Sali, Andrej - Department of Biochemistry and Biophysics, University of California at San Francisco

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Sali, Andrej - Department of Biochemistry and Biophysics, University of California at San Francisco

proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS STRUCTURE NOTE
Function of human Rh based on structure of RhCG at 2.1
Molecular Docking Screens Using Comparative Models of Proteins John J. Irwin,
nature structural biology volume 8 number 9 september 2001 745 Paoli's analysis of archaeal and eukaryotic
Protein production and purification Structural Genomics Consortium13,Architecture et Fonction des Macromolcules
BioMed Central Page 1 of 8
New York-Structural GenomiX Research Consortium (NYSGXRC): a large scale center for the protein structure initiative
The third, use of quantum mechanics to evaluate the molecular energy and forces, holds promise for future refinements when applied wholesale,
Determination of Cancer Risk Associated with Germ Line BRCA1 Missense Variants by Functional Analysis
THEJOURNALOF BIOLOGICALCHEMISTRY 0 1993by The American Societyfor Biochemistry and Moleculal' Biology, Inc
Comparative protein structure modeling Andrs Fiser and Andrej Sali
INVITED ARTICLE Structural genomics: A pipeline for providing
Classifying Variants of Undetermined Significance in BRCA2 with Protein Likelihood Ratios
Proc. Natl. Acad. Sci. USA Vol. 95, pp. 1359713602, November 1998
2 -28NSLS Activity Report 2001 Structural Genomics at the National Synchrotron
Cell, Vol. 91, 335345, October 31, 1997, Copyright 1997 by Cell Press Crystal Structure of the Subunit
This article was originally published in a journal published by Elsevier, and the attached copy is provided by Elsevier for the
986 nature structural biology structural genomics supplement november 2000 Evolution has produced families of pro-
The Tryptase, Mouse Mast Cell Protease 7, Exhibits Anticoagulant Activity in Vivo and in Vitro Due to Its Ability to Degrade
BIOINFORMATICS APPLICATIONS NOTE Vol. 19 no. 18 2003, pages 25002501
4.10 Comparative Modeling of Drug Target N Eswar and A Sali, University of California at San Francisco, San Francisco, CA, USA
10.1110/ps.072855507Access the most recent version at doi: 2007 16: 2030-2041Protein Sci.
COCEBI-649; NO OF PAGES 12 Please cite this article in press as: Russel D, et al. The structural dynamics of macromolecular processes, Curr Opin Cell Biol (2009), doi:10.1016/j.ceb.2009.01.022
Journal of Biomolecular NMR, 19: 289290, 2001. KLUWER/ESCOM
SHORT COMMUNICATION Variable gap penalty for protein sequencestructure
Neuron, Vol. 23, 105114, May, 1999, Copyright 1999 by Cell Press lynx1, an Endogenous Toxin-like Modulator
meeting review nature structural biology volume 5 number 12 december 1998 1029
[CANCER RESEARCH 64, 37903797, June 1, 2004] Structure-Based Assessment of Missense Mutations in Human BRCA1: Implications
Protein Structure Fitting and Refinement Guided by cryoEM Maya Topf1,*, Keren Lasker2,3, Ben Webb2, Haim Wolfson3, Wah Chiu4, and Andrej Sali2,*
Protein Science (1992), I , 216-226. Cambridge University Press. Printed in the USA Copyright 0 1992 The Protein Society 0961-8368/92 $5.00 + .OO
1999 Macmillan Magazines Ltd (orT)violationarisesonlyfromeffectsofthe
insight review articles 216 NATURE | VOL 422 | 13 MARCH 2003 | www.nature.com/nature
Structure of the Mammalian 80S Ribosome at 8.7 A Resolution
Integrative Structure Modeling of Macromolecular Assemblies from Proteomics Data*
10.1110/ps.062095806Access the most recent version at doi: 2006 15: 1653-1666; originally published online Jun 2, 2006;Protein Sci.
Biol. Chem., Vol. 385, pp. 363372, May 2004 Copyright by Walter de Gruyter Berlin New York 2004/311140
Functional hot spots in human ATP-binding cassette transporter
Selecting Optimum Eukaryotic Integral Membrane Proteins for Structure Determination by Rapid
Role of organic cation transporter 3 (SLC22A3) and its missense variants in the pharmacologic action of metformin
Comparative Protein Structure Modeling and its Applications to Drug Discovery
Detecting remotely related proteins by their interactions and sequence similarity
The Structure of Chagasin in Complex with a Cysteine Protease Clarifies the Binding
Tryptase 4, a New Member of the Chromosome 17 Family of Mouse Serine Proteases*
Components of Coated Vesicles and Nuclear Pore Complexes
A novel conformation of E. coli Hsp90 in solution: insights into the conformational dynamics of Hsp90
FoXS: a web server for rapid computation and fitting of SAXS profiles
Functional Impact of Missense Variants in BRCA1 Predicted by Supervised Learning
Human Tryptase (PRSS22), a New Member of the Chromosome 16p13.3 Family of Human Serine Proteases Expressed in Airway
Structural genomics of enzymes involved in sterol isoprenoid biosynthesis
heavily penalized, since in this case chances of having Livermore, California 94551 Sanger Centremodels in common with other groups are lower. One
Proc. Natl. Acad. Sci. USA Vol. 96, pp. 62856290, May 1999
Protein Engineering vol 5 no 1 pp.43-51. 1992 A variable gap penalty function and feature weights for protein
Ligand Specificity of Brain Lipid-binding Protein* (Received for publication, April 19, and in revised from, July 10, 1996)
Detection of homologous proteins by an intermediate sequence search
Genomic-scale prioritization of drug targets: the TDR Targets database
Structure determination of macromolecular complexes by experiment and computation
BIOINFORMATICS ORIGINAL PAPER Vol. 25 no. 12 2009, pages 15061512
Mol. Biol. Evol. 17(8):11561163. 2000 2000 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038
Modeling of loops in protein structures ANDRS FISER, RICHARD KINH GIAN DO, and ANDREJ SALI
Inferential Optimization for Simultaneous Fitting of Multiple Components into a CryoEM Map of
PROTEIN INTERACTIONS AND DISEASE PHENOTYPES IN THE ABC TRANSPORTER SUPERFAMILY
COMMUNICATION Crystallographic Conformers of Actin in a Biologically
Global Motions of the Nuclear Pore Complex: Insights from Elastic Network Models
Published: January 28, 2011 r 2011 American Chemical Society 2080 dx.doi.org/10.1021/ja110157u |J. Am. Chem. Soc. 2011, 133, 20802083
High-Throughput Computational and Experimental Techniques in Structural Genomics
10.1110/ps.062247506Access the most recent version at doi: 2006 15: 2366-2380; originally published online Sep 8, 2006;Protein Sci.
Domain Organization of Escherichia coli Transcript Cleavage Factors GreA and GreB*
Proc. Natl. Acad. Sci. USA Vol. 93, pp. 83568361, August 1996
Stereochemical Criteria for Prediction of the Effects of Proline Mutations
Global Sequencing of Proteolytic Cleavage Sites in Apoptosis by
2007 Annual progress report synopsis of the Center for Structures of Membrane Proteins
Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy
Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT Christopher R Booth1,2,5, Anne S Meyer3,5, Yao Cong2, Maya Topf4,5, Andrej Sali4, Steven
Fold assessment for comparative protein structure FRANCISCO MELO1
Identification of a New Member of the Tryptase Family of Mouse and Human Mast Cell Proteases Which Possesses a
Identification and characterization of a p53 homologue in Drosophila melanogaster
IMPRO VING FUNC TIO NAL ANNO TATIO N O F NO N-S YNO NO MO US S NPs
320 volume 27 number 4 april 2009 nature biotechnology Table 1 TDI kernel genomes
proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS Determining macromolecular assembly
A cell consists of hundreds of different functional modules, such as the RNA exosome, the proteasome and the nuclear pore complex
10.1110/ps.062416606Access the most recent version at doi: 2006 15: 2507-2524Protein Sci.
PharmGKB Submission Update: IV. PMT Submissions of Genetic Variations in ATP-
MODBASE: a database of annotated comparative protein structure models and associated resources
Insights into the molecular architecture of the 26S proteasome
Statistical potentials for fold assessment FRANCISCO MELO,1
Journal of Clinical Immunology, Vol. 18, No. 3, 1998 Special Article
Advances in comparative protein-structure modelling Roberto Sanchez and Andrej Sali
Temperature dependence of the folding rate in a simple protein model: Search for a ``glass'' transition
Tools for comparative protein structure modeling and analysis
RasGRP4, a New Mast Cell-restricted Ras Guanine Nucleotide-releasing Protein with Calcium-and Diacylglycerol-binding Motifs
Alignment of multiple protein structures based on sequence and structure features
Evolutionary constraints on structural similarity in orthologs and paralogs
HEMOSTASIS, THROMBOSIS, AND VASCULAR BIOLOGY Urokinase-type plasminogen activator is a preferred substrate of the human
BIOINFORMATICS APPLICATIONS NOTE Vol. 17 no. 8 2001
nature genetics volume 27 march 2001 337 Homology-based annotation yields 1,042 new candidate
Prediction of Protease Substrates Using Sequence and Structure David T. Barkan1,2,3,+, Daniel R. Hostetter3,+, Sami Mahrus3, Ursula Pieper2,3, James A.
Subscriber access provided by -Access paid by the | UCSF Library Biochemistry is published by the American Chemical Society. 1155 Sixteenth Street
ModBase, a database of annotated comparative protein structure models, and associated resources
Response to "PREDICTABLE DIFFICULTY OR DIFFICULTY TO PREDICT" by Tams Arnyi, Krisztina Fulop, Orsolya Symmons, Viola Pomozi, and Andrs Vradi
Macromolecular docking restrained by a small angle X-ray scattering profile Dina Schneidman-Duhovny a,
Toward an Integrated Structural Model of the 26S Proteasome*
An atomic model AAA-ATPase/20S core particle sub-complex of the 26S Friedrich Frster a,b
A survey of integral a-helical membrane proteins Libusha Kelly Ursula Pieper Narayanan Eswar
Regulatory Elements within the Prodomain of Falcipain-2, a Cysteine Protease of the Malaria Parasite
A Kernel for Open Source Drug Discovery in Tropical Leticia Orti1,2
Ratiocinative screen of eukaryotic integral membrane protein expression and solubilization for structure determination
Published online 23 October 2008 Nucleic Acids Research, 2009, Vol. 37, Database issue D347D354 doi:10.1093/nar/gkn791
Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies
Subnanometer-resolution electron cryomicroscopy-based domain models for the
Evolutionarily Conserved Substrate Substructures for Automated Annotation of Enzyme Superfamilies
10.1101/gad.1646208Access the most recent version at doi: 2008 22: 854-859 originally published online March 11, 2008Genes Dev.
Integration of Small-Angle X-Ray Scattering Data into Structural Modeling of Proteins and Their Assemblies
10.1110/ps.036061.108Access the most recent version at doi: 2008 17: 1881-1893; originally published online Oct 1, 2008;Protein Sci.
Integrating Diverse Data for Structure Determination of
Gene Expression Profiling of the Human Maternal-Fetal Interface Reveals Dramatic Changes between
Structural Genomics Structural genomics is an ongoing worldwide effort that is attempting to characterize the structures of most proteins
Structural genomics of protein phosphatases Steven C. Almo Jeffrey B. Bonanno J. Michael Sauder Spencer Emtage
Characterization of Protein Hubs by Inferring Interacting Motifs from Protein Interactions
Epilepsia, **(*):110, 2007 Blackwell Publishing, Inc.
UNIT 5.6Comparative Protein Structure Modeling Using Modeller
UNIT 5.6Comparative Protein Structure Modeling Using Modeller
Refinement of Protein Structures by Iterative Comparative Modeling and CryoEM Density Fitting
Combining electron microscopy and comparative protein structure modeling
Multiple cathepsin B isoforms in schistosomula of Trichobilharzia regenti: identification, characterisation and putative role
BIOINFORMATICS ORIGINAL PAPER Vol. 21 no. 12 2005, pages 28142820
Comparative Protein Structure Modeling 831 From: The Proteomics Protocols Handbook
PLoS Medicine | www.plosmedicine.org 180 nly about 1% of newly developed drugs are for
Computation plays an increasing role in biol-ogy. The convergence between computing and
Alignment of protein sequences by their profiles MARC A. MARTI-RENOM, M.S. MADHUSUDHAN, AND ANDREJ SALI
INTRODUCTION One central question in vertebrate development is how
Cell, Vol. 113, 789801, June 13, 2003, Copyright 2003 by Cell Press Study of the Structural Dynamics of the E. coli
Comparative protein structure modeling by iterative alignment, model building and model assessment
UNIT 5.1Modeling Protein Structure from Its Sequence Functional characterization of a protein sequence is one of the most frequent problems
BIOINFORMATICS APPLICATIONS NOTE Vol. 19 no. 1 2003
Use of Single Point Mutations in Domain I of 2-Glycoprotein I to Determine Fine Antigenic Specificity of Antiphospholipid
Probing the specificity of a trypanosomal aromatic a-hydroxy acid dehydrogenase by site-directed mutagenesisq
news and views 482 nature structural biology volume 8 number 6 june 2001
1156 nature structural biology volume 7 number 12 december 2000 Protein synthesis in eukaryotes depends critically on the avail-
Formation of Enzymatically Active, Homotypic, and Heterotypic Tetramers of Mouse Mast Cell Tryptases
o understand fully the workings of the cell, we face the challenge of describing the three-dimensional structures of
Cell, Vol. 94, 439449, August 21, 1998, Copyright 1998 by Cell Press Crystal Structure of a GCN5-Related
Site-directedMutagenesis of Recombinant Human Pz-GlycoproteinI
Mouse Mast Cell Protease 9, a Novel Member of the Chromosome 14 Family of Serine Proteases that is Selectively Expressed in
Site-Directed Mutagenesis of Recombinant Human &-Glycoprotein I Identifies a Cluster of LysineResidues That
Protein Science (1992), I , 322-328. Cambridge University Press. Printed in the USA. Copyright 0 1992 The Protein Society
Protein Structure Modeling With MODELLER Narayanan Eswar$
Genetic Polymorphisms in Organic Cation Transporter 1 (OCT1) in Chinese and Japanese Populations Exhibit Altered
A knowledge of the potential
nature genetics volume 23 october 1999 151 Structural genomics
Comparison of human solute carriers Avner Schlessinger,1,2,3
Evolution and Physics in Comparative Protein Structure
Comprehensive Molecular Structure of the Eukaryotic Ribosome
Structure-based discovery of prescription drugs that interact with the norepinephrine transporter, NET
The Rockefeller University Press J. Cell Biol. Vol. 193 No. 6 963972
MultiFit: a web server for fitting multiple protein structures into their electron microscopy
Macromolecular assembly structures by comparative modeling and electron microscopy
Modeling of proteins and their assemblies with the Integrative
r XXXX American Chemical Society A dx.doi.org/10.1021/cb200198c |ACS Chem. Biol. XXXX, XXX, 000000 pubs.acs.org/acschemicalbiology
Virtual Ligand Screening Against Comparative Protein Structure Models , John J. Irwin2
2011NatureAmerica,Inc.Allrightsreserved. nature CHeMICaL BIOLOGY | AdvAnce online publicAtion | www.nature.com/naturechemicalbiology 1
CliniCal pharmaCology & TherapeuTiCs 1 articlesnature publishing group
Subscriber access provided by -Access paid by the | UCSF Library Journal of Chemical Information and Modeling is published by the American
UCSF Chimera, MODELLER, and IMP: An integrated modeling system Zheng Yang a
The Enzyme Function Initiative John A. Gerlt,*,,
Meeting Review Outcome of the First Electron Microscopy
Biol. Chem., Vol. 393, pp. 177186, March 2012 Copyright by Walter de Gruyter Berlin Boston. DOI 10.1515/hsz-2011-0219 Biochemical characterization and structural modeling
Community Page Putting the Pieces Together: Integrative Modeling
The proteasomal subunit Rpn6 is a molecular clamp holding the core and regulatory
Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach
JCB: Article The Rockefeller University Press $30.00