Andrej Sali

Summary

Affiliation: University of California
Country: USA

Publications

  1. 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
  2. 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
  3. 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
  4. 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
  5. pmc A kernel for open source drug discovery in tropical diseases
    Leticia Ortí
    Structural Genomics Unit, Bioinformatics and Genomics Department, Centro de Investigacion Principe Felipe, Valencia, Spain
    PLoS Negl Trop Dis 3:e418. 2009
  6. pmc FoXS: a web server for rapid computation and fitting of SAXS profiles
    Dina Schneidman-Duhovny
    Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, CA 94158, USA
    Nucleic Acids Res 38:W540-4. 2010
  7. 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, and California Institute for Quantitative Biosciences, University of California at San Francisco, CA 94158, USA
    Nucleic Acids Res 39:D465-74. 2011
  8. 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
  9. 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
  10. 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

Collaborators

Detail Information

Publications125 found, 100 shown here

  1. 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/)...
  2. 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
    ....
  3. 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)...
  4. 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/...
  5. pmc A kernel for open source drug discovery in tropical diseases
    Leticia Ortí
    Structural Genomics Unit, Bioinformatics and Genomics Department, Centro de Investigacion Principe Felipe, Valencia, Spain
    PLoS Negl Trop Dis 3:e418. 2009
    ..Historically, open source software collaborations have almost never succeeded without such "kernels"...
  6. pmc FoXS: a web server for rapid computation and fitting of SAXS profiles
    Dina Schneidman-Duhovny
    Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, CA 94158, USA
    Nucleic Acids Res 38:W540-4. 2010
    ..Here, we describe the interface and capabilities of the FoXS web server (http://salilab.org/foxs)...
  7. 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, and California Institute for Quantitative Biosciences, University of California at San Francisco, CA 94158, USA
    Nucleic Acids Res 39:D465-74. 2011
    ..org/modeval), the PCSS server for predicting which peptides bind to a given protein (http://salilab.org/pcss) and the FoXS server for calculating and fitting Small Angle X-ray Scattering profiles (http://salilab.org/foxs)...
  8. 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...
  9. 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...
  10. 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
    ....
  11. 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)...
  12. 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...
  13. 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...
  14. 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...
  15. 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...
  16. 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...
  17. 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
    ....
  18. 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
    ....
  19. 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
    ....
  20. 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...
  21. ncbi 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. ..
  22. 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...
  23. 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...
  24. pmc 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
    ....
  25. 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...
  26. 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...
  27. 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...
  28. ncbi 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...
  29. pmc How well can the accuracy of comparative protein structure models be predicted?
    David Eramian
    Graduate Group in Biophysics, University of California at San Francisco, California 94158, USA
    Protein Sci 17:1881-93. 2008
    ..84 and 0.86, respectively, to the actual errors. This scoring function achieves the best correlation compared to 13 other tested assessment criteria that achieved correlations ranging from 0.35 to 0.71...
  30. 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/)...
  31. 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)...
  32. 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
    ....
  33. 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...
  34. 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...
  35. 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...
  36. 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...
  37. 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...
  38. ncbi 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...
  39. pmc Regulatory elements within the prodomain of Falcipain-2, a cysteine protease of the malaria parasite Plasmodium falciparum
    Kailash C Pandey
    Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
    PLoS ONE 4:e5694. 2009
    ....
  40. 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...
  41. 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
    ....
  42. 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...
  43. 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...
  44. pmc 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...
  45. 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...
  46. 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...
  47. 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...
  48. ncbi request reprint Variable gap penalty for protein sequence-structure alignment
    M S Madhusudhan
    Department of Biopharmaceutical Sciences and Pharmaceutical Chemistry, University of California at San Francisco, 94143, USA
    Protein Eng Des Sel 19:129-33. 2006
    ..We estimate that the new algorithm allows us to produce comparative models with an additional approximately 7 million accurately modeled residues in the approximately 1.1 million proteins that are detectably related to a known structure...
  49. 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...
  50. 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...
  51. 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...
  52. 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...
  53. 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...
  54. 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...
  55. 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...
  56. 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...
  57. 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...
  58. 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...
  59. 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...
  60. 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...
  61. 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...
  62. 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...
  63. 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...
  64. 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...
  65. 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...
  66. 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
    ....
  67. 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...
  68. 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...
  69. 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...
  70. pmc 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...
  71. 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...
  72. 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...
  73. 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...
  74. 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...
  75. 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...
  76. 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...
  77. 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...
  78. 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...
  79. 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...
  80. 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...
  81. 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...
  82. 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...
  83. 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...
  84. 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...
  85. 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...
  86. 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
    ....
  87. 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...
  88. 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
  89. 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...
  90. 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...
  91. 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...
  92. 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
    ....
  93. pmc 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. ..
  94. 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
  95. 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...
  96. 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
    ....
  97. 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
    ....
  98. 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)...
  99. pmc Functional impact of missense variants in BRCA1 predicted by supervised learning
    Rachel Karchin
    Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
    PLoS Comput Biol 3:e26. 2007
    ..These classifiers can be adapted to other cancer susceptibility genes and systematically applied to prioritize the growing number of potential causative loci and variants found by large-scale disease association studies...
  100. 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...
  101. ncbi request reprint Minimalist representations and the importance of nearest neighbor effects in protein folding simulations
    Andres Colubri
    Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
    J Mol Biol 363:835-57. 2006
    ....

Research Grants12

  1. PROTEIN MODELING BY SATISFACTION OF SPATIAL RESTRAINTS
    Andrej Sali; Fiscal Year: 2001
    ..The improvements will leverage the genomics effort by significantly increasing both the number of modeled proteins and the model accuracy. ..
  2. PROTEIN MODELING BY SATISFACTION OF SPATIAL RESTRAINTS
    Andrej Sali; Fiscal Year: 2006
    ..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. ..
  3. PROTEIN MODELING BY SATISFACTION OF SPATIAL RESTRAINTS
    Andrej Sali; Fiscal Year: 2005
    ..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. ..
  4. 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. ..
  5. PROTEIN MODELING BY SATISFACTION OF SPATIAL RESTRAINTS
    Andrej Sali; Fiscal Year: 2003
    ..The improvements will leverage the genomics effort by significantly increasing both the number of modeled proteins and the model accuracy. ..
  6. 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. ..
  7. PROTEIN MODELING BY SATISFACTION OF SPATIAL RESTRAINTS
    Andrej Sali; Fiscal Year: 2002
    ..The improvements will leverage the genomics effort by significantly increasing both the number of modeled proteins and the model accuracy. ..
  8. 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. ..
  9. PROTEIN MODELING BY SATISFACTION OF SPATIAL RESTRAINTS
    Andrej Sali; Fiscal Year: 2002
    ..The improvements will leverage the genomics effort by significantly increasing both the number of modeled proteins and the model accuracy. ..
  10. IMP: Software for Hybrid Determination of Macromolecular Assembly Structures
    Andrej Sali; Fiscal Year: 2009
    ..These structures will allow us to better understand the workings of the cell, both under normal and disease conditions. ..