana L Smith; Svetlana Makovets; Jeffrey J. Seidel; Andrej Sali; Elizabeth H Blackburn
Tel2 mediates activation and localization of ATM/Tel1 kinase to a double-strand break.
Genes & development 2008;22(7):854-9.
2008: Maya Topf; Keren Lasker; Ben Webb; Haim Wolfson; Wah Chiu; Andrej Sali
Protein structure fitting and refinement guided by cryo-EM density.
Structure (London, England : 1993) 2008;16(2):295-307.
2008: Yao Cong; Maya Topf; Andrej Sali; Paul Matsudaira; Matthew Dougherty; Wah Chiu; Michael F Schmid
Crystallographic conformers of actin in a biologically active bundle of filaments.
Journal of molecular biology 2008;375(2):331-6.
2008: Ranyee A Chiang; Andrej Sali; Patricia C Babbitt
Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies.
PLoS computational biology 2008;4(8):e1000142.
2008: Narayanan Eswar; David Eramian; Ben Webb; Min-Yi Shen; Andrej Sali
Protein structure modeling with MODELLER.
Methods in molecular biology (Clifton, N.J.) 2008;426():145-59.
2008: Jordi Espadaler; Narayanan Eswar; Enrique Querol; Francesc X Avilés; Andrej Sali; maricus MR; baldomero oliva
Prediction of enzyme function by combining sequence similarity and protein interactions.
BMC bioinformatics 2008;9():249.
2008: Frank Alber; Friedrich Förster; Dmitry Korkin; Maya Topf; Andrej Sali
Integrating diverse data for structure determination of macromolecular assemblies.
Annual review of biochemistry 2008;77():443-77.
2007: Carol V Robinson; Andrej Sali; Wolfgang Baumeister
The molecular sociology of the cell.
Nature 2007;450(7172):973-82.
2007: Kanika Bajaj; MS Madhusudhan; Bharat Adkar; Purbani Chakrabarti; C Ramakrishnan; Andrej Sali; Raghavan Varadarajan
Stereochemical criteria for prediction of the effects of proline mutations on protein stability.
PLoS computational biology 2007;3(12):e241.
2007: Fred P Davis; David T Barkan; Narayanan Eswar; James H McKerrow; Andrej Sali
Host pathogen protein interactions predicted by comparative modeling.
Protein science : a publication of the Protein Society 2007;16(12):2585-96.
2007: Frank Alber; Svetlana Dokudovskaya; Liesbeth M Veenhoff; Wenzhu Zhang; Julia Kipper; Damien Devos; Adisetyantari Suprapto; Orit Karni-Schmidt; Rosemary Williams; Brian T Chait; Andrej Sali; Michael P Rout
The molecular architecture of the nuclear pore complex.
Nature 2007;450(7170):695-701.
2007: Frank Alber; Svetlana Dokudovskaya; Liesbeth M Veenhoff; Wenzhu Zhang; Julia Kipper; Damien Devos; Adisetyantari Suprapto; Orit Karni-Schmidt; Rosemary Williams; Brian T Chait; Michael P Rout; Andrej Sali
Determining the architectures of macromolecular assemblies.
Nature 2007;450(7170):683-94.
2007: Narayanan Eswar; Ben Webb; maricus MR; Mallur S Madhusudhan; David Eramian; Min-Yi Shen; Ursula Pieper; Andrej Sali
Comparative protein structure modeling using MODELLER.
Current protocols in protein science / editorial board, John E. Coligan ... [et al.] 2007;Chapter 2():Unit 2.9.
2007: Andrej Sali; Christopher D Lima; Milka Kostic
Structural genomics.
Structure (London, England : 1993) 2007;15(11):1341.
2007: Francisco Melo; Andrej Sali
Fold assessment for comparative protein structure modeling.
Protein science : a publication of the Protein Society 2007;16(11):2412-26.
2007: Steven C Almo; Jeffrey B Bonanno; J Michael Sauder; Spencer Emtage; Teresa P DiLorenzo; Vladimir N Malashkevich; Steven R Wasserman; S Swaminathan; Subramaniam Eswaramoorthy; Rakhi Agarwal; Desigan Kumaran; Mahendra Madegowda; Sugadev Ragumani; Yury Patskovsky; Johnjeff Alvarado; Udupi A Ramagopal; Joana Faber-Barata; Mark R Chance; Andrej Sali; András Fiser; Zhong-Yin Zhang; David S Lawrence; Stephen K Burley
Structural genomics of protein phosphatases.
Journal of structural and functional genomics 2007;8(2-3):121-40.
2007: Ramon Aragues; Andrej Sali; Jaume Bonet; maricus MR; baldomero oliva
Characterization of protein hubs by inferring interacting motifs from protein interactions.
PLoS computational biology 2007;3(9):1761-71.
2007: Eric Feyfant; Andrej Sali; András Fiser
Modeling mutations in protein structures.
Protein science : a publication of the Protein Society 2007;16(9):2030-41.
2007: maricus MR; Ursula Pieper; Mallur S Madhusudhan; Andrea Rossi; Narayanan Eswar; Fred P Davis; Fátima Al-Shahrour; Joaquín Dopazo; Andrej Sali
DBAli tools: mining the protein structure space.
Nucleic acids research 2007;35(Web Server issue):W393-7.
2007: Stephanie X Wang; Kailash C Pandey; Julio Scharfstein; James C Whisstock; Rick K Huang; Jordan Jacobelli; Robert J Fletterick; Philip J Rosenthal; Magnus Abrahamson; Linda S Brinen; Andrea Rossi; Andrej Sali; James H McKerrow
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.
2007: Nicole Soranzo; Libusha Kelly; Lillian Martinian; Mari-Wyn Burley; Maria Thom; Andrej Sali; Deanna L Kroetz; David B Goldstein; Sanjay M Sisodiya
Lack of support for a role for RLIP76 (RALBP1) in response to treatment or predisposition to epilepsy.
Epilepsia 2007;48(4):674-83.
2007: Virginia D Winn; Ronit Haimov-Kochman; Agnes C Paquet; Y Jean Yang; M S Madhusudhan; Matthew Gormley; Kui-Tzu V Feng; David A Bernlohr; Susan McDonagh; Lenore Pereira; Andrej Sali; Susan J Fisher
Gene expression profiling of the human maternal-fetal interface reveals dramatic changes between midgestation and term.
Endocrinology 2007;148(3):1059-79.
2007: Rachel Karchin; Alvaro Monteiro; Sean V Tavtigian; Marcelo A Carvalho; Andrej Sali
Functional impact of missense variants in BRCA1 predicted by supervised learning.
PLoS computational biology 2007;3(2):e26.
2007: Marcelo A Carvalho; Sylvia M Marsillac; Rachel Karchin; Siranoush Manoukian; Scott Grist; Ramona F Swaby; Turan P Urmenyi; Edson Rondinelli; Rosane Silva; Luis Gayol; Lisa Baumbach; Rebecca Sutphen; Jennifer L Pickard-Brzosowicz; Katherine L Nathanson; Andrej Sali; David E Goldgar; Fergus J. Couch; Paolo Radice; Alvaro Monteiro
Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis.
Cancer research 2007;67(4):1494-501.
2007: Libusha Kelly; Rachel Karchin; Andrej Sali
Protein interactions and disease phenotypes in the ABC transporter superfamily.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2007;():51-63.
2007: maricus MR; Andrea Rossi; Fátima Al-Shahrour; Fred P Davis; Ursula Pieper; Joaquín Dopazo; Andrej Sali
The AnnoLite and AnnoLyze programs for comparative annotation of protein structures.
BMC bioinformatics 2007;8 Suppl 4():S4.
2006: Dmitry Korkin; Fred P Davis; Frank Alber; Tinh Luong; Min-Yi Shen; Vladan Lucic; Mary B Kennedy; Andrej Sali
Structural modeling of protein interactions by analogy: application to PSD-95.
PLoS computational biology 2006;2(11):e153.
2006: Andrés Colubri; Abhishek K Jha; Min-Yi Shen; Andrej Sali; R Stephen Berry; Tobin R Sosnick; Karl F Freed
Minimalist representations and the importance of nearest neighbor effects in protein folding simulations.
Journal of molecular biology 2006;363(4):835-57.
2006: Min-Yi Shen; Andrej Sali
Statistical potential for assessment and prediction of protein structures.
Protein science : a publication of the Protein Society 2006;15(11):2507-24.
2006: Narayanan Eswar; Ben Webb; maricus MR; Mallur S Madhusudhan; David Eramian; Min-Yi Shen; Ursula Pieper; Andrej Sali
Comparative protein structure modeling using Modeller.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 2006;Chapter 5():Unit 5.6.
2006: Andrea Rossi; maricus MR; Andrej Sali
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.
2006: Helen M Berman; Stephen K Burley; Wah Chiu; Andrej Sali; Alexei A Adzhubei; Philip Bourne; Stephen H Bryant; Roland L Dunbrack; Krzysztof Fidelis; Joachim Frank; Adam Godzik; Kim Henrick; Andrzej Joachimiak; Bernard Heymann; David Jones; John Lute Markley; John Moult; Gaetano T Montelione; Christine Orengo; Michael G Rossmann; Burkhard Rost; Helen R Saibil; Torsten Schwede; Daron M Standley; John D Westbrook
Outcome of a workshop on archiving structural models of biological macromolecules.
Structure (London, England : 1993) 2006;14(8):1211-7.
2006: David Eramian; Min-yi Shen; Damien Devos; Francisco Melo; Andrej Sali; maricus MR
A composite score for predicting errors in protein structure models.
Protein science : a publication of the Protein Society 2006;15(7):1653-66.
2006: Maya Topf; Matthew Baker; maricus MR; Wah Chiu; Andrej Sali
Refinement of protein structures by iterative comparative modeling and CryoEM density fitting.
Journal of molecular biology 2006;357(5):1655-68.
2006: Svetlana Dokudovskaya; Rosemary Williams; Damien Devos; Andrej Sali; Brian T Chait; Michael P Rout
Protease accessibility laddering: a proteomic tool for probing protein structure.
Structure (London, England : 1993) 2006;14(4):653-60.
2006: Tan D Nguyen; Jason M Gow; Leslie W Chinn; Libusha Kelly; Hotcherl Jeong; Conrad C Huang; Doug Stryke; Michiko Kawamoto; Susan J Johns; Elaine Carlson; Travis Taylor; Thomas E Ferrin; Andrej Sali; Kathleen M Giacomini; Deanna L Kroetz
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.
2006: Mallur S Madhusudhan; maricus MR; Roberto Sanchez; Andrej Sali
Variable gap penalty for protein sequence-structure alignment.
Protein engineering, design & selection : PEDS 2006;19(3):129-33.
2006: Damien Devos; Svetlana Dokudovskaya; Rosemary Williams; Frank Alber; Narayanan Eswar; Brian T Chait; Michael P Rout; Andrej Sali
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.
2006: Fred P Davis; Hannes Braberg; Min-Yi Shen; Ursula Pieper; Andrej Sali; Mallur S Madhusudhan
Protein complex compositions predicted by structural similarity.
Nucleic acids research 2006;34(10):2943-52.
2006: Ursula Pieper; Narayanan Eswar; Fred P Davis; Hannes Braberg; Mallur S Madhusudhan; Andrea Rossi; maricus MR; Rachel Karchin; Ben M Webb; David Eramian; Min-Yi Shen; Libusha Kelly; Francisco Melo; Andrej Sali
MODBASE: a database of annotated comparative protein structure models and associated resources.
Nucleic acids research 2006;34(Database issue):D291-5.
2005: Stephen McMahon; Jason L Miller; Jeffrey A Lawton; Donald E Kerkow; Asher Hodes; maricus MR; Sergei R Doulatov; Eswar Narayanan; Andrej Sali; Jeff F Miller; Partho Ghosh
The C-type lectin fold as an evolutionary solution for massive sequence variation.
Nature structural & molecular biology 2005;12(10):886-92.
2005: Maya Topf; Andrej Sali
Combining electron microscopy and comparative protein structure modeling.
Current opinion in structural biology 2005;15(5):578-85.
2005: Dmitry Korkin; Fred P Davis; Andrej Sali
Localization of protein-binding sites within families of proteins.
Protein science : a publication of the Protein Society 2005;14(9):2350-60.
2005: Josef Dvorák; Melaine Delcroix; Andrea Rossi; Václav Vopálenský; Martin Pospísek; Miroslava Sedinová; Libor Mikes; Mohammed Sajid; Andrej Sali; James H McKerrow; Petr Horák; Conor R Caffrey
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.
2005: Rachel Karchin; Mark Diekhans; Libusha Kelly; Daryl J Thomas; Ursula Pieper; Narayanan Eswar; David Haussler; Andrej Sali
LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources.
Bioinformatics (Oxford, England) 2005;21(12):2814-20.
2005: Jordi Espadaler; Ramón Aragüés; Narayanan Eswar; maricus MR; Enrique Querol; Francesc X Avilés; Andrej Sali; baldomero oliva
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.
2005: Shinsuke Yasuda; Nasa Morokawa; GUANG WILLIAM WONG; Andrea Rossi; Mallur S Madhusudhan; Andrej Sali; Yuko S Askew; Roberto Adachi; Gary A Silverman; Steven A Krilis; Richard L Stevens
Urokinase-type plasminogen activator is a preferred substrate of the human epithelium serine protease tryptase epsilon/PRSS22.
Blood 2005;105(10):3893-901.
2005: Fred P Davis; Andrej Sali
PIBASE: a comprehensive database of structurally defined protein interfaces.
Bioinformatics (Oxford, England) 2005;21(9):1901-7.
2005: Frank Alber; Michael F Kim; Andrej Sali
Structural characterization of assemblies from overall shape and subcomplex compositions.
Structure (London, England : 1993) 2005;13(3):435-45.
2005: Maya Topf; Matthew Baker; Bino John; Wah Chiu; Andrej Sali
Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy.
Journal of structural biology 2005;149(2):191-203.
2005: Jeffrey B Bonanno; Steven C Almo; Anne R Bresnick; Mark R Chance; András Fiser; S Swaminathan; J Jiang; F William Studier; Lawrence Shapiro; Christopher D Lima; Theresa M Gaasterland; Andrej Sali; Kevin Bain; Ingeborg K Feil; Xia Gao; Don Lorimer; Aurora Ramos; J Michael Sauder; Steven R Wasserman; Spencer Emtage; Kevin L D'Amico; Stephen K Burley
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.
2005: Rachel Karchin; Libusha Kelly; Andrej Sali
Improving functional annotation of non-synonomous SNPs with information theory.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2005;():397-408.
2004: Stephen M Maurer; Arti Rai; Andrej Sali
Finding cures for tropical diseases: is open source an answer?
PLoS medicine 2004;1(3):e56.
2004: Damien Devos; Svetlana Dokudovskaya; Frank Alber; Rosemary Williams; Brian T Chait; Andrej Sali; Michael P Rout
Components of coated vesicles and nuclear pore complexes share a common molecular architecture.
PLoS biology 2004;2(12):e380.
2004: Mark R Chance; András Fiser; Andrej Sali; Ursula Pieper; Narayanan Eswar; Guiping Xu; Jorge Fajardo; Thirumuruhan Radhakannan; Nebojsa Marinkovic
High-throughput computational and experimental techniques in structural genomics.
Genome research 2004;14(10B):2145-54.
2004: Robert B Russell; Frank Alber; Patrick Aloy; Fred P Davis; Dmitry Korkin; Matthieu Pichaud; Maya Topf; Andrej Sali
A structural perspective on protein-protein interactions.
Current opinion in structural biology 2004;14(3):313-24.
2004: Nebojsa Mirkovic; maricus MR; Barbara L Weber; Andrej Sali; Alvaro Monteiro
Structure-based assessment of missense mutations in human BRCA1: implications for breast and ovarian cancer predisposition.
Cancer research 2004;64(11):3790-7.
2004: Andrea Rossi; Quinn Deveraux; Boris Turk; Andrej Sali
Comprehensive search for cysteine cathepsins in the human genome.
Biological chemistry 2004;385(5):363-72.
2004: maricus MR; Mallur S Madhusudhan; Andrej Sali
Alignment of protein sequences by their profiles.
Protein science : a publication of the Protein Society 2004;13(4):1071-87.
2004: Bino John; Andrej Sali
Detection of homologous proteins by an intermediate sequence search.
Protein science : a publication of the Protein Society 2004;13(1):54-62.
2004: Ursula Pieper; Narayanan Eswar; Hannes Braberg; Mallur S Madhusudhan; Fred P Davis; Ashley C Stuart; Nebojsa Mirkovic; Andrea Rossi; maricus MR; András Fiser; Ben Webb; Daniel Greenblatt; Conrad C Huang; Thomas E Ferrin; Andrej Sali
MODBASE, a database of annotated comparative protein structure models, and associated resources.
Nucleic acids research 2004;32(Database issue):D217-22.
2003: András Fiser; Andrej Sali
ModLoop: automated modeling of loops in protein structures.
Bioinformatics (Oxford, England) 2003;19(18):2500-1.
2003: Andrej Sali
NIH workshop on structural proteomics of biological complexes.
Structure (London, England : 1993) 2003;11(9):1043-7.
2003: Bino John; Andrej Sali
Comparative protein structure modeling by iterative alignment, model building and model assessment.
Nucleic acids research 2003;31(14):3982-92.
2003: Narayanan Eswar; Bino John; Nebojsa Mirkovic; András Fiser; Valentin A Ilyin; Ursula Pieper; Ashley C Stuart; maricus MR; Mallur S Madhusudhan; Bozidar Yerkovich; Andrej Sali
Tools for comparative protein structure modeling and analysis.
Nucleic acids research 2003;31(13):3375-80.
2003: Ingrid Y Y Koh; Volker A Eyrich; maricus MR; Dariusz Przybylski; Mallur S Madhusudhan; Narayanan Eswar; Osvaldo Graña; Florencio Pazos; Carmen Galvez; Andrej Sali; Burkhard Rost
EVA: Evaluation of protein structure prediction servers.
Nucleic acids research 2003;31(13):3311-5.
2003: Haixiao Gao; Jayati Sengupta; Mikel Valle; Andrei Korostelev; Narayanan Eswar; Scott M Stagg; Patrick Van Roey; Rajendra K Agrawal; Stephen C Harvey; Andrej Sali; Michael S Chapman; Joachim Frank
Study of the structural dynamics of the E coli 70S ribosome using real-space refinement.
Cell 2003;113(6):789-801.
2003: Susie A Lee; Ellen L Shen; András Fiser; Andrej Sali; Su Guo
The zebrafish forkhead transcription factor Foxi1 specifies epibranchial placode-derived sensory neurons.
Development (Cambridge, England) 2003;130(12):2669-79.
2003: Andrej Sali; Robert Glaeser; Thomas Earnest; Wolfgang Baumeister
From words to literature in structural proteomics.
Nature 2003;422(6928):216-25.
2003: András Fiser; Andrej Sali
Modeller: generation and refinement of homology-based protein structure models.
Methods in enzymology 2003;374():461-91.
2003: Valentin A Ilyin; Ursula Pieper; Ashley C Stuart; maricus MR; Linda McMahan; Andrej Sali
ModView, visualization of multiple protein sequences and structures.
Bioinformatics (Oxford, England) 2003;19(1):165-6.
2002: G Michael Iverson; Stephen Reddel; Edward J Victoria; Keith A Cockerill; Ying-Xia Wang; maricus MR; Andrej Sali; David M Marquis; Steven A Krilis; Matthew D Linnik
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.
2002: Yi Yang; Lixin Li; GUANG WILLIAM WONG; Steven A Krilis; Mallur S Madhusudhan; Andrej Sali; Richard L Stevens
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.
2002: András Fiser; Michael Feig; Charles L Brooks; Andrej Sali
Evolution and physics in comparative protein structure modeling.
Accounts of chemical research 2002;35(6):413-21.
2002: Javier Vernal; András Fiser; Andrej Sali; Miklós Müller; Juan J Cazzulo; Cristina Nowicki
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.
2002: Mark R Chance; Anne R Bresnick; Stephen K Burley; Jian-Sheng Jiang; Christopher D Lima; Andrej Sali; Steven C Almo; Jeffrey B Bonanno; John A Buglino; Simon J Boulton; Hua Chen; Narayanan Eswar; Guoshun He; Raymond Huang; Valentin A Ilyin; Linda McMahan; Ursula Pieper; Soumya Ray; Marc Vidal; Li Kai Wang
Structural genomics: a pipeline for providing structures for the biologist.
Protein science : a publication of the Protein Society 2002;11(4):723-38.
2002: maricus MR; Mallur S Madhusudhan; András Fiser; Burkhard Rost; Andrej Sali
Reliability of assessment of protein structure prediction methods.
Structure (London, England : 1993) 2002;10(3):435-40.
2002: Francisco Melo; Roberto Sánchez; Andrej Sali
Statistical potentials for fold assessment.
Protein science : a publication of the Protein Society 2002;11(2):430-48.
2002: Ashley C Stuart; Valentin A Ilyin; Andrej Sali
LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures.
Bioinformatics (Oxford, England) 2002;18(1):200-1.
2002: Ursula Pieper; Narayanan Eswar; Ashley C Stuart; Valentin A Ilyin; Andrej Sali
MODBASE, a database of annotated comparative protein structure models.
Nucleic acids research 2002;30(1):255-9.
2001: GUANG WILLIAM WONG; Shinsuke Yasuda; Mallur S Madhusudhan; Lixin Li; Yi Yang; Steven A Krilis; Andrej Sali; Richard L Stevens
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.
2001: Volker A Eyrich; MA Martí-Renom; Dariusz Przybylski; Mallur S Madhusudhan; András Fiser; Florencio Pazos; Carmen Galvez; Andrej Sali; Burkhard Rost
EVA: continuous automatic evaluation of protein structure prediction servers.
Bioinformatics (Oxford, England) 2001;17(12):1242-3.
2001: Jeffrey B Bonanno; C Edo; Narayanan Eswar; Ursula Pieper; Michael J Romanowski; Valentin A Ilyin; Sue Ellen Gerchman; Helen Kycia; F William Studier; Andrej Sali; Stephen K Burley
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.
2001: Christian M T Spahn; Roland Beckmann; Narayanan Eswar; Pawel A Penczek; Andrej Sali; Günter Blobel; Joachim Frank
Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions.
Cell 2001;107(3):373-86.
2001: Roland Beckmann; Christian M T Spahn; Narayanan Eswar; J Helmers; Pawel A Penczek; Andrej Sali; J Frank; Günter Blobel
Architecture of the protein-conducting channel associated with the translating 80S ribosome.
Cell 2001;107(3):361-72.
2001: David Baker; Andrej Sali
Protein structure prediction and structural genomics.
Science (New York, N.Y.) 2001;294(5540):93-6.
2001: MA Martí-Renom; Valentin A Ilyin; Andrej Sali
DBAli: a database of protein structure alignments.
Bioinformatics (Oxford, England) 2001;17(8):746-7.
2001: GUANG WILLIAM WONG; Lixin Li; Mallur S Madhusudhan; Steven A Krilis; Michael F Gurish; M E Rothenberg; Andrej Sali; Richard L Stevens
Tryptase 4, a new member of the chromosome 17 family of mouse serine proteases.
The Journal of biological chemistry 2001;276(23):20648-58.
2001: Andrej Sali
Target practice.
Nature structural biology 2001;8(6):482-4.
2001: Laura G Barrientos; Ramón Campos-Olivas; John M Louis; András Fiser; Andrej Sali; Angela M Gronenborn
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.
2001: Shuba Gopal; M Schroeder; Ursula Pieper; Alexander Sczyrba; G Aytekin-Kurban; Stefan Bekiranov; Jorge Fajardo; Narayanan Eswar; R Sanchez; Andrej Sali; Terry Gaasterland
Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome.
Nature genetics 2001;27(3):337-40.
2000: Caroline M Groft; Roland Beckmann; Andrej Sali; Stephen K Burley
Crystal structures of ribosome anti-association factor IF6.
Nature structural biology 2000;7(12):1156-64.
2000: R Sánchez; Ursula Pieper; Francisco Melo; Narayanan Eswar; MA Martí-Renom; Mallur S Madhusudhan; N Mirković; Andrej Sali
Protein structure modeling for structural genomics.
Nature structural biology 2000;7 Suppl():986-90.
2000: Wolfgang Liedtke; Yong Choe; MA Martí-Renom; Andrea M Bell; Charlotte S Denis; Andrej Sali; AJ Hudspeth; Jeffrey M Friedman; Stefan Heller
Vanilloid receptor-related osmotically activated channel (VR-OAC), a candidate vertebrate osmoreceptor.
Cell 2000;103(3):525-35.
2000: András Fiser; Richard K G Do; Andrej Sali
Modeling of loops in protein structures.
Protein science : a publication of the Protein Society 2000;9(9):1753-73.
2000: G Wu; Andrew G McArthur; András Fiser; Andrej Sali; Mitchell L Sogin; M Mllerm
Core histones of the amitochondriate protist, Giardia lamblia.
Molecular biology and evolution 2000;17(8):1156-63.
2000: AR Dinner; Andrej Sali; L J Smith; Christopher M Dobson; M Karplus
Understanding protein folding via free-energy surfaces from theory and experiment.
Trends in biochemical sciences 2000;25(7):331-9.
2000: Shengkan Jin; S Martinek; W S Joo; Jennifer Wortman; Nebojsa Mirkovic; Andrej Sali; M D Yandell; Nikola P Pavletich; Michael W Young; Arnold J Levine
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.
2000: Chao Huang; G Morales; A Vagi; K Chanasyk; M Ferrazzi; C Burklow; WT Qiu; E Feyfant; Andrej Sali; Richard L Stevens
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.
2000: R Sánchez; Andrej Sali
Comparative protein structure modeling. Introduction and practical examples with modeller.
Methods in molecular biology (Clifton, N.J.) 2000;143():97-129.
2000: MA Martí-Renom; Ashley C Stuart; András Fiser; R Sánchez; Francisco Melo; Andrej Sali
Comparative protein structure modeling of genes and genomes.
Annual review of biophysics and biomolecular structure 2000;29():291-325.
2000: R Sánchez; Ursula Pieper; N Mirković; P I de Bakker; E Wittenstein; Andrej Sali
MODBASE, a database of annotated comparative protein structure models.
Nucleic acids research 2000;28(1):250-3.
1999: R Sánchez; Andrej Sali
ModBase: a database of comparative protein structure models.
Bioinformatics (Oxford, England) 1999;15(12):1060-1.
1999: Andrej Sali; John Kuriyan
Challenges at the frontiers of structural biology.
Trends in cell biology 1999;9(12):M20-4.
1999: Andrej Sali
Functional links between proteins.
Nature 1999;402(6757):23, 25-6.
1999: GUANG WILLIAM WONG; Y Tang; E Feyfant; Andrej Sali; Ling Li; Y Li; Chao Huang; Daniel S Friend; Steven A Krilis; Richard L Stevens
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.
1999: Stephen K Burley; Steven C Almo; Jeffrey B Bonanno; M Capel; Mark R Chance; T Gaasterland; D Lin; Andrej Sali; F William Studier; Subramanyam Swaminathan
Structural genomics: beyond the human genome project.
Nature genetics 1999;23(2):151-7.
1999: T Nagata; Vineet Gupta; D Sorce; W Y Kim; Andrej Sali; Brian T Chait; Shigesada Katsuya; Y Ito; Milton H Werner
Immunoglobulin motif DNA recognition and heterodimerization of the PEBP2/CBF Runt domain.
Nature structural biology 1999;6(7):615-9.
1999: Gang Wu; András Fiser; BH ter Kuile; Andrej Sali; Miklós Müller
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.
1999: Julie M Miwa; I Ibanez-Tallon; G W Crabtree; R Sánchez; Andrej Sali; L W Role; Nathaniel Heintz
lynx1, an endogenous toxin-like modulator of nicotinic acetylcholine receptors in the mammalian CNS.
Neuron 1999;23(1):105-14.
1998: Andrej Sali
100,000 protein structures for the biologist.
Nature structural biology 1998;5(12):1029-32.
1998: R Sánchez; Andrej Sali
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.
1998: E Wolf; A Vassilev; Y Makino; Andrej Sali; Y Nakatani; Stephen K Burley
Crystal structure of a GCN5-related N-acetyltransferase: Serratia marcescens aminoglycoside 3-N-acetyltransferase.
Cell 1998;94(4):439-49.
1998: C Huang; Andrej Sali; R L Stevens
Regulation and function of mast cell proteases in inflammation.
Journal of clinical immunology 1998;18(3):169-83.
1998: DA Kandiah; Andrej Sali; Yonghua Sheng; Edward J Victoria; David M Marquis; coutts stephen; Steven A Krilis
Current insights into the "antiphospholipid" syndrome: clinical, immunological, and molecular aspects.
Advances in immunology 1998;70():507-63.
1997: Chao Huang; GUANG WILLIAM WONG; N Ghildyal; Michael F Gurish; Andrej Sali; R Matsumoto; WT Qiu; Richard L Stevens
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.
1997: J E Hunt; Daniel S Friend; Michael F Gurish; E Feyfant; Andrej Sali; Chao Huang; N Ghildyal; S Stechschulte; K Frank Austen; Richard L Stevens
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.
1997: B Guenther; R Onrust; Andrej Sali; Mike O'Donnell; John Kuriyan
Crystal structure of the delta' subunit of the clamp-loader complex of E. coli DNA polymerase III.
Cell 1997;91(3):335-45.
1997: Marjorie Russel; NA Linderoth; Andrej Sali
Filamentous phage assembly: variation on a protein export theme.
Gene 1997;192(1):23-32.
1997: Yonghua Sheng; Steven A Krilis; Andrej Sali
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.
1997: R Sánchez; Andrej Sali
Advances in comparative protein-structure modelling.
Current opinion in structural biology 1997;7(2):206-14.
1997: D Koulich; M Orlova; Arun Malhotra; Andrej Sali; Seth A Darst; Sergei Borukhov
Domain organization of Escherichia coli transcript cleavage factors GreA and GreB.
The Journal of biological chemistry 1997;272(11):7201-10.
1997: R Sánchez; Andrej Sali
Evaluation of comparative protein structure modeling by MODELLER-3.
Proteins 1997;Suppl 1():50-8.
1996: Yonghua Sheng; Andrej Sali; Herbert Herzog; J Lahnstein; Steven A Krilis
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.
1996: L Z Xu; R Sánchez; Andrej Sali; Nathaniel Heintz
Ligand specificity of brain lipid-binding protein.
The Journal of biological chemistry 1996;271(40):24711-9.
1996: N Ghildyal; Daniel S Friend; Richard L Stevens; K Frank Austen; Chao Huang; John F Penrose; Andrej Sali; Michael F Gurish
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.
1996: A R Dinner; Andrej Sali; M Karplus
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.
1996: S Wu; Hermínia de Lencastre; Andrej Sali; Alexander Tomasz
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.
1995: Andrej Sali; L Potterton; F Yuan; Herman van Vlijmen; M Karplus
Evaluation of comparative protein modeling by MODELLER.
Proteins 1995;23(3):318-26.
1995: Andrej Sali
Comparative protein modeling by satisfaction of spatial restraints.
Molecular medicine today 1995;1(6):270-7.
1995: R Matsumoto; Andrej Sali; N Ghildyal; M Karplus; Richard L Stevens
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.
1995: Andrej Sali
Modeling mutations and homologous proteins.
Current opinion in biotechnology 1995;6(4):437-51.
1995: X Wu; B Knudsen; Stephan M Feller; J Zheng; Andrej Sali; David Cowburn; Hidesaburo Hanafusa; John Kuriyan
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.
1995: M Karplus; Andrej Sali
Theoretical studies of protein folding and unfolding.
Current opinion in structural biology 1995;5(1):58-73.
1994: Andrej Sali; John Overington
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.
1994: Andrej Sali; Eugene I Shakhnovich; M Karplus
How does a protein fold?
Nature 1994;369(6477):248-51.
1994: Andrej Sali; Eugene I Shakhnovich; M Karplus
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.
1993: Andrej Sali; Tom L Blundell
Comparative protein modelling by satisfaction of spatial restraints.
Journal of molecular biology 1993;234(3):779-815.
1993: John Overington; Z Y Zhu; Andrej Sali; M S Johnson; R Sowdhamini; G V Louie; Tom L Blundell
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.
1993: Andrej Sali; R Matsumoto; H P McNeil; M Karplus; R L Stevens
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.
1992: B Veerapandian; Jonathan B Cooper; Andrej Sali; Tom L Blundell; R L Rosati; B W Dominy; D B Damon; D J Hoover
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.
1992: Andrej Sali; B Veerapandian; Jonathan B Cooper; David S Moss; T Hofmann; Tom L Blundell
Domain flexibility in aspartic proteinases.
Proteins 1992;12(2):158-70.
1992: J Overington; D Donnelly; M S Johnson; Andrej Sali; Tom L Blundell
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.
1992: Z Y Zhu; Andrej Sali; Tom L Blundell
A variable gap penalty function and feature weights for protein 3-D structure comparisons.
Protein engineering 1992;5(1):43-51.
1991: Tom L Blundell; Jonathan B Cooper; Andrej Sali; Z Y Zhu
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.
1990: B Veerapandian; Jonathan B Cooper; Andrej Sali; Tom L Blundell
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.
1990: J Overington; M S Johnson; Andrej Sali; T L Blundell
Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction.
Proceedings. Biological sciences / The Royal Society 1990;241(1301):132-45.
1990: Andrej Sali; John Overington; M S Johnson; Tom L Blundell
From comparisons of protein sequences and structures to protein modelling and design.
Trends in biochemical sciences 1990;15(6):235-40.
1990: Andrej Sali; Tom L Blundell
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.
1990: M S Johnson; Andrej Sali; T L Blundell
Phylogenetic relationships from three-dimensional protein structures.
Methods in enzymology 1990;183():670-90.
1989: Andrej Sali; B Veerapandian; Jonathan B Cooper; SI Foundling; D J Hoover; Tom L Blundell
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.
1987: Andrej Sali; V Turk
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.