AlphaFold protein structures & ChimeraX cryoEM modeling

  • Presenter: Tom Goddard, UCSF Resource for Biocomputing, Visualization, and Informatics - Topic: Using AlphaFold protein structures in ChimeraX for cryoEM modeling

    Linked to presented materials: https://www.rbvi.ucsf.edu/chimerax/data/sbgrid-mar2022/alphafold_pae.html

    Learn more on the ChimeraX website:

    This talk was presented as part of the SBGrid Spring Mini-series - Cryo-electron microscopy of membrane proteins: from sample to structure. See the full series lineup at https://sbgrid.org/webinars/

    Organized by
    Prof. Jamaine Davis, Meharry Medical College
    Prof. Piotr Sliz, Harvard Medical School
    Prof. Patrick Sexton, ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash University

    Recorded on March 29, 2022

    CAVER 3.0

  • Topic: CAVER 3.0: Analysis of Tunnels in Static and Dynamic Protein Structures
    Presenter: Jan Brezovsky, Ph.D., Team Leader, Loschmidt Laboratories, Czech Republic

    Host: Jason Key
    Recorded on June 13, 2013

    CCP4 Molecular Graphics (CCP4-MG)

  • Topic: The CCP4 Molecular Graphics Program
    Presenter: Stuart McNicholas, Research Fellow and CCP4-funded Developer, Dept of Chemistry, University of York

    Host: Piotr Sliz
    Recorded on January 24, 2013


  • Topic: Making Augmented Reality Videos with ChimeraX
    Presenter: Tom Goddard, University of California, San Francisco, Resource for Biocomputing, Visualization, and Informatics

    The Zoom recording of this presentation is pretty choppy. We recommend you also check out the video Tom recorded and posted on his own channel here: https://youtu.be/dKNbRRRFhqY

    Slides from talk available at https://www.rbvi.ucsf.edu/chimerax/data/sbgrid-july2020/

    Host: Pete Meyer
    Recorded on July 7, 2020


  • Topic: Movie Making for cryoEM using ChimeraX
    Presenter: Tom Goddard, Programmer/Analyst, UCSF Resource for Biocomputing, Visualization, and Informatics

    Hosted by Pete Meyer
    Recorded on April 11, 2017


  • Topic: What's New in Coot?

    Presenter: Paul Emsley, Ph.D., MRC Laboratory of Molecular Biology

    Recorded on February 16, 2021
    Host: Jason Key

    Coot Cryo-EM

  • Topic: Breezing Through the Coot Cryo-EM Tutorial
    Speaker: Paul Emsley - MRC Laboratory of Molecular Biology

    Recorded March 2019


  • Topic: DireX - Cross-validated Real-space Refinement to Density Map
    Presenter: Gunnar Schröder, PhD, Assistant Professor, University of Düsseldorf, Jülich, Germany

    Host: Pete Meyer
    Recorded on May 10, 2016


  • Topic: DSSR, a new 3DNA program for Defining the Secondary Structures of RNA from three-dimensional coordinates
    Presenter: Xiang-Jun Lu, Ph.D., Associate Research Scientist, Columbia University

    Host: Jason Key
    Recorded on June 26, 2014


  • Topic: In-situ and in-vitro subtomogram averaging to subnanometer resolution using EMAN2.3
    Presenter: Steven J Ludtke, Ph.D., Professor, Baylor College of Medicine

    Recorded on November 12, 2019
    Host: Jason Key


  • Topic: EMAN2
    Presenter: Steven Ludtke, Ph.D. Baylor College of Medicine

    Host: Jason Key
    Recorded on May 11, 2021


  • Topic: A quick introduction to EMAN2.1 for CryoEM Single Particle Analysis
    Presenter: Steven Ludtke, Ph.D., Professor, Baylor College of Medicine

    Host: Jason Key
    Recorded on April 15, 2015


  • Topic: EMAN2.2 for Single Particle Analysis and In-situ Structural Biology
    Presenter: Steven Ludtke, Ph.D.
    Professor of Biochemistry - Baylor College of Medicine
    Co-Director - National Center for Macromolecular Imaging
    Co-Director - Center for Computational and Integrative Biomedical Research

    Date Recorded: November 14, 2017
    Host: Jason Key


  • Topic: EVcouplings: Using evolution to determine structure and function
    Presenters: Kelly Brock, Ph.D., Laboratory of Debora Marks, Harvard Medical School and Thomas Hopf, Ph.D., Scientific Consultant

    Host: Pete Meyer
    Recorded on May 12, 2020


  • Topic: Haddock

    Presenter: Prof. Alexandre Bonvin, University Utrecht

    Host: Jason Key
    Recorded on: June 29, 2021


  • Topic: Modelling biomolecular complexes using HADDOCK: local vs server mode.
    Presenter: Alexandre Bonvin, Computational Structural Biology group, Bijvoet Center for Biomolecular Research, University of Utrecht, The Netherlands

    Host: Jason Key
    Recorded on September 8, 2015


  • Topic: Creating and analyzing multiple sequence alignments with the Jalview Desktop Application
    Presenter: Jim Procter, Ph.D., Jalview Coordinator, College of Life Sciences, University of Dundee Scotland, UK

    Host: Jason Key
    Recorded on July 11, 2013


  • Topic: OpenMM
    Speaker: Peter Eastman, Senior Software Engineer, Vijay Pande's Group, Stanford University

    Host: Jason Key
    Recorded on February 28, 2017


  • Topic: PDBStat
    Presenter: Roberto Tejero, Associate Professor, University of Valencia, Spain

    Host: Jason Key
    Recorded on January 28, 2016


  • Presenter: Thomas Stewart, Ph.D., Schrödinger
    Topic: A new approach to visual presets in PyMOL (upcoming in PyMOL 3.0)

    Recorded on March 1, 2022
    Host: Pete Meyer