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SBGrid Consortium
United States
Registrace 13. 06. 2013
For structural biologists, by structural biologists!
The SBGrid TV channel was developed with participation from many members of the structural biology community. We welcome suggestions for topics to cover or speakers to hear from in future sessions. Contact us at info@sbgrid.org.
The project was developed with support from the National Science Foundation.
For more information on SBGrid, please visit us at www.sbgrid.org.
The SBGrid TV channel was developed with participation from many members of the structural biology community. We welcome suggestions for topics to cover or speakers to hear from in future sessions. Contact us at info@sbgrid.org.
The project was developed with support from the National Science Foundation.
For more information on SBGrid, please visit us at www.sbgrid.org.
matchmaps
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: matchmaps - a general approach to isomorphous, near-isomorphous, and non-isomorphous difference maps for crystallography
Presenter: Dennis Brookner, Ph.D. Student, Hekstra Lab, Harvard University
Host: Jason Key
Recorded on July 9, 2024
For more information on matchmaps:
sbgrid.org/software/titles/matchmaps
github.com/rs-station/matchmaps
rs-station.github.io
Topic: matchmaps - a general approach to isomorphous, near-isomorphous, and non-isomorphous difference maps for crystallography
Presenter: Dennis Brookner, Ph.D. Student, Hekstra Lab, Harvard University
Host: Jason Key
Recorded on July 9, 2024
For more information on matchmaps:
sbgrid.org/software/titles/matchmaps
github.com/rs-station/matchmaps
rs-station.github.io
zhlédnutí: 111
Video
TomoDRGN
zhlédnutí 302Před 2 měsíci
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: TomoDRGN - Visualizing molecular machines in motion through cryoET and deep learning Presenter: Professor Joseph Davis, Department of Biology, MIT Host: Jason Key Recorded on June 11, 2024 For...
Amber
zhlédnutí 269Před 3 měsíci
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: Free energy methods in Amber. Presenter: Professor Darrin York, Rutgers University. Host: Jason Key Recorded on May 14, 2024 For more information on Amber: sbgrid.org/software/titles/amber the...
RFdiffusion
zhlédnutí 2,3KPřed 4 měsíci
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...
RELION-5.0
zhlédnutí 2,1KPřed 5 měsíci
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: RELION-5.0: Recent developments Presenter: Prof. Sjors Scheres, MRC Laboratory of Molecular Biology Host: Shaun Rawson Recorded on March 12, 2024 For more information on RELION: sbgrid.org/sof...
OccuPy
zhlédnutí 669Před 6 měsíci
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: OccuPy: A software tool for heterogeneity - and occupancy analysis of cryo-EM reconstructions based on spatial filtering. Presenter: Björn Forsberg, Ph.D, Postdoctoral Fellow, Karolinska Insti...
DIALS
zhlédnutí 402Před 7 měsíci
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: DIALS - what’s new - with a focus on treatment of multi-crystal data sets. Presenter: Graeme Winter, Ph.D., Senior Software Scientist / Team Lead, Diamond Light Source Host: Pete Meyer Recorde...
DeepFoldRNA
zhlédnutí 339Před 8 měsíci
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: A deep-learning based method for de novo RNA tertiary structure prediction. Presenter: Robin Pearce, Ph.D. student, Yang Zhang's lab, University of Michigan Medical School. Host: Jason Key Rec...
DiffDock
zhlédnutí 1,9KPřed 9 měsíci
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...
Scipion
zhlédnutí 315Před 10 měsíci
Topic: ScipionTomo: Towards cryo-electron tomography software integration, reproducibility, and validation. Presenter: Pablo Conesa Team Leader, Spanish National Research Council Host: Jason Key Recorded on October 10, 2023 For more information on Scipion: sbgrid.org/software/titles/scipion github.com/pconesa
POKY
zhlédnutí 1,2KPřed rokem
Topic: POKY: a software suite for multidimensional NMR and 3D structure calculation of biomolecules. Presenter: Prof. Woonghee Lee - Assistant Professor, University of Colorado, Denver. Host: Jason Key Recorded on June 13, 2023. For more information on POKY: sbgrid.org/software/titles/poky sites.google.com/view/pokynmr/team?authuser=0
careless
zhlédnutí 664Před rokem
Topic: careless: Modern Machine Learning for Diffraction Data. Presenter: Kevin Dalton, Ph.D., Hekstra Laboratory, Harvard University. Host: Jason Key Recorded on May 9, 2023. For more information on careless: - sbgrid.org/wiki/examples/careless.md - sbgrid.org/software/titles/careless - github.com/rs-station/careless-examples Presentation Slides: docs.google.com/presentation/d/1UkXy2LQJWiB-QjW...
OpenFold
zhlédnutí 1,9KPřed rokem
Topic: Retraining AlphaFold2 yields new insights into its learning mechanism and capacity for generalization. Presenter: Gustaf Ahdritz, Ph.D. Student, AlQuraishi Laboratory Columbia University. Host: Jason Key Recorded on April 11, 2023 For more information on OpenFold: sbgrid.org/software/titles/openfold github.com/aqlaboratory/openfold
ModelAngelo
zhlédnutí 2,2KPřed rokem
Topic: Automated atomic modeling for cryo-EM maps. Presenter: Kiarash Jamali, PhD student, Scheres group, MRC Laboratory of Molecular Biology, Cambridge, UK. Host: Jason Key Recorded on: March 14, 2023 For more information on ModelAngelo: github.com/3dem/model-angelo
Foldseek
zhlédnutí 10KPřed rokem
Topic: Fast and accurate protein structure search with Foldseek Presenter: Prof. Martin Steinegger, Asst Professor of Bioinformatics, Seoul National University Host: Pete Meyer Recorded on Feb 14, 2023 For more information on Foldseek: github.com/steineggerlab/foldseek
Integrative structural modeling of macromolecular complexes using Assembline
zhlédnutí 820Před rokem
Integrative structural modeling of macromolecular complexes using Assembline
On the fly and downstream processing of CryoEM data
zhlédnutí 874Před 2 lety
On the fly and downstream processing of CryoEM data
AlphaFold protein structures & ChimeraX cryoEM modeling
zhlédnutí 1,6KPřed 2 lety
AlphaFold protein structures & ChimeraX cryoEM modeling
Florent Delhommel - Co-chaperone structural characterization in client-transfer heat shock proteins
zhlédnutí 298Před 2 lety
Florent Delhommel - Co-chaperone structural characterization in client-transfer heat shock proteins
Regional CryoEM infrastructure in Australia
zhlédnutí 320Před 2 lety
Regional CryoEM infrastructure in Australia
Effective on-the-fly and downstream processing of CryoEM data
zhlédnutí 996Před 2 lety
Effective on-the-fly and downstream processing of CryoEM data
Really excellent. How do I obtain the 3Di files for my protein and its matches? I think that they would be useful for identifying where matches occur.
please guide which option is used in new version for strip aliment
amazing! so quick! thanks!
Excellent talk❤
This is what I have been looking for! Thank you so much.
Thank you very much Dr. Bovin! this is very helpful!
Thanks for the explaination.
Thanks for sharing!
Nicolas*
thanks video. classes
Very useful! Thanks!
Very interesting! 👍
you are a hero keep up your good work
Great tutorial, if you need to see its technical detail, visit us
Ligands can be macromolecules? I mean large proteins or peptides?
Amazing!
How one can extract data from 3D NMR process spectra?
that is great please continue these useful training program.
Absolutely amazing staff! Thankyou! Can LiDAR sensor devices (i-phone, i-pad) be used instead of the special camera? For instance using DroidCam to replace your webcam with your I-phone 12?
If you are looking for particular parts of the webinar, timings are as follows: AnalysisAssign demo 14:15 NEF demo 37:48 AnalysisScreen demo 40:45
👍👍👍👍👍👍👍👍👍👍👍👍👍👍
great talk Dan
Wonderful wonderful piece of software... Thank you, Tristan! :)
Is the SARS strain in the 2015 Nature paper (See: www.nature.com/articles/nm.3985 ) the same strain of SARS as Covid-19?
Can SAXS be used for detergent-solubilized membrane proteins?
Please note: The validation paper for the MovableType fast free energy method is available from JCIM under OpenAccess: pubs.acs.org/doi/10.1021/acs.jcim.0c00618
So exciting
Thank you for sharing! These scientific talks should haven been worthy of more attention and applause!
12:30 ProDy
How is the ProSMART added?
2 months too late, but the menu item it now called "Restraints" and is loaded from Calculate -> Modules. This video is a bit out of date now.
Thanks you for presented nice session regarding structure based drug design approach, best regards.
@Brody Ben Does it helps to dock my girlfriend in a specific receptor too ?
very easy, explanatry and informative. thnx
Are there still extensions in Version 9.0 EL? I cannot find these extensions including RCrane.
Hi Wu, I found the RCrane extension under 'Calculate' second from the bottom. However, I am on 0.8.9.2 EL.
Thanks. I think it depends on the versions.@@MrEatteapee
powerful tool
Is this like pymol ?
Tom, I love how you keep innovating. The idea with using an ordinary webcam is brilliant. Clearly, it has its limitations but with a bit of creativity it can be very useful. I can't wait to try it for a supporting info of one of my papers!
r we just gonna ignore corona_cactus and 6u42_guts on Tom's desktop???
this is cuttin edge here
5 days ago I left a comment asking for more vids on ChimeraX and then this webinar happens, coincidence?.. Thx Tom Goddard
We aim to please! It was, in fact, a coincidence, but we do always welcome suggestions for future topics, so please let us know what software you'd like to hear about.
Great, thanks
Impressive grace under pressure from our speaker, Evan Worden, who took the fire alarm in stride, donned a mask, relocated, reconnected, and finished his talk. Thanks Evan!
best
Hi Dr. Mahfuz , It was great talk. I was wondering , How affinity reagent works and could you please (if any way you can see my comment) explain how this affinity materials used to purify this protein ?
Hi, can you send me or Ryan (PI) an email for further discussion? Thank you. Mahfuz
You can also find the detail in our recently published article “Rahman et al. 2020 Neuron”. Thank you for your interest.
Thanks for the video. Can you help me with the software? Because i'm having some difficult to designing a primer and simulating cloning
Hi -- for this kind of support, we would suggest contacting Geneious directly or checking the Geneious website where they have a nice selection of tutorials www.geneious.com/tutorials/
Would you please upload a basic tutorial for COOT operation and Phenix operation? I am struggling to learn it
THIS SAVED ME THANK YOU!!
I would really like to hear that questions… Also, great talk Ellen!
1
How to prepare reference pdb file and whome CA should be choosen....please explain if possible. Thankyou. I'm facein trouble like "It looks like weights used for displacement are zero. Check your reference PDB file"
Hi, Thanks for sharing your video. Could you please upload a tutorial for beginner. I recently downloaded in my workstation, but looks like time consuming to discover everything. Please upload tutorial for beginner. Thanks.
Hi Rejaul, please check our tutorials page. You'll find pdf tutorials and video tutorial as well. scipion-em.github.io/docs/docs/user/user-documentation.html#tutorials