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.
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
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
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
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
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.