Bluesky

SBGridTV

Button for mobile navigation

Webinars

  • Page 1 of 1

AlphaFold protein structures & ChimeraX cryoEM modeling

  • 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:
    https://www.rbvi.ucsf.edu/chimerax/data/alphafold-nov2021/af_sbgrid.html

    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

    De novo design of protein structure and function with RFdiffusion.

  • De novo design of protein structure and function with RFdiffusion.
  • SBGrid webinars are hosted with partial support from the NIH R25 Continuing Education for Structural Biology Mentors #GM151273, in collaboration with Co-PI Jamaine Davis of Meharry Medical College.

    Topic: De novo design of protein structure and function with RFdiffusion.

    Presenter: Brian Trippe, Ph.D., Postdoctoral Fellow, Columbia University.

    Host: Pete Meyer
    Recorded on April 9, 2024

    For more information on RFdiffusion:

    https://sbgrid.org/software/titles/rfdiffusion
    https://github.com/RosettaCommons/RFdiffusion

    DiffDock

  • DiffDock
  • SBGrid webinars are hosted with partial support from the NIH R25 Continuing Education for Structural Biology Mentors #GM151273, in collaboration with Co-PI Jamaine Davis of Meharry Medical College.

    Topic: DiffDock: a state-of-the-art method for molecular docking.

    Presenter: Gabriele Corso, Hannes Staerk, and Bowen Jing, Ph.D. students, MIT Computer Science and Artificial Intelligence Laboratory (CSAIL).

    Host: Pete Meyer
    Recorded on November 14, 2023

    For more information on DiffDock:

    https://sbgrid.org/software/titles/diffdock
    https://github.com/gcorso/DiffDock

    Dock

  • Dock
  • Topic: DOCK: Where it is and where its going
    Presenter: Trent Balius, Ph.D. , Postdoctoral Scholar, Shoichet Lab, University of California, San Francisco

    Recorded on June 20, 2017
    Host: Jason Key

    GROMACS

  • GROMACS
  • Topic: GROMACS
    Presnter: Alessandra Villa, Ph.D., KTH Royal Institute of Technology, Sweden

    GROMACS


    Host: Jason Key
    Recorded on September 29, 2021

    GROMACS

  • GROMACS
  • Topic: Molecular Simulations with GROMACS: Possibilities and Pitfalls
    Presenter: Erik Lindahl, Professor, Stockholm University and KTH Royal Institute of Technology

    Date Recorded: May 28, 2015
    Host: Jason Key

    Haddock

  • Haddock
  • Topic: Haddock

    Presenter: Prof. Alexandre Bonvin, University Utrecht


    Host: Jason Key
    Recorded on: June 29, 2021

    HADDOCK

  • HADDOCK
  • 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

    LightDock

  • LightDock
  • Topic: LightDock: Shedding light into the dark fraction of the protein interactome

    Presenters:
    Brian Jimenez-Garcia, Ph.D., University Utrecht, and
    Jorge Roel, Ph.D., Department of Structural Biology, Protein Design and Modeling group, IBMB-CSIC, Barcelona

    Host: Pete Meyer

    Recorded on May 18, 2021

    MovableType Software for Fast Free Energy-based Virtual Screening

  • MovableType Software for Fast Free Energy-based Virtual Screening
  • Topic: MovableType Software for Fast Free Energy-based Virtual Screening
    Presenter: Lance Westerhoff, Ph.D., QuantumBio, Inc.

    Host: Jason Key
    Recorded on October 6, 2020

    OpenMM

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

    Host: Jason Key
    Recorded on February 28, 2017

    Phenix-Amber Integration

  • Phenix-Amber Integration
  • Topic: Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix
    Presenter: Nigel Moriarty, Lawrence Berkeley National Labs

    Host: Pete Meyer
    Recorded on: October 8, 2019

    Phenix/DivCon

  • Phenix/DivCon
  • Topic: Phenix/DivCon: accurate macromolecular crystallographic refinement using linear scaling, semiempirical quantum-mechanics.
    Presenter: Lance Westerhoff, President and General Manager

    Host: Jason Key
    Recorded on September 22, 2015

    Phenix/DivCon

  • Phenix/DivCon
  • Topic: XModeScore: using crystallography to determine protonation states, fragment binding modes, and flip-states.
    Speaker: Lance Westerhoff, President and General Manager at QuantumBio Inc.

    Date: recorded: Oct 2, 2018
    Host: Jason Key

    PLUMED

  • PLUMED
  • Topic: Analyzing and enhancing molecular dynamics simulations with PLUMED
    Presenters: Giovanni Bussi -- Associate Professor, SISSA, Trieste, Italy
    Massimiliano Bonomi -- Postdoc, University of Cambridge, Vendruscolo Group

    Recorded on May 22, 2018
    Host: Jason Key

    ProDy

  • ProDy
  • Topic: Elastic Network Models and ProDy for Bimolecular Systems Dynamics
    Presenter: Ivet Bahar, University of Pittsburgh

    Host: Jason Key
    Recorded on June 26, 2016

    Schrödinger

  • Schrödinger
  • "Recent Enhancements and Scientific Advancements in the Schrödinger Suite"
    Presenter: Woody Sherman, Schrödinger Vice President of Applications Science.
    SBGrid Host: Piotr Sliz
    Recorded on: June 12, 2012

    Schrödinger website: http://www.schrodinger.com

    Schrodinger Glide with ICCB Library

  • Schrodinger Glide with ICCB Library
  • Topic: A basic primer for docking and similarity searching against the ICCB-Longwood databases on the SBGrid Goldfinger cluster
    Presenter: Paul Sanschagrin

    SBGrid Host: Jason Key
    Recorded on March 28, 2013

    Using AlphaFold protein structures in ChimeraX for cryoEM modeling

  • Using AlphaFold protein structures in ChimeraX for cryoEM modeling
  • Topic: Using AlphaFold protein structures in ChimeraX for cryoEM modeling

    Presenter: Tom Goddard, UCSF Resource for Biocomputing, Visualization, and Informatics

    Q&A session also includes Shaun Rawson, who presented during this session on "Effective on-the-fly and downstream processing of CryoEM data." See https://youtu.be/ra2sVFEPtN8

    Learn more on the ChimeraX website:
    https://www.rbvi.ucsf.edu/chimerax/data/alphafold-nov2021/af_sbgrid.html

    This talk was presented as part of the SBGrid Australasian III Mini-series - CryoEM: from Sample to Structure and should appeal to both novice and expert structural biologists.
    See the full mini-series lineup at https://sbgrid.org/news/sbgrid-university-otago-webinar-series.

    Scroll