SBGrid Consortium
SBGrid Consortium
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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
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
NMR TITAN
zhlédnutí 686Před rokem
NMR TITAN
Proteus
zhlédnutí 430Před rokem
Proteus
TomoTwin-cryoet
zhlédnutí 636Před rokem
TomoTwin-cryoet
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
PyMOL
zhlédnutí 2,7KPřed 2 lety
PyMOL
CCP4 Cloud Part I
zhlédnutí 708Před 2 lety
CCP4 Cloud Part I
CCP4 Cloud Part II
zhlédnutí 354Před 2 lety
CCP4 Cloud Part II
BioXTAS RAW
zhlédnutí 372Před 2 lety
BioXTAS RAW
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
RELION-4.0
zhlédnutí 5KPřed 2 lety
RELION-4.0
Regional CryoEM infrastructure in Australia
zhlédnutí 320Před 2 lety
Regional CryoEM infrastructure in Australia
IsoNet
zhlédnutí 972Před 2 lety
IsoNet
Effective on-the-fly and downstream processing of CryoEM data
zhlédnutí 996Před 2 lety
Effective on-the-fly and downstream processing of CryoEM data

Komentáře

  • @fruitflylikeabanana
    @fruitflylikeabanana Před 10 měsíci

    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.

  • @riffatsultana1100
    @riffatsultana1100 Před 10 měsíci

    please guide which option is used in new version for strip aliment

  • @MJ-hj8wz
    @MJ-hj8wz Před 10 měsíci

    amazing! so quick! thanks!

  • @thejaswinib.g.2570
    @thejaswinib.g.2570 Před 11 měsíci

    Excellent talk❤

  • @eugeniaclerico5008
    @eugeniaclerico5008 Před 11 měsíci

    This is what I have been looking for! Thank you so much.

  • @zairapalominojara5391
    @zairapalominojara5391 Před 11 měsíci

    Thank you very much Dr. Bovin! this is very helpful!

  • @manishdas6525
    @manishdas6525 Před rokem

    Thanks for the explaination.

  • @jimmyyoung1657
    @jimmyyoung1657 Před 2 lety

    Thanks for sharing!

  • @williamnicolas122
    @williamnicolas122 Před 2 lety

    Nicolas*

  • @castilloh.gianmarco1048

    thanks video. classes

  • @MJ-hj8wz
    @MJ-hj8wz Před 2 lety

    Very useful! Thanks!

  • @philippebenas5721
    @philippebenas5721 Před 2 lety

    Very interesting! 👍

  • @danirurajapaksha7990
    @danirurajapaksha7990 Před 3 lety

    you are a hero keep up your good work

  • @infomen8128
    @infomen8128 Před 3 lety

    Great tutorial, if you need to see its technical detail, visit us

  • @imrocknreeling
    @imrocknreeling Před 3 lety

    Ligands can be macromolecules? I mean large proteins or peptides?

  • @JonaszBP
    @JonaszBP Před 3 lety

    Amazing!

  • @debashismajhi386
    @debashismajhi386 Před 3 lety

    How one can extract data from 3D NMR process spectra?

  • @soheilmahmoudi3015
    @soheilmahmoudi3015 Před 3 lety

    that is great please continue these useful training program.

  • @biomodelos3d995
    @biomodelos3d995 Před 3 lety

    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?

  • @CcpNmr
    @CcpNmr Před 3 lety

    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

  • @baisun9088
    @baisun9088 Před 3 lety

    👍👍👍👍👍👍👍👍👍👍👍👍👍👍

  • @offmeds2nite
    @offmeds2nite Před 3 lety

    great talk Dan

  • @billyfisher1539
    @billyfisher1539 Před 3 lety

    Wonderful wonderful piece of software... Thank you, Tristan! :)

  • @InfiniteUniverse88
    @InfiniteUniverse88 Před 3 lety

    Is the SARS strain in the 2015 Nature paper (See: www.nature.com/articles/nm.3985 ) the same strain of SARS as Covid-19?

  • @erik_carter_art
    @erik_carter_art Před 3 lety

    Can SAXS be used for detergent-solubilized membrane proteins?

  • @quantumbioinc.9533
    @quantumbioinc.9533 Před 3 lety

    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

  • @lipingliao3421
    @lipingliao3421 Před 3 lety

    So exciting

  • @andylau7268
    @andylau7268 Před 3 lety

    Thank you for sharing! These scientific talks should haven been worthy of more attention and applause!

  • @summerxia7474
    @summerxia7474 Před 3 lety

    12:30 ProDy

  • @MJ-hj8wz
    @MJ-hj8wz Před 4 lety

    How is the ProSMART added?

    • @PaulEmsley
      @PaulEmsley Před 3 lety

      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.

  • @jamilualiyu7565
    @jamilualiyu7565 Před 4 lety

    Thanks you for presented nice session regarding structure based drug design approach, best regards.

    • @NellioStyle
      @NellioStyle Před 3 lety

      @Brody Ben Does it helps to dock my girlfriend in a specific receptor too ?

  • @rabeyatafsire9062
    @rabeyatafsire9062 Před 4 lety

    very easy, explanatry and informative. thnx

  • @wujian7791
    @wujian7791 Před 4 lety

    Are there still extensions in Version 9.0 EL? I cannot find these extensions including RCrane.

    • @MrEatteapee
      @MrEatteapee Před 4 lety

      Hi Wu, I found the RCrane extension under 'Calculate' second from the bottom. However, I am on 0.8.9.2 EL.

    • @wujian7791
      @wujian7791 Před 4 lety

      Thanks. I think it depends on the versions.@@MrEatteapee

  • @offmeds2nite
    @offmeds2nite Před 4 lety

    powerful tool

  • @shilpinagpal1738
    @shilpinagpal1738 Před 4 lety

    Is this like pymol ?

  • @jozeflewandowski7608
    @jozeflewandowski7608 Před 4 lety

    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!

  • @authorXS
    @authorXS Před 4 lety

    r we just gonna ignore corona_cactus and 6u42_guts on Tom's desktop???

  • @authorXS
    @authorXS Před 4 lety

    this is cuttin edge here

  • @authorXS
    @authorXS Před 4 lety

    5 days ago I left a comment asking for more vids on ChimeraX and then this webinar happens, coincidence?.. Thx Tom Goddard

    • @SBGridTV
      @SBGridTV Před 4 lety

      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.

  • @physicalandquantumchemistr5054

    Great, thanks

  • @michelleottaviano3928

    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!

  • @authorXS
    @authorXS Před 4 lety

    best

  • @chemobiologist2527
    @chemobiologist2527 Před 4 lety

    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 ?

    • @mahfuzrahman1093
      @mahfuzrahman1093 Před 4 lety

      Hi, can you send me or Ryan (PI) an email for further discussion? Thank you. Mahfuz

    • @mahfuzrahman1093
      @mahfuzrahman1093 Před 4 lety

      You can also find the detail in our recently published article “Rahman et al. 2020 Neuron”. Thank you for your interest.

  • @skatedededo17
    @skatedededo17 Před 4 lety

    Thanks for the video. Can you help me with the software? Because i'm having some difficult to designing a primer and simulating cloning

    • @SBGridTV
      @SBGridTV Před 4 lety

      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/

  • @nayem1chem
    @nayem1chem Před 4 lety

    Would you please upload a basic tutorial for COOT operation and Phenix operation? I am struggling to learn it

  • @ariusmaximilian8291
    @ariusmaximilian8291 Před 4 lety

    THIS SAVED ME THANK YOU!!

  • @piwowarczyk94
    @piwowarczyk94 Před 4 lety

    I would really like to hear that questions… Also, great talk Ellen!

  • @usaassole5739
    @usaassole5739 Před 4 lety

    1

  • @gmx_qk
    @gmx_qk Před 4 lety

    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"

  • @nayem1chem
    @nayem1chem Před 4 lety

    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.

    • @PabloConesa
      @PabloConesa Před 4 lety

      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