Webinars
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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
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
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
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
Topic: GROMACS
Presnter: Alessandra Villa, Ph.D., KTH Royal Institute of Technology, Sweden
GROMACS
Host: Jason Key
Recorded on September 29, 2021
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
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: 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
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
Topic: OpenMM
Speaker: Peter Eastman, Senior Software Engineer, Vijay Pande's Group, Stanford University
Host: Jason Key
Recorded on February 28, 2017
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
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
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
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
Topic: Elastic Network Models and ProDy for Bimolecular Systems Dynamics
Presenter: Ivet Bahar, University of Pittsburgh
Host: Jason Key
Recorded on June 26, 2016
"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
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
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.