Andrej Sali

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Components of coated vesicles and nuclear pore complexes share a common molecular architecture
    Damien Devos
    Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, University of California, San Francisco, USA
    PLoS Biol 2:e380. 2004
  2. pmc Prediction of enzyme function by combining sequence similarity and protein interactions
    Jordi Espadaler
    Laboratori de Bioinformàtica Estructural GRIB, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra IMIM, 08003 Barcelona, Catalonia, Spain
    BMC Bioinformatics 9:249. 2008
  3. pmc The AnnoLite and AnnoLyze programs for comparative annotation of protein structures
    Marc A Marti-Renom
    Structural Genomics Unit, Bioinformatics Department, Centro de Investigacion Principe Felipe, Valencia, Spain
    BMC Bioinformatics 8:S4. 2007
  4. ncbi request reprint NIH workshop on structural proteomics of biological complexes
    Andrej Sali
    Department of Biopharmaceutical Sciences and California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94143, USA
    Structure 11:1043-7. 2003
  5. pmc DBAli tools: mining the protein structure space
    Marc A Marti-Renom
    Structural Genomics Unit, and California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, CA 94158 2330, USA
    Nucleic Acids Res 35:W393-7. 2007
  6. pmc MODBASE: a database of annotated comparative protein structure models and associated resources
    Ursula Pieper
    Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, QB3 at Mission Bay, Office 503B, University of California at San Francisco 1700 4th Street, San Francisco, CA 94158, USA
    Nucleic Acids Res 34:D291-5. 2006
  7. pmc Simple fold composition and modular architecture of the nuclear pore complex
    Damien Devos
    Department of Biopharmaceutical Sciences, University of California, Mission Bay QB3, 1700 4th Street, Suite 503B, San Francisco, CA 94143 2552, USA
    Proc Natl Acad Sci U S A 103:2172-7. 2006
  8. ncbi request reprint The molecular architecture of the nuclear pore complex
    Frank Alber
    Department of Bioengineering and Therapeutic Sciences, and California Institute for Quantitative Biosciences, Mission Bay QB3, 1700 4th Street, Suite 503B, University of California at San Francisco, San Francisco, California 94158 2330, USA
    Nature 450:695-701. 2007
  9. pmc Structural basis for alternating access of a eukaryotic calcium/proton exchanger
    Andrew B Waight
    Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158, USA
    Nature 499:107-10. 2013
  10. pmc Structural modeling of protein interactions by analogy: application to PSD-95
    Dmitry Korkin
    Department of Biopharmaceutical Sciences, University of California San Francisco, San Francisco, California, United States of America
    PLoS Comput Biol 2:e153. 2006

Collaborators

Detail Information

Publications120 found, 100 shown here

  1. pmc Components of coated vesicles and nuclear pore complexes share a common molecular architecture
    Damien Devos
    Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, University of California, San Francisco, USA
    PLoS Biol 2:e380. 2004
    ..These similarities suggest a common evolutionary origin for nuclear pore complexes and coated vesicles in an early membrane-curving module that led to the formation of the internal membrane systems in modern eukaryotes...
  2. pmc Prediction of enzyme function by combining sequence similarity and protein interactions
    Jordi Espadaler
    Laboratori de Bioinformàtica Estructural GRIB, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra IMIM, 08003 Barcelona, Catalonia, Spain
    BMC Bioinformatics 9:249. 2008
    ..Here, we introduce a computational approach for annotation of enzymes, based on the observation that similar protein sequences are more likely to perform the same function if they share similar interacting partners...
  3. pmc The AnnoLite and AnnoLyze programs for comparative annotation of protein structures
    Marc A Marti-Renom
    Structural Genomics Unit, Bioinformatics Department, Centro de Investigacion Principe Felipe, Valencia, Spain
    BMC Bioinformatics 8:S4. 2007
    ..Here we introduce two programs, AnnoLite and AnnoLyze, which use the structural alignments deposited in the DBAli database...
  4. ncbi request reprint NIH workshop on structural proteomics of biological complexes
    Andrej Sali
    Department of Biopharmaceutical Sciences and California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94143, USA
    Structure 11:1043-7. 2003
    ....
  5. pmc DBAli tools: mining the protein structure space
    Marc A Marti-Renom
    Structural Genomics Unit, and California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, CA 94158 2330, USA
    Nucleic Acids Res 35:W393-7. 2007
    ..Thus, the DBAli tools, which are freely accessible via the World Wide Web at http://salilab.org/DBAli/, allow users to mine the protein structure space by establishing relationships between protein structures and their functions...
  6. pmc MODBASE: a database of annotated comparative protein structure models and associated resources
    Ursula Pieper
    Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, QB3 at Mission Bay, Office 503B, University of California at San Francisco 1700 4th Street, San Francisco, CA 94158, USA
    Nucleic Acids Res 34:D291-5. 2006
    ..org/pibase) as well as predictions of ligand binding sites, interactions between yeast proteins, and functional consequences of human nsSNPs (LS-SNP, http://salilab.org/LS-SNP)...
  7. pmc Simple fold composition and modular architecture of the nuclear pore complex
    Damien Devos
    Department of Biopharmaceutical Sciences, University of California, Mission Bay QB3, 1700 4th Street, Suite 503B, San Francisco, CA 94143 2552, USA
    Proc Natl Acad Sci U S A 103:2172-7. 2006
    ..The small number of predicted fold types in the NPC and their internal symmetries suggest that the bulk of the NPC structure has evolved through extensive motif and gene duplication from a simple precursor set of only a few proteins...
  8. ncbi request reprint The molecular architecture of the nuclear pore complex
    Frank Alber
    Department of Bioengineering and Therapeutic Sciences, and California Institute for Quantitative Biosciences, Mission Bay QB3, 1700 4th Street, Suite 503B, University of California at San Francisco, San Francisco, California 94158 2330, USA
    Nature 450:695-701. 2007
    ..These findings provide clues to the evolutionary origins of the NPC...
  9. pmc Structural basis for alternating access of a eukaryotic calcium/proton exchanger
    Andrew B Waight
    Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158, USA
    Nature 499:107-10. 2013
    ....
  10. pmc Structural modeling of protein interactions by analogy: application to PSD-95
    Dmitry Korkin
    Department of Biopharmaceutical Sciences, University of California San Francisco, San Francisco, California, United States of America
    PLoS Comput Biol 2:e153. 2006
    ..More generally, we expect that comparative patch analysis will provide useful spatial restraints for the structural characterization of an increasing number of binary and higher-order protein complexes...
  11. pmc Protein complex compositions predicted by structural similarity
    Fred P Davis
    Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, University of California San Francisco, 1700 4th Street, Byers Hall, San Francisco, CA 94143 2552, USA
    Nucleic Acids Res 34:2943-52. 2006
    ..cerevisiae will contribute to expansion of the structural and functional coverage of protein interaction space. The predicted complexes are deposited in MODBASE (http://salilab.org/modbase)...
  12. doi request reprint Modeling of proteins and their assemblies with the integrative modeling platform
    Benjamin Webb
    Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, USA
    Methods Mol Biol 781:377-97. 2011
    ..We also demonstrate the Integrative Modeling Platform (IMP) software, which provides the necessary computational framework to implement this protocol, and several applications for specific-use cases...
  13. pmc A survey of integral alpha-helical membrane proteins
    Libusha Kelly
    Graduate Group in Bioinformatics, University of California at San Francisco, San Francisco, CA, USA
    J Struct Funct Genomics 10:269-80. 2009
    ....
  14. pmc Structure-based discovery of prescription drugs that interact with the norepinephrine transporter, NET
    Avner Schlessinger
    Department of Bioengineering and Therapeutic Sciences, and California Institute for Quantitative Biosciences, University of California, San Francisco, CA 94158, USA
    Proc Natl Acad Sci U S A 108:15810-5. 2011
    ..The observations highlight the utility of virtual screening against a comparative model, even when the target shares less than 30% sequence identity with its template structure and no known ligands in the primary binding site...
  15. pmc Host pathogen protein interactions predicted by comparative modeling
    Fred P Davis
    Department of Biopharmaceutical Sciences, University of California at San Francisco, San Francisco, California 94158, USA
    Protein Sci 16:2585-96. 2007
    ..Our computational method provides a means to mine whole-genome data and is complementary to experimental efforts in elucidating networks of host-pathogen protein interactions...
  16. pmc UCSF Chimera, MODELLER, and IMP: an integrated modeling system
    Zheng Yang
    Resource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
    J Struct Biol 179:269-78. 2012
    ....
  17. pmc Statistical potential for modeling and ranking of protein-ligand interactions
    Hao Fan
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, USA
    J Chem Inf Model 51:3078-92. 2011
    ..The statistical potentials are available through the Integrative Modeling Platform (IMP) software package (http://salilab.org/imp) and the LigScore Web server (http://salilab.org/ligscore/)...
  18. pmc MODBASE, a database of annotated comparative protein structure models and associated resources
    Ursula Pieper
    Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, USA
    Nucleic Acids Res 37:D347-54. 2009
    ..MODBASE models are also available through the Protein Model Portal (http://www.proteinmodelportal.org/)...
  19. pmc Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies
    Daniel Russel
    Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences QB3, University of California, San Francisco, San Francisco, California, United States of America
    PLoS Biol 10:e1001244. 2012
    ....
  20. doi request reprint Macromolecular assembly structures by comparative modeling and electron microscopy
    Keren Lasker
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
    Methods Mol Biol 857:331-50. 2012
    ..In particular, we provide detailed instructions for density map-guided modeling using the Integrative Modeling Platform (IMP), MODELLER, and UCSF Chimera...
  21. pmc MODBASE, a database of annotated comparative protein structure models, and associated resources
    Ursula Pieper
    Department of Biopharmaceutical Sciences, and California Institute for Quantitative Biomedical Research, Mission Bay Genentech Hall, 600 16th Street, Suite N472D, University of California San Francisco, San Francisco, CA 94143 2240, USA
    Nucleic Acids Res 32:D217-22. 2004
    ..org/modweb), modeling of loops in protein structures (MODLOOP, http://salilab.org/modloop) and predicting functional consequences of single nucleotide polymorphisms (SNPWEB, http://salilab. org/snpweb)...
  22. ncbi request reprint LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources
    Rachel Karchin
    Department of Biopharmaceutical Sciences, University of California at San Francisco, San Francisco, CA 94143, USA
    Bioinformatics 21:2814-20. 2005
    ..SNPs that result in amino acid residue changes (nsSNPs) are of critical importance in variation between individuals, including disease and drug sensitivity...
  23. pmc SALIGN: a web server for alignment of multiple protein sequences and structures
    Hannes Braberg
    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
    Bioinformatics 28:2072-3. 2012
    ..All features of the server have been previously optimized for accuracy, especially in the contexts of comparative modeling and identification of interacting protein partners...
  24. pmc Alignment of protein sequences by their profiles
    Marc A Marti-Renom
    Mission Bay Genentech Hall, University of California, San Francisco, San Francisco, CA 94143, USA
    Protein Sci 13:1071-87. 2004
    ..The new method is currently applied to large-scale comparative protein structure modeling of all known sequences...
  25. pmc Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies
    Ursula Pieper
    Department of Biopharmaceutical Sciences, California Institute for Quantitative Biosciences, University of California at San Francisco, San Francisco, CA 94158, USA
    J Struct Funct Genomics 10:107-25. 2009
    ....
  26. pmc Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies
    Ranyee A Chiang
    Department of Biopharmaceutical Sciences, California Institute for Quantitative Biosciences, University of California at San Francisco, San Francisco, California, United States of America
    PLoS Comput Biol 4:e1000142. 2008
    ..Because the method is automated, it is suitable for large-scale characterization and comparison of fundamental functional capabilities of both characterized and uncharacterized enzyme superfamilies...
  27. pmc Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies
    Friedrich Förster
    Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, CA 94158, USA
    J Mol Biol 382:1089-106. 2008
    ..Our integration of a SAXS profile into modeling by satisfaction of spatial restraints will facilitate further integration of different kinds of data for structure determination of proteins and their assemblies...
  28. doi request reprint ModBase, a database of annotated comparative protein structure models and associated resources
    Ursula Pieper
    Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, Byers Hall at Mission Bay, Office 503B, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, USA, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall at Mission Bay, Office 503B, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, USA, Graduate Group in Biophysics, University of California at San Francisco, CA 94158, USA, Structural Bioinformatics Unit, Structural Biology and Chemistry Department, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France, Universite Paris Diderot Paris 7, école doctorale iViv, Paris Rive Gauche, 5 rue Thomas Mann, 75013 Paris, France, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, Department of Molecular Biology, Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA, Life Sciences Division, Department of Molecular Biology, Stanford
    Nucleic Acids Res 42:D336-46. 2014
    ....
  29. doi request reprint Protein structure modeling with MODELLER
    Narayanan Eswar
    Department of Biopharmaceutical Sciences and California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, CA, USA
    Methods Mol Biol 426:145-59. 2008
    ..Automation of similar protocols (correction of protcols) has resulted in models of useful accuracy for domains in more than half of all known protein sequences...
  30. doi request reprint Comparative protein structure modeling using MODELLER
    Narayanan Eswar
    University of California at San Francisco, San Francisco, California, USA
    Curr Protoc Protein Sci . 2007
    ..Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described...
  31. pmc Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images
    Javier Velázquez-Muriel
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158 2552, USA
    Proc Natl Acad Sci U S A 109:18821-6. 2012
    ..Thus, integrative structural biology can now benefit from the relative ease with which the EM class averages are determined...
  32. pmc High selectivity of the γ-aminobutyric acid transporter 2 (GAT-2, SLC6A13) revealed by structure-based approach
    Avner Schlessinger
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94158, USA
    J Biol Chem 287:37745-56. 2012
    ..Our combined approach may be useful for characterizing interactions between small molecules and other membrane proteins, as well as for describing substrate specificities in other protein families...
  33. pmc Localization of protein-binding sites within families of proteins
    Dmitry Korkin
    Department of Biopharmaceutical Sciences, University of California at San Francisco, San Francisco, CA 94143 2552, USA
    Protein Sci 14:2350-60. 2005
    ..Consideration of the binding site localization may also result in spatial restraints for the modeling of protein assembly structures...
  34. doi request reprint Integrating diverse data for structure determination of macromolecular assemblies
    Frank Alber
    Department of Biopharmaceutical Sciences, and California Institute for Quantitative Biosciences, University of California at San Francisco, CA 94158 2330, USA
    Annu Rev Biochem 77:443-77. 2008
    ..With these tools, we are poised to integrate structural information gathered at multiple levels of the biological hierarchy--from atoms to cells--into a common framework...
  35. pmc Ligand discovery from a dopamine D3 receptor homology model and crystal structure
    Jens Carlsson
    Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
    Nat Chem Biol 7:769-78. 2011
    ..3 to 3.0 μM. One of the new ligands from the homology model screen was optimized for affinity to 81 nM. The feasibility of docking screens against modeled GPCRs more generally is considered...
  36. pmc Prediction of protease substrates using sequence and structure features
    David T Barkan
    Graduate Group in Bioinformatics, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
    Bioinformatics 26:1714-22. 2010
    ..Our approach can act as a convenient hypothesis generator, guiding future experiments by high-confidence identification of peptide-protein partners...
  37. ncbi request reprint PIBASE: a comprehensive database of structurally defined protein interfaces
    Fred P Davis
    Graduate Group in Biophysics, California Institute for Quantitative Biomedical Research, University of California, San Francisco, 94143, USA
    Bioinformatics 21:1901-7. 2005
    ..It is composed of binary interfaces extracted from structures in the PDB and the Probable Quaternary Structure server using domain assignments from the Structural Classification of Proteins and CATH fold classification systems...
  38. pmc Alignment of multiple protein structures based on sequence and structure features
    M S Madhusudhan
    Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, CA 94158, USA
    Protein Eng Des Sel 22:569-74. 2009
    ..The utility of accurate multiple structure alignment is illustrated by its application to comparative protein structure modeling...
  39. pmc Crystal structure of a eukaryotic phosphate transporter
    Bjørn P Pedersen
    Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158, USA
    Nature 496:533-6. 2013
    ..The PiPT structure demonstrates and expands on principles of substrate transport by the MFS transporters and illuminates principles of phosphate uptake in particular...
  40. pmc Impact of mutations on the allosteric conformational equilibrium
    Patrick Weinkam
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
    J Mol Biol 425:647-61. 2013
    ..We also assess which calculated thermodynamic properties contribute most to the accuracy of the prediction...
  41. ncbi request reprint Refinement of protein structures by iterative comparative modeling and CryoEM density fitting
    Maya Topf
    Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, QB3, 1700 4th Street, Suite 503B, University of California at San Francisco, San Francisco, CA 94143 2552, USA
    J Mol Biol 357:1655-68. 2006
    ..The method is being implemented in our program MODELLER for protein structure modeling by satisfaction of spatial restraints and will be applicable to the rapidly increasing number of cryoEM density maps of macromolecular assemblies...
  42. pmc Integrative structure modeling of macromolecular assemblies from proteomics data
    Keren Lasker
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94158, USA
    Mol Cell Proteomics 9:1689-702. 2010
    ..Correspondingly, integrative computational methods are being developed to provide descriptions of protein complexes at varying levels of accuracy and resolution, ranging from complex compositions to detailed atomic structures...
  43. doi request reprint Modeling of proteins and their assemblies with the Integrative Modeling Platform
    Benjamin Webb
    Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quanstitative Biosciences QB3, University of California San Francisco, San Francisco, CA, USA
    Methods Mol Biol 1091:277-95. 2014
    ..We also demonstrate the Integrative Modeling Platform (IMP) software, which provides the necessary computational framework to implement this protocol, and several applications for specific use cases. ..
  44. pmc Institutional Profile: The University of California Pharmacogenomics Center: at the interface of genomics, biological mechanisms and drug therapy
    Deanna L Kroetz
    Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, CA, USA
    Pharmacogenomics 10:1569-76. 2009
    ..A key emphasis of the Center is on biological mechanisms with a goal of facilitating the development of safer and more effective medications...
  45. pmc Function of human Rh based on structure of RhCG at 2.1 A
    Franz Gruswitz
    Department of Biochemistry and Biophysics, S412C Genentech Hall, Center for the Structure of Membrane Proteins, and Membrane Protein Expression Center, University of California, San Francisco, CA 94158, USA
    Proc Natl Acad Sci U S A 107:9638-43. 2010
    ..Models of the erythrocyte Rh complex based on our RhCG structure suggest that the erythrocytic Rh complex is composed of stochastically assembled heterotrimers of RhAG, RhD, and RhCE...
  46. pmc Virtual ligand screening against comparative protein structure models
    Hao Fan
    Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, USA
    Methods Mol Biol 819:105-26. 2012
    ..Here, we describe an integrated modeling and docking protocol, combining comparative modeling by MODELLER and virtual ligand screening by DOCK...
  47. pmc Global identification and characterization of both O-GlcNAcylation and phosphorylation at the murine synapse
    Jonathan C Trinidad
    Department of Pharmaceutical Chemistry, UCSF, San Francisco, California 94158, USA
    Mol Cell Proteomics 11:215-29. 2012
    ..As a class, protein kinases are found to be more extensively O-GlcNAcylated than proteins in general, indicating the potential for crosstalk of phosphorylation with O-GlcNAcylation via regulation of enzymatic activity...
  48. pmc Localization of binding sites in protein structures by optimization of a composite scoring function
    Andrea Rossi
    Department of Biopharmaceutical Sciences and Pharmaceutical Chemistry, California Institute for Quantitative Biomedical Research, University of California, San Francisco, California 94143 2552, USA
    Protein Sci 15:2366-80. 2006
    ..The method is completely automated (http://salilab.org/patcher) and can be applied on a large scale in a structural genomics setting...
  49. pmc A composite score for predicting errors in protein structure models
    David Eramian
    Graduate Group in Biophysics, Department of Biopharmaceutical Sciences, University of California at San Francisco 94158, USA
    Protein Sci 15:1653-66. 2006
    ..It was implemented in the SVMod program, which can now be applied to select the final model in various modeling problems, including fold assignment, target-template alignment, and loop modeling...
  50. pmc Statistical potential for assessment and prediction of protein structures
    Min Yi Shen
    Department of Biopharmaceutical Sciences, Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94158, USA
    Protein Sci 15:2507-24. 2006
    ....
  51. pmc Functional hot spots in human ATP-binding cassette transporter nucleotide binding domains
    Libusha Kelly
    Graduate Group in Bioinformatics, University of California at San Francisco, San Francisco, California, USA
    Protein Sci 19:2110-21. 2010
    ..Our analysis provides a structural and evolutionary framework for rationalizing and predicting the functional effects of nsSNPs in this clinically important membrane transporter superfamily...
  52. pmc MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map
    Elina Tjioe
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
    Nucleic Acids Res 39:W167-70. 2011
    ..The models can be viewed online or downloaded from the website. The service is available at; http://salilab.org/multifit/ and http://bioinfo3d.cs.tau.ac.il/...
  53. pmc Selecting optimum eukaryotic integral membrane proteins for structure determination by rapid expression and solubilization screening
    Min Li
    Membrane Protein Expression Center, University of California at San Francisco, San Francisco, CA 94158 2517, USA
    J Mol Biol 385:820-30. 2009
    ..This discovery-oriented pipeline provides an efficient way to select proteins from particular membrane protein classes, families, or organisms that may be more suited to structure analysis than others...
  54. pmc 2007 annual progress report synopsis of the Center for Structures of Membrane Proteins
    Robert M Stroud
    The Center for Structures of Membrane Proteins CSMP, UCSF, San Francisco, CA 94158 2517, USA
    J Struct Funct Genomics 10:193-208. 2009
    ..A synopsis of the 2007 annual progress report for the Center for Structures of Membrane Proteins, a specialized center of the Protein Structure Initiative...
  55. doi request reprint Discovery of potent, selective multidrug and toxin extrusion transporter 1 (MATE1, SLC47A1) inhibitors through prescription drug profiling and computational modeling
    Matthias B Wittwer
    University of California, San Francisco, Department of Bioengineering and Therapeutic Sciences RH 581, 1550 Fourth Street, San Francisco, California 94158, USA
    J Med Chem 56:781-95. 2013
    ..In parallel, a QSAR model identified distinct molecular properties of MATE1 versus OCT2 inhibitors and was used to screen the DrugBank in silico library for new hits in a larger chemical space...
  56. pmc Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach
    Keren Lasker
    Department of Bioengineering and Therapeutic Sciences, California Institute of Quantitative Biosciences, 1700 4th Street, University of California, San Francisco, CA 94158, USA
    Proc Natl Acad Sci U S A 109:1380-7. 2012
    ..The modular structure of the 26S proteasome provides insights into the sequence of events prior to the degradation of ubiquitylated substrates...
  57. pmc A method for integrative structure determination of protein-protein complexes
    Dina Schneidman-Duhovny
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
    Bioinformatics 28:3282-9. 2012
    ..On the other hand, computational methods for modeling assembly structures from individual components frequently suffer from high false-positive rate, rarely resulting in a unique solution...
  58. pmc Assignment of pterin deaminase activity to an enzyme of unknown function guided by homology modeling and docking
    Hao Fan
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94143, USA
    J Am Chem Soc 135:795-803. 2013
    ..Homology model-based virtual screening, especially with modeling of protein backbone flexibility, may be broadly useful for enzyme function annotation and discovering new pathways and drug targets...
  59. pmc Evolutionary constraints on structural similarity in orthologs and paralogs
    Mark E Peterson
    Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1700 4th Street, San Francisco, CA 94158, USA
    Protein Sci 18:1306-15. 2009
    ..These differences between orthologs and paralogs are expected to be useful for selecting template structures in comparative modeling and target proteins in structural genomics...
  60. pmc Structure-based ligand discovery for the Large-neutral Amino Acid Transporter 1, LAT-1
    Ethan G Geier
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
    Proc Natl Acad Sci U S A 110:5480-5. 2013
    ..Finally, two of our hits inhibited proliferation of a cancer cell line by distinct mechanisms, providing useful chemical tools to characterize the role of LAT-1 in cancer metabolism...
  61. pmc Vif hijacks CBF-β to degrade APOBEC3G and promote HIV-1 infection
    Stefanie Jäger
    Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, USA
    Nature 481:371-5. 2012
    ..Methods of disrupting the CBF-β-Vif interaction might enable HIV-1 restriction and provide a supplement to current antiviral therapies that primarily target viral proteins...
  62. ncbi request reprint Structural characterization of assemblies from overall shape and subcomplex compositions
    Frank Alber
    Department of Biopharmaceutical Sciences and, California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, California 94143, USA
    Structure 13:435-45. 2005
    ..Testing of the approach with model systems suggests its feasibility...
  63. pmc Molecular docking screens using comparative models of proteins
    Hao Fan
    Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, San Francisco, California 94158, USA
    J Chem Inf Model 49:2512-27. 2009
    ..Even for single models, the models are significantly more enriching than the template structure if the template is paralogous and shares more than 25% sequence identity with the target...
  64. pmc Comparison of human solute carriers
    Avner Schlessinger
    Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, California
    Protein Sci 19:412-28. 2010
    ..The classification scheme will inform future attempts directed at modeling the structures of the solute carriers, a prerequisite for describing the substrate specificities of the individual families...
  65. ncbi request reprint Comprehensive search for cysteine cathepsins in the human genome
    Andrea Rossi
    Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, CA 94143 2240, USA
    Biol Chem 385:363-72. 2004
    ..No expression of any of the three cathepsin L-like pseudogenes was found. Based on these results, it is likely that to date all human cysteine cathepsins are known...
  66. pmc Macromolecular docking restrained by a small angle X-ray scattering profile
    Dina Schneidman-Duhovny
    Department of Bioengineering and Therapeutic Sciences, and California Institute for Quantitative Biosciences QB3, University of California at San Francisco, CA 94158, USA
    J Struct Biol 173:461-71. 2011
    ..Thus, the integrative approach significantly improves on molecular docking alone. The improvement arises from an increased resolution of rigid docking sampling and more accurate scoring...
  67. pmc Tel2 mediates activation and localization of ATM/Tel1 kinase to a double-strand break
    Carol M Anderson
    Department of Biochemistry, University of California, San Francisco, California 94143, USA
    Genes Dev 22:854-9. 2008
    ..Computational analysis revealed structural homology between Tel2 and Ddc2 (ATRIP in vertebrates), a partner of Mec1, suggesting a common structural principle used by partners of phoshoinositide 3-kinase-like kinases...
  68. pmc Integrative structural modeling with small angle X-ray scattering profiles
    Dina Schneidman-Duhovny
    Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, USA
    BMC Struct Biol 12:17. 2012
    ..Third, we discuss the use of SAXS profiles in integrative structure modeling approaches that depend simultaneously on several data types...
  69. ncbi request reprint Molecular modeling and ligand docking for solute carrier (SLC) transporters
    Avner Schlessinger
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, 1700 4th Street, San Francisco, CA 94158, USA
    Curr Top Med Chem 13:843-56. 2013
    ..We conclude by discussing future directions in the discovery of the SLC transporter ligands...
  70. pmc Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini
    Sami Mahrus
    Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
    Cell 134:866-76. 2008
    ..Strikingly, we also find that a disproportionate number of caspase substrates physically interact, suggesting that these dimeric proteases target protein complexes and networks to elicit apoptosis...
  71. pmc Ratiocinative screen of eukaryotic integral membrane protein expression and solubilization for structure determination
    Franklin A Hays
    Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94158 2517, USA
    J Struct Funct Genomics 10:9-16. 2009
    ..A screen of 384 rationally selected eukaryotic IMPs in baker's yeast Saccharomyces cerevisiae is outlined to demonstrate the results expected when applying this discovery-oriented pipeline to whole-organism membrane proteomes...
  72. pmc Optimized atomic statistical potentials: assessment of protein interfaces and loops
    Guang Qiang Dong
    Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry and California Institute for Quantitative Biosciences QB3, University of California, San Francisco, CA 94158, USA
    Bioinformatics 29:3158-66. 2013
    ..Here, we formulate the statistical potentials entirely within a statistical framework, avoiding questionable statistical mechanical assumptions and approximations, including a definition of the reference state...
  73. ncbi request reprint Combining electron microscopy and comparative protein structure modeling
    Maya Topf
    Department of Biopharmaceutical Sciences, University of California San Francisco, San Francisco, CA 94143, USA
    Curr Opin Struct Biol 15:578-85. 2005
    ..Also, comparative modeling can benefit from electron microscopy through the use of intermediate-resolution density maps in fold recognition, template selection and sequence-structure alignment...
  74. ncbi request reprint Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy
    Maya Topf
    Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, Mission Bay Genentech Hall, 600 16th Street, Suite N472D, University of California, San Francisco, CA 94143, USA
    J Struct Biol 149:191-203. 2005
    ..Moreover, a pseudo-atomic model of a component in an assembly may be built better with comparative models of the native subunit sequences than with experimentally determined structures of their homologs...
  75. pmc Role of organic cation transporter 3 (SLC22A3) and its missense variants in the pharmacologic action of metformin
    Ligong Chen
    Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, California 94158, USA
    Pharmacogenet Genomics 20:687-99. 2010
    ....
  76. pmc Self-assembly of filamentous amelogenin requires calcium and phosphate: from dimers via nanoribbons to fibrils
    Olga Martinez-Avila
    Department of Preventative and Restorative Dental Sciences, University of California, 707 Parnassus Avenue, San Francisco, CA 94143, USA
    Biomacromolecules 13:3494-502. 2012
    ..These observations confirm reports of filamentous organic components in developing enamel and provide a new model for matrix-templated enamel mineralization...
  77. pmc Global landscape of HIV-human protein complexes
    Stefanie Jäger
    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, USA
    Nature 481:365-70. 2012
    ..This data set facilitates a more comprehensive and detailed understanding of how the host machinery is manipulated during the course of HIV infection...
  78. ncbi request reprint The structure of chagasin in complex with a cysteine protease clarifies the binding mode and evolution of an inhibitor family
    Stephanie X Wang
    Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
    Structure 15:535-43. 2007
    ..Interactions of chagasin with a target protease are reminiscent of the cystatin family inhibitors. Protein inhibitors of cysteine proteases may have evolved more than once on nonhomologous scaffolds...
  79. ncbi request reprint PharmGKB submission update: IV. PMT submissions of genetic variations in ATP-Binding cassette transporters to the PharmGKB network
    Tan D Nguyen
    Department of Biopharmaceutical Sciences, University of California, San Francisco, USA
    Pharmacol Rev 58:1-2. 2006
  80. pmc The structural dynamics of macromolecular processes
    Daniel Russel
    Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158 2330, USA
    Curr Opin Cell Biol 21:97-108. 2009
    ..We review the relevant sources of information and introduce a framework for integrating the data to produce representations of dynamic processes...
  81. doi request reprint Comparative protein structure modeling using Modeller
    Narayanan Eswar
    University of California at San Francisco, San Francisco, California, USA
    Curr Protoc Bioinformatics . 2006
    ..Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described...
  82. ncbi request reprint Determining the architectures of macromolecular assemblies
    Frank Alber
    Department of Bioengineering and Therapeutic Sciences, and California Institute for Quantitative Biosciences, Byers Hall, Suite 503B, 1700 4th Street, University of California at San Francisco, San Francisco, California 94158 2330, USA
    Nature 450:683-94. 2007
    ..The present approach should be applicable to many other macromolecular assemblies...
  83. doi request reprint Mapping polymerization and allostery of hemoglobin S using point mutations
    Patrick Weinkam
    Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences QB3, University of California, San Francisco, San Francisco, California 94158, United States
    J Phys Chem B 117:13058-68. 2013
    ..Finally, our analysis of allostery allows us to hypothesize why hemoglobin evolved to have multiple subunits and a persistent low frequency sickle cell mutation. ..
  84. pmc Accurate SAXS profile computation and its assessment by contrast variation experiments
    Dina Schneidman-Duhovny
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
    Biophys J 105:962-74. 2013
    ....
  85. pmc Multiple conformations of E. coli Hsp90 in solution: insights into the conformational dynamics of Hsp90
    Kristin A Krukenberg
    Graduate Program in Chemistry and Chemical Biology, Department of Biochemistry and Biophysics and the Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
    Structure 16:755-65. 2008
    ..These studies provide a unique view of Hsp90 conformational dynamics and provide a model for the role of nucleotide in effecting conformational change...
  86. pmc Structure-based model of allostery predicts coupling between distant sites
    Patrick Weinkam
    Department of Bioengineering and Therapeutic Sciences, and California Institute for Quantitative Biosciences, University of California, San Francisco, CA 94158, USA
    Proc Natl Acad Sci U S A 109:4875-80. 2012
    ..Remarkably, the model is able to reproduce allosteric motion and predict coupling in a manner consistent with experiment...
  87. pmc Tools for comparative protein structure modeling and analysis
    Narayanan Eswar
    Department of Biopharmaceutical Sciences and California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94143 2240, USA
    Nucleic Acids Res 31:3375-80. 2003
    ....
  88. pmc Finding cures for tropical diseases: is open source an answer?
    Stephen M Maurer
    Goldman School of Public Policy, University of California, Berkeley, California, USA
    PLoS Med 1:e56. 2004
  89. ncbi request reprint From words to literature in structural proteomics
    Andrej Sali
    Department of Biopharmaceutical Sciences, and California Institute for Quantitative Biomedical Research, University of California, San Francisco, California 94143, USA
    Nature 422:216-25. 2003
    ..The goal is a comprehensive description of the multitude of interactions between molecular entities, which in turn is a prerequisite for the discovery of general structural principles that underlie all cellular processes...
  90. ncbi request reprint Modeller: generation and refinement of homology-based protein structure models
    Andras Fiser
    Department of Biochemistry and Seaver Foundation Center for Bioinformatics, Albert Einstein College of Medicine, Bronz, New York 10461, USA
    Methods Enzymol 374:461-91. 2003
  91. pmc Detection of homologous proteins by an intermediate sequence search
    Bino John
    Laboratory of Molecular Biophysics, Pels Family Center for Biochemistry and Structural Biology, The Rockefeller University, New York, New York 10021, USA
    Protein Sci 13:54-62. 2004
    ..In addition, we show that the 15 alignments with the most significant BLAST E-values include the nearly best alignments constructed by ISS(new)...
  92. ncbi request reprint ModLoop: automated modeling of loops in protein structures
    Andras Fiser
    Department of Biochemistry and Seaver Foundation Center for Bioinformatics, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA
    Bioinformatics 19:2500-1. 2003
    ..For a rapid response, ModLoop runs on a cluster of Linux PC computers...
  93. pmc Comparative protein structure modeling by iterative alignment, model building and model assessment
    Bino John
    Laboratory of Molecular Biophysics, Pels Family Center for Biochemistry and Structural Biology, The Rockefeller University, New York, NY 10021, USA
    Nucleic Acids Res 31:3982-92. 2003
    ..The accuracy of the final models would be increased further if a better method for ranking of the models were available...
  94. pmc EVA: Evaluation of protein structure prediction servers
    Ingrid Y Y Koh
    Columbia University Center for Computational Biology and Bioinformatics C2B2, Russ Berrie Pavilion, 1150 St Nicholas Avenue, New York, NY 10032, USA
    Nucleic Acids Res 31:3311-5. 2003
    ..This large sample assures that methods are compared reliably. As a result, EVA provides useful information to developers as well as users of prediction methods...
  95. pmc MODBASE, a database of annotated comparative protein structure models
    Ursula Pieper
    Laboratories of Molecular Biophysics, The Pels Family Center for Biochemistry and Structural Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Nucleic Acids Res 30:255-9. 2002
    ....
  96. ncbi request reprint ModView, visualization of multiple protein sequences and structures
    Valentin A Ilyin
    The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Bioinformatics 19:165-6. 2003
    ..ModView is also suitable as a graphical interface to various databases because it can be controlled through JavaScript commands and called from CGI scripts...
  97. ncbi request reprint Evolution and physics in comparative protein structure modeling
    Andras Fiser
    Laboratory of Molecular Biophysics, Pels Family Center for Biochemistry and Structural Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
    Acc Chem Res 35:413-21. 2002
    ..Incorporation of physical considerations is illustrated by an inclusion of solvation effects into the modeling of loops...
  98. ncbi request reprint Reliability of assessment of protein structure prediction methods
    Marc A Marti-Renom
    Laboratories of Molecular Biophysics, Pels Family Center for Biochemistry and Structural Biology, The Rockefeller University, New York, New York 10021, USA
    Structure 10:435-40. 2002
    ....
  99. pmc Structural genomics: a pipeline for providing structures for the biologist
    Mark R Chance
    Center for Synchrotron Biosciences, Albert Einstein College of Medicine, Bronx, New York 10461, USA
    Protein Sci 11:723-38. 2002
  100. ncbi request reprint LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures
    Ashley C Stuart
    Laboratories of Molecular Biophysics, Pels Family Center for Biochemistry and Structural Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Bioinformatics 18:200-1. 2002
    ..Residues in the binding sites are graphically depicted for comparison with other structurally defined family members. LigBase provides a resource for the analysis of families of related binding sites...
  101. pmc Statistical potentials for fold assessment
    Francisco Melo
    Laboratories of Molecular Biophysics, Pels Family Center for Biochemistry and Structural Biology, The Rockefeller University, New York, New York 10021, USA
    Protein Sci 11:430-48. 2002
    ..The results described in this study provide a basis for an optimal use of statistical potentials in fold assessment...

Research Grants12

  1. PROTEIN MODELING BY SATISFACTION OF SPATIAL RESTRAINTS
    Andrej Sali; Fiscal Year: 2007
    ..More broadly, these aims are especially timely due to the advent of structural and functional genomics of proteins and their complexes, which will benefit from increased accuracy, applicability, and efficiency of comparative modeling. ..
  2. PROTEIN MODELING BY SATISFACTION OF SPATIAL RESTRAINTS
    Andrej Sali; Fiscal Year: 2004
    ..The improvements will leverage the genomics effort by significantly increasing both the number of modeled proteins and the model accuracy. ..
  3. IMP: Software for Hybrid Determination of Macromolecular Assembly Structures
    Andrej Sali; Fiscal Year: 2010
    ..These structures will allow us to better understand the workings of the cell, both under normal and disease conditions. ..