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Andrej Sali

UC, San Francisco - Dept. of Biopharmaceutical Sciences and Pharmaceutical Chemistry

600 16th Street, Suite N472D

Mission Bay Genentech Hall

San Francisco, CA 94143-0446

United States

http://salilab.org

UCSF, California Institute for Quantitative Biomedical Research

San Francisco, CA 94107

United States

  • UC, San Francisco - Dept. of Biopharmaceutical Sciences and Pharmaceutical Chemistry

    • Email
    • Tel: 415-514-4227
    • Fax: 415-514-4231
SCHOLARLY PAPERS

7

DOWNLOADS

264

TOTAL CITATIONS

1

Scholarly Papers (7)

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1.

IHMValidation: Assessment of Integrative Structure Models Deposited to the Protein Data Bank

Number of pages: 25 Posted: 15 Oct 2025
Arthur Zalevsky, Brinda Vallat, Benjamin M. Webb, Hongsuda Tangmunarunkit, Monica Sekharan, Aref Shafaeibejestan, Sai Ganesan, Jared Sagendorf, Cy M. Jeffries, Jill Trewhella, Andrea Graziadei, Juan Antonio Vizcaíno, Alexander Leitner, Juri Rappsilber, Ezra Peisach, Justin W. Flatt, Jasmine Y. Young, Kartik Majila, Shruthi Viswanath, Carl Kesselman, Jeffrey C. Hoch, Genji Kurisu, Kyle Morris, Sameer Velnankar, Helen M. Berman, Stephen K. Burley and Andrej Sali
affiliation not provided to SSRN, Rutgers, The State University of New Jersey - Research Collaboratory for Structural Bioinformatics Protein Data Bank, affiliation not provided to SSRN, University of Southern California, Rutgers, The State University of New Jersey - Research Collaboratory for Structural Bioinformatics Protein Data Bank, University of Southern California, affiliation not provided to SSRN, affiliation not provided to SSRN, affiliation not provided to SSRN, affiliation not provided to SSRN, affiliation not provided to SSRN, affiliation not provided to SSRN, affiliation not provided to SSRN, Technische Universität Berlin (TU Berlin) - Chair of Bioanalytics, Rutgers, The State University of New Jersey - Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey - Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey - Research Collaboratory for Structural Bioinformatics Protein Data Bank, Tata Institute of Fundamental Research (TIFR), Tata Institute of Fundamental Research (TIFR), University of Southern California, University of Connecticut - Department of Molecular Biology and Biophysics, The University of Osaka, European Bioinformatics Institute, European Bioinformatics Institute, Rutgers, The State University of New Jersey - Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey - Research Collaboratory for Structural Bioinformatics Protein Data Bank and UC, San Francisco - Dept. of Biopharmaceutical Sciences and Pharmaceutical Chemistry
Downloads 57 (989,921)

Abstract:

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Integrative modeling, Protein Data Bank (PDB), Small-angle X-ray scattering (SAXS), Crosslinking mass spectrometry (crosslinking-MS), Three-dimensional cryo-electron microscopy (3DEM)

2.

ModelCIF update: Supporting Emerging Classes of Computational Macromolecular Models

Number of pages: 15 Posted: 06 Nov 2025
Gerardo Tauriello, Yoriko Lill, Jacopo Sgrignani, Vincent Zoete, Benedikt Singer, Brinda Vallat, Benjamin M. Webb, Thomas Garello, Stefan Bienert, Michael Feig, Stephen K. Burley, Andrej Sali, Markus A. Lill, Andrea Cavalli, Matteo Dal Pararo and Torsten Schwede
Swiss Institute of Bioinformatics, affiliation not provided to SSRN, affiliation not provided to SSRN, affiliation not provided to SSRN, affiliation not provided to SSRN, Rutgers, The State University of New Jersey - Research Collaboratory for Structural Bioinformatics Protein Data Bank, affiliation not provided to SSRN, University of Basel - Biozentrum, Swiss Institute of Bioinformatics, affiliation not provided to SSRN, Rutgers, The State University of New Jersey - Research Collaboratory for Structural Bioinformatics Protein Data Bank, UC, San Francisco - Dept. of Biopharmaceutical Sciences and Pharmaceutical Chemistry, affiliation not provided to SSRN, Universita della Svizzera Italiana (USI Lugano) - Institute for Research in Biomedicine, École Polytechnique Fédérale de Lausanne (EPFL) - Institute of Bioengineering and University of Basel - Biozentrum
Downloads 47 (1,097,529)

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data standard, macromolecular structure prediction, protein complexes, conformational states, protein design

3.

Data-Driven Cell Modeling Reveals Regulatory Mechanisms of Insulin Secretion in Pancreatic β-Cells

Number of pages: 23 Posted: 03 Nov 2025
Xianni Zhong, Weimin Li, Xiaoyan Liu, Huaiqing Cao, Barak Raveh, Andrej Sali, Angdi Li, Liping Sun and Sneak Peek Administrator
ShanghaiTech University, Chinese Academy of Sciences (CAS), ShanghaiTech University, Shandong Institute of Advanced Technology, Hebrew University of Jerusalem, UC, San Francisco - Dept. of Biopharmaceutical Sciences and Pharmaceutical Chemistry, ShanghaiTech University, ShanghaiTech University and Independent
Downloads 45 (1,121,190)

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Data-driven modeling, Cell modeling, Brownian dynamics simulations, Pancreatic β-cells, Glucose-stimulated insulin secretion, Regulatory mechanisms

4.

Pdb-Ihm: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures

Number of pages: 15 Posted: 26 Nov 2024
Brinda Vallat, Benjamin M. Webb, Arthur Zalevsky, Hongsuda Tangmunarunkit, Monica Sekharan, Serban Voinea, Aref Shafaeibejestan, Jared Sagendorf, Jeffrey C. Hoch, Genji Kurisu, Kyle Morris, Sameer Velnankar, Carl Kesselman, Stephen K. Burley, Helen M. Berman and Andrej Sali
Rutgers, The State University of New Jersey - Research Collaboratory for Structural Bioinformatics Protein Data Bank, affiliation not provided to SSRN, affiliation not provided to SSRN, University of Southern California, Rutgers, The State University of New Jersey - Research Collaboratory for Structural Bioinformatics Protein Data Bank, University of Southern California, University of Southern California, affiliation not provided to SSRN, University of Connecticut - Department of Molecular Biology and Biophysics, The University of Osaka, European Bioinformatics Institute, European Bioinformatics Institute, University of Southern California, affiliation not provided to SSRN, Rutgers, The State University of New Jersey - Department of Chemistry and Chemical Biology and UC, San Francisco - Dept. of Biopharmaceutical Sciences and Pharmaceutical Chemistry
Downloads 39 (1,196,171)
Citation 1

Abstract:

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PDB, PDBx/mmCIF, integrative modeling, IHMCIF, structure validation, PDB-Dev, PDB-IHM

5.

Unique Mechanisms to Increase Structural Stability and Enhance Antigen Binding in Nanobodies

Number of pages: 53 Posted: 22 Oct 2024
Natalia Elena Ketaren, Peter Fridy, Vladimir Malashkevich, Tanmoy Sanyal, Marc Brillantes, Mary Thompson, Deena Oren, Jeffrey Bonanno, Andrej Sali, Steven Almo, Brian T. Chait, Michael P. Rout and Sneak Peek Administrator
Rockefeller University - Laboratory of Cellular and Structural Biology, Rockefeller University - Laboratory of Cellular and Structural Biology, Yeshiva University - Albert Einstein College of Medicine, University of California, San Francisco (UCSF), Rockefeller University - Laboratory of Cellular and Structural Biology, Rockefeller University - Laboratory of Cellular and Structural Biology, Rockefeller University, Yeshiva University - Albert Einstein College of Medicine, UC, San Francisco - Dept. of Biopharmaceutical Sciences and Pharmaceutical Chemistry, Yeshiva University - Albert Einstein College of Medicine, Rockefeller University - Laboratory of Cellular and Structural Biology, Rockefeller University - Laboratory of Cellular and Structural Biology and Independent
Downloads 39 (1,196,171)

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Nanobody, nanobody engineering, single-domain antibody, SARS-COV-2, Green Fluorescent Protein, nanobody optimization, X-ray crystallography, nanobody stability, nanobody affinity optimization

6.

The Active DNA-PK Holoenzyme Occupies a Tensed State in a Staggered Synaptic Complex

Number of pages: 66 Posted: 21 Oct 2020
Morgan Hepburn, Daniel J. Saltzberg, Linda Lee, Shujuan Fang, Claire Atkinson, Natalie C.J. Strynadka, Andrej Sali, Susan Lees-Miller and David C. Schriemer
University of Calgary - Department of Biochemistry and Molecular Biology, University of California, San Francisco (UCSF) - Department of Bioengineering and Therapeutic Sciences, University of Calgary - Department of Biochemistry and Molecular Biology, University of Calgary - Department of Biochemistry and Molecular Biology, University of British Columbia (UBC) - Department of Biochemistry and Molecular Biology, University of British Columbia (UBC) - Department of Biochemistry and Molecular Biology, UC, San Francisco - Dept. of Biopharmaceutical Sciences and Pharmaceutical Chemistry, University of Calgary - Department of Biochemistry and Molecular Biology and University of Calgary - Department of Biochemistry and Molecular Biology
Downloads 37 (1,222,651)

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DNA repair, non-homologous end joining, DNA-PK, structure, synaptic complex, crosslinking mass spectrometry, hydrogen/deuterium exchange, modeling

7.

Finding Cures for Tropical Diseases: Is Open Source an Answer?

PLOS Medicine, Vol. 1, p. 183, 2004, Duke Science, Technology & Innovation Paper No. 4
Posted: 06 Apr 2005
Stephen M. Maurer, Arti K. Rai and Andrej Sali
University of California, Berkeley, Duke University School of Law and UC, San Francisco - Dept. of Biopharmaceutical Sciences and Pharmaceutical Chemistry

Abstract:

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open source, neglected disease, patent