Join us for our weekly webinar series --- Tuesdays at 12pm ET hear from developers and scientists about what's new in structural biology. Community members can connect via Zoom and directly ask questions of presenters. Be sure to subscribe to SBGridTV to receive alerts when we post new recordings and view our full collection of past tutorials. Events are also posted on SBGrid's public calendar. To subscribe visit https://sbgrid.org/calendar/.
Up next: Johannes Elferich
Oct 26th at 12pm ET
University of Massachusetts Medical School, Niko Grigorieff's Laboratory
Webinar connection instructions: We are now using Zoom to connect for webinars. Connection instructions:
- Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/6170001111
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Telephone password: 851323 - Or look up an international access number
WEBINAR LINEUP
UPCOMING
| Tues, Oct 26, 2021 | Johannes Elferich, Ph.D., University of Massachusetts Medical School, Niko Grigorieff's Laboratory |
| Tues, Nov 9, 2021 | Andrey Lebedev, Ph.D., Science and Technology Facilities Council, UK |
| Tues, Nov 16, 2021 | Prof. Yi-Wei Chang, Ph.D., Perelman School of Medicine, University of Pennsylvania |
| Tues, Nov 30, 2021 | Jarrett Johnson, Ph.D., Senior Developer, Schrödinger |
| Tues, Dec 7, 2021 | Prof. Sjors Scheres, MRC Laboratory of Molecular Biology |
| Tues, Jan 18, 2022 | Jesse Hopkins, Ph.D., BioCAT |
| Tues, Feb 15, 2022 | Thorsten Wagner, Ph.D., Max Planck Institute of Molecular Physiology |
PAST WEBINARS
| Tues, Sept 28, 2021 | Alessandra Villa, Ph.D., KTH Royal Institute of Technology, Sweden GROMACS |
| Tues, Oct 5, 2021 | Kirill Nadezhdin, Ph.D., and Arthur Neuberger, Ph.D. Columbia University, Alexander Sobolevsky's Laboratory Structural mechanism of heat-induced opening of a temperature-sensitive TRP channel |
| Tues, Oct 12, 2021 | Jim Vincent, Ph.D., Harvard Medical School BioGrids for SBGrid Users |
2020-2021
| Tues, Sept 15, 2020 | Prof. Daniel Minor, University of California, San Francisco K2P channel gating caught in the act: asymmetric pinching and dilation of a potassium channel selectivity filter |
| Tues, Sept 22, 2020 | Daniel Wrapp, Graduate student, Jason McLellan's lab The University of Texas at Austin Structural insights into SARS-CoV-2 S and implications for therapeutic development |
| Tues, Sept 29, 2020 | Prof. Qing Fan, Columbia University Cryo-EM structure of human GABAB receptor |
| Tues, Oct 6, 2020 | Lance Westerhoff, Ph.D., QuantumBio, Inc. MovableType Software for Fast Free Energy-based Virtual Screening |
| Tues, Oct 13, 2020 | From Priyamvada Acharya's group at Duke Human Vaccine Institute Sophie Gobeil, Ph.D. Structural, biophysical, and biochemical studies of SARS-CoV-2 spike variants |
| Kartik Manne, Ph.D. Structural studies on HIV-1 Env for vaccine design | |
| Tues, Oct 20, 2020 | Jose Miguel de la Rosa Trevin, Ph.D., Research Engineer, Science for Life Laboratory, Stockholm University Scipion 3.0 |
| Tues, Oct 27, 2020 | Markus Stabrin, Max Planck Institute of Molecular Physiology TranSPHIRE |
| Tues, Nov 3, 2020 | Vicky Higman, Ph.D., Research Fellow, University of Leicester CcpNmr Analysis Version 3: Assign & Screen |
| Tues, Nov 10, 2020 | POSTPONED - Yilai Li, Ph.D., Research Fellow, University of Michigan CryoAssess: Automatic data assessment for cryoEM by pretrained neural networks |
| Tues, Nov 17, 2020 | Radhika Malik, Ph.D., Assistant Professor, Icahn School of Medicine at Mt. Sinai Cryo-EM Structures of DNA Polymerase Zeta in Translesion DNA Synthesis |
| Rinku Jain, Ph.D., Assistant Professor, Icahn School of Medicine at Mt. Sinai Cryo-EM Structure and Dynamics of DNA Polymerase Delta in High-Fidelity DNA Synthesis | |
| Tues, Dec 1, 2020 | Vera Moiseenkova-Bell, Ph.D., University of Pennsylvania Perelman School of Medicine Structural insights into TRP channels gating |
| Tues, Dec 8, 2020 | Matt Jaremko, Ph.D., Leemor Joshua-Tor's group, Cold Spring Harbor Laboratory Twist and Pinch, Rock and Roll: Uncovering the dynamic states of the human Origin Recognition Complex |
| Tues, Dec 15, 2020 | Prof. Lejla Zubcevic, University of Kansas Medical Center The role of the cytoplasmic inter-protomer interface in thermoTRPV channel gating |
| Tues, Jan 19, 2021 | Benjamin Himes, Ph.D., University of Massachusetts Medical School Multi-scale classification of the floppy bits; using biological priors in emClarity |
| Tues, Jan 26, 2021 | Rubén Sánchez Garcia, Ph.D., The National Centre for Biotechnolgy, Spanish National Research Council DeepEMhancer: exploiting previous knowledge to enhance map visualization |
| Tues, Feb 2, 2021 | Fabian Schoenfeld, Ph.D., Max Planck Instiutute of Molecular Physiology Computing 2D class averages on a single machine using GPU ISAC |
| Tues, Feb 9, 2021 | Jason Key, Ph.D., SBGrid, Harvard Medical School SBGrid Installation Tools Carol Herre, M.Sc., SBGrid, Harvard Medical School SBGrid Capsule Environment |
| Tues, Feb 16, 2021 | Paul Emsley, Ph.D., MRC Laboratory of Molecular Biology Coot |
| Tues, Feb 23, 2021 | Yilai Li, Ph.D., University of Michigan CryoAssess: Automatic data assessment for cryoEM by pretrained neural networks |
| Tues, Mar 2, 2021 | Prof. Willy Wriggers, Old Dominion University, Integrative Structural Biology with SITUS |
| Tues, Mar 9, 2021 | Florent Delhommel, Ph.D., Michael Sattler's group, Technical University of Munich, Structural characterization of a new co-chaperone involved in client-transfer between heat shock proteins |
| Tues, Mar 16, 2021 | Prof. Marcos Sotomayor, Ohio State University The Molecular Machinery of Hearing |
| Tues, Mar 23, 2021 | Woody Sherman, Ph.D., Silicon Therapeutics Physics-Driven Discovery of SNX281, a Novel Small Molecule Sting Agonist in Clinical Trials for Solid Tumors or Lymphoma |
| Tues, Mar 30, 2021 | Prof. Daniela Fera, Swarthmore College Uncovering an Allosteric Site Critical for the Interaction between B-Raf and MEK Kinases and Downstream MAPK Signaling |
| Tues, Apr 6, 2021 | Steve Meisburger, Ph.D., Nozomi Ando's group, Cornell University Deconvolving protein dynamics in solution and crystals with X-ray scattering |
| Tues, Apr 13 | Jason Key, Ph.D., SBGrid, Harvard Medical School New SBGrid GUI-based software installation manager |
| Tues, Apr 20, 2021 | Dr. Dhirendra Simanshu, NCI RAS Initiative, Frederick National Laboratory for Cancer Research Structural and mechanistic insights into the RAS biology |
| Tues, Apr 27, 2021 | Prof. Evris Gavathiotis, Albert Einstein College of Medicine Conformations, dynamics and allostery in targeting pro-apoptotic BAX |
| Tues, May 4, 2021 | Prof. Yoel Shkolnisky, and Amitay Eldar, Ph.D., Tel Aviv University KLT picker |
| Tues, May 11, 2021 | Steven Ludtke, Baylor College of Medicine EMAN2 |
| Tues, May 18, 2021 | Brian Jimenez-Garcia, Ph.D., University Utrecht, and Jorge Roel, Ph.D., Department of Structural Biology, Protein Design and Modeling group, IBMB-CSIC, Barcelona LightDock: Shedding light into the dark fraction of the protein interactome |
| Tues, Jun 8, 2021 | Daniel Castaño Díez, Ph.D., Biozentrum, University of Basel Dynamo |
| Tues, Jun 29, 2021 | Prof. Alexandre Bonvin, University Utrecht HADDOCK |
2019-2020
| Tues, Sept. 24, 2019 | Tristan Croll, Ph.D., ISOLDE: Bringing structural biology to life | |
| Tues, Oct. 8, 2019 | Nigel Moriarty, Ph.D., Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix | |
| Tues, Nov. 2, 2019 | Prof. Steven Ludtke, In-situ and in-vitro subtomogram averaging to subnanometer resolution using EMAN2.3 | |
| Tues, Mar 24, 2020 | Dr. James Vincent, SBGrid / Harvard Medical School Using the SBGrid Software Client for Remote Work | |
| Fri, Mar 27, 2020 | Dr. Pete Meyer, SBGrid / Harvard Medical School Remote work and structural biology computing | |
| Tues, Mar 31, 2020 | Dr. Tom Terwilliger, Los Alamos National Laboratory Density modification and model building with cryo-EM maps | |
| Fri, Apr 3, 2020 | Dr. Pavel Afonine, Berkeley Lab Atomic model refinement and validation in Phenix | |
| Tues, Apr 7, 2020 | Dr. Dorothee Liebschner, Berkeley Lab Map Sharpening; Model Building; other cryo-EM tools in Phenix | |
| Fri, Apr 9, 2020 | No webinar today -- we'll be back on Tuesday | |
| Tues, Apr 14, 2020 | Dr. Pavel Afonine, Berkeley Lab Atomic model, map and model-to-map fit validation | |
| Fri, Apr 17, 2020 | Prof. Daniel Panne, University of Leicester Structural insights into genome folding by CTCF and cohesin | |
| Tues, Apr 21, 2020 | Dr. Pablo Conesa, National Center for Biotechnology Quo Vadis Scipion | |
| Fri, Apr 24, 2020 | Dr. Tristan Croll, Cambridge Institute for Medical Research ISOLDE | |
| Tues, Apr 28, 2020 | Dr. Shawn Zheng, University of California, San Francisco The recent progress of high-throughput cryo electron microscopy and cryo electron tomography at UCSF | |
| Fri, May 1, 2020 | Trainee Presentations (10 min each with Q&A) Goran Bajic, PhD, Stephen Harrison's group, Harvard Medical School - Structure-guided influenza virus antigen engineering focuses immune responses Ryan Feathers, Chris Fromme's group, Cornell University - Structural analysis of regulated Ypt6 (Rab6) activation by the Ric1/Rgp1 complex | |
| Tues, May 5, 2020 | Dr. Kay Diederichs, Universität Konstanz Crystallographic data processing with XDS, using XDSGUI | |
| Fri, May 8, 2020 | SBGrid Technology Tutorial Carol Herre, Software Release Engineer, SBGrid/Harvard Medical School - Introduction to SBGrid Capsules Dr. Jason Key, Assoc Director of Technology & Innovation, SBGrid/Harvard Medical School - Sneak Peek: SBGrid Installer v2 | |
| Tues, May 12, 2020 | Kelly Brock, PhD and Thomas Hopf, PhD, Laboratory of Debora Marks, Harvard Medical School EVCouplings | |
| Fri, May 15, 2020 | Ellen Zhong, Bonnie Berger's Lab, MIT CryoDRGN: Deep generative models for reconstructing heterogeneous protein structures from cryo-EM | |
| Tues, May 19, 2020 | Trainee Presentations (10 min each with Q&A) Mayukh Chakrabarti, Sandra Gabelli's group, Johns Hopkins University - Dynamic Allostery in PI3Kɑ activation: A computational approach Liron David, PhD, Hao Wu's group, Boston Children's Hospital - Assembly Mechanism of the CBM signalosome Mike Fenwick, PhD, Steve Ealick's group, Cornell University - Structural basis of substrate selectivity of viperin, an antiviral radical SAM enzyme | |
| Fri, May 22, 2020 | Dr. Colin Palmer, Science and Technology Facilities Council CCP-EM: software for cryo-EM | |
| Tues, May 26, 2020 | Prof. Karin Reinisch, Yale School of Medicine Structural insights into interorganelle lipid transport | |
| Fri, May 29, 2020 | Dr. Thorsten Wagner, Max-Planck-Institute of Molecular Physiology crYOLO and its utilization in feedback guided real-time processing | |
| Tues, Jun 2, 2020 | Dari Kimanius, Ph.D., MRC Laboratory of Molecular Biology RELION: Exploiting prior knowledge about biological macromolecules in cryo-EM structure determination | |
| Tues, Jun 9, 2020 | Prof. Steve Reichow, Portland State University Connexin-46/50 gap junction channels in a dynamic lipid environment resolved by CryoEM at 1.9 Å | |
| Tues, Jun 16, 2020 | Prof. Chris Hill, University of Utah School of Medicine Structural insights to the mechanism of AAA unfoldases | |
| Tues, Jun 23, 2020 | Trainee Presentations (10 min each with Q&A) Michael Robertson, PhD, Georgios Skiniotis's group, Stanford University - GemSpot: A Pipeline for Robust Modeling of Ligands into CryoEM Maps Md. Mahfuzur Rahman, PhD, Ryan Hibbs's group, UT Southwestern - Cryo-EM structure of native muscle-type nicotinic acetylcholine receptor and inhibition by snake venom toxins | |
| Tues, Jun 30, 2020 | Evan Worden, Cynthia Wolberger's Laboratory, Johns Hopkins University School of Medicine Mechanisms of crosstalk between histone ubiquitination and methylation | |
| Tues, Jul 7, 2020 | Tom Goddard, University of California, San Francisco, Resource for Biocomputing, Visualization, and Informatics Making Augmented Reality Videos with ChimeraX | |
| Tues, Jul 14, 2020 | Lightning Talks (15 min each with Q&A) Makaia Papasergi-Scott, PhD, Georgios Skiniotis's group, Stanford University - Structures of metabotropic GABAB receptors Q&A with SBGrid Technical Team: | |
| Tues, Jul 21, 2020 | Prof. Brent Nannenga, Arizona State University MicroED methodology and application | |
| Tues, Jul 28, 2020 | Michael Sheedlo, PhD, Vanderbilt University, Borden Lacy's group Structural Characterization of Bacterial Translocases |
2018-2019
| Tues, Oct 2, 2018 | Lance Westerhoff, Ph.D., XModeScore: using crystallography to determine protonation states, fragment binding modes, and flip-states |
| Tues, Nov 6, 2018 | Sjors Scheres, Ph.D., RELION-3: new tools for automated high-resolution cryo-EM structure determination |
| Tues, Dec 4, 2018 | Nicholas Pearce, Ph.D., PanDDA: extracting ligand-bound protein states from conventionally uninterpretable crystallographic electron density |
| Tues, Jan 22, 2019 | Thomas Grant, Ph.D., DENSS: Ab Initio Electron Density Maps from Biological SAXS Data |
| Tues, Feb 26, 2019 | Tristan Bepler, Ph.D., Topaz: particle picking with positive-unlabeled learning |
| Tues, Apr 2, 2019 | Prof. Jose-Jesus Fernandez, TomoAlign: Consideration of sample motion in cryoET |
| Tues, May 28, 2019 | Thorsten Wagner, Ph.D., Fast, accurate and easy particle picking with crYOLO |
| Tues, Jul 23, 2019 | Colin Palmer, Ph.D., Model building and validation in CCP-EM |
2017-2018
| Tues, Sept 19, 2017 | Jason Key, Ph.D., What's new at SBGrid: SBGrid Environment and Installation Tools |
| Tues, Oct 10, 2017 | Prof. Toshio Moriya Ludtke, SPHIRE: User-friendly pipeline for near-atomic resolution Cryo-EM structure determination with automatic validation mechanisms |
| Tues, Nov 14, 2017 | Prof. Steven Ludtke, EMAN2.2 for Single Particle Analysis and In-situ Structural Biology |
| Tues, Dec 5, 2017 | Frank Delaglio, Ph.D., Concepts in Spectral Processing of Conventional and Non-Uniformly Sampled NMR Data |
| Tues, Dec 12, 2017 | Frank Delaglio, Ph.D., Processing of Conventional and Non-Uniformly Sampled NMR Data with NMRPipe |
| Tues, Mar 27, 2018 | Prof. Michael Cianfrocco, Software tools to manage cryo-EM jobs on the cloud |
| Tues, Apr 3, 2018 | Woonghee Lee, Ph.D., NMRFAM-Sparky |
| Tues, May 22, 2018 | Giovanni Bussi, Ph.D., Analyzing and enhancing molecular dynamics simulations with PLUMED |
| Tues, Jun 12, 2018 | Jose Miguel de la Rosa Trevin, Using Scipion for Stream Image Processing at Cryo-EM Facilities |
2011-2017
| Sept 27, 2011 | Jason Vertrees,Ph.D. Hints, Tips and New Features for PyMOL v1.4 |
| Oct 31, 2011 | Daniel O'Donovan, Ph.D. Low Resolution refinement with DEN |
| Nov 11, 2011 | Kevin Keating, Ph.D. RCrane: Semi-automated RNA model building within Coot |
| Dec 12, 2011 | Name, Institution Title |
| Jan 9, 2012 | Wladek Minor, Ph.D. HKL2000 |
| Feb 27, 2012 | Tim Stevens, Ph.D. CcpNmr SpecView and ChemBuild: the first next-generation CCPN software |
| Mar 13, 2012 | Jose-Maria Carazo, Ph.D. Primer on the XMIPP software suite: its contribution to 3-dimensional electron microscopy and future directions |
| Apr 23, 2012 | Randy Read,Ph.D. Extending the reach of molecular replacement in Phaser |
| Jun 12, 2012 | Woody Sherman, Ph.D. Recent Enhancements and Scientific Advancements in the Schrödinger Suite |
| Jun 19, 2012 | Clemens Vornhein, Ph.D. Experimental phasing and structure solution with SHARP/autoSHARP |
| Oct 4, 2012 | James Chen, Ph.D. PARTICLE: an Integrated Computing Platform for Single-Particle Electron Microscopy |
| Nov 1, 2012 | Ronan Keegan, Ph.D. What's new in CCP4 6.3.0 |
| Jan 24, 2013 | Stuart McNicholas, Ph.D. The CCP4 Molecular Graphics Program (CCP4-MG) |
| Feb 7, 2013 | Thomas Goddard, Ph.D. Analyzing Molecular Assemblies with UCSF Chimera |
| Apr 18, 2013 | Graeme Winter, Ph.D. Automated Data Analysis with xia2 |
| Jun 13, 2013 | Jan Brezovsky, Ph.D. CAVER 3.0: Analysis of Tunnels in Static and Dynamic Protein Structures |
| July 11, 2013 | Jim Procter, Ph.D. Creating and analyzing multiple sequence alignments with the Jalview Desktop Application |
| Sept 19, 2013 | Andrea Thorn, Ph.D. New features in SHELX_2013 |
| Oct 3, 2013 | Christian Olsen, Ph.D. Geneious R7: A bioinformatics platform for biologists |
| Nov 7, 2013 | Frank Delaglio, Ph.D. Spectral Processing Concepts for Biomolecular NMR |
| Nov 14, 2013 | Frank Delaglio, Ph.D. Introduction to NMR Spectral Processing with NMRPipe |
| Dec 5, 2013 | Homayoun Valafar, Ph.D. Structure Validation of Proteins using REDCAT |
| Feb 6, 2014 | Wladek Minor, Ph.D. HKL-2000/HKL-3000: Toward the Future of Structural Biology |
| Mar 21, 2014 | Thomas Grant, Ph.D. SAXS Part I: Introduction to Biological Small Angle Scattering |
| Apr 10, 2014 | Matthew Baker, Ph.D. Modeling Macromolecular Structures with Gorgon |
| May 13, 2014 | Nat Echols, Ph.D. Refinement of challenging structures with Rosetta and Phenix |
| June 26, 2014 | Xiang-Jun Lu, Ph.D. DSSR, a new 3DNA program for Defining the Secondary Structures of RNA from three-dimensional coordinates |
| July 17, 2014 | Daron Standley, Ph.D. MAFFT/MAFFTash: Web services for structure-informed multiple sequence alignment |
| Sept 9, 2014 | Christian Olsen, Ph.D. Geneious R7: Sequence Analysis Tool for Biologists |
| Nov 18, 2014 | Thomas Grant, Ph.D. Advanced Applications of Biological Small Angle Scattering |
| Feb 17, 2015 | Harry Powell, Ph.D. iMosflm - a tool for data reduction |
| Mar 24, 2015 | Sjors Scheres, Ph.D. RELION |
| Apr 14, 2015 | Steven Ludtke, Ph.D. A quick introduction to EMAN2.1 for CryoEM Single Particle Analysis |
| May 19, 2015 | Erek Lindahl, Ph.D. Molecular Simulations with GROMACS: Possibilities and Pitfalls |
| July 7, 2015 | Woody Sherman, Ph.D. Schrodinger Small Molecule Suite |
| July 14, 2015 | Thomas White, Ph.D. CrystFEL - data processing for serial crystallography |
| Sept 8, 2015 | Prof. Alexandre Bonvin Modelling biomolecular complexes using HADDOCK: local vs server mode. |
| Sept 22, 2015 | Lance Westerhoff, Ph.D. Phenix/DivCon: accurate macromolecular crystallographic refinement using linear scaling, semiempirical quantum-mechanics |
| Nov 10, 2015 | Woody Sherman, Ph.D. Docking Tools within the Schrodinger Suite |
| Nov 17, 2015 | Graeme Winter, Ph.D. DIALS |
| Jan 12, 2016 | Woody Sherman, Ph.D. The role of water molecules in protein preparation, docking, and scoring |
| Jan 26, 2016 | Roberto Tejero, Ph.D. PDBStat: Features for NMR structure and constraint satisfaction analysis |
| Feb 9, 2016 | Jamse Foadi, Ph.D. Assembling data from multiple crystals with BLEND |
| Mar 8, 2016 | Raj Pannu, Ph.D. Automated macromolecular structure solution from SAD and MR-SAD experiments with Crank2 |
| Mar 29, 2016 | Jas Bhachoo, Ph.D. The Importance of Protein Preparation for Modeling Applications |
| Apr 26, 2016 | Daniel Rigden, Ph.D. AMPLE: a pipeline for unconventional Molecular Replacement |
| May 10, 2016 | Gunnar Schroeder, Ph.D. DireX - Cross-validated Real-space Refinement to Density Map |
| June 21, 2016 | Ivet Behar, Ph.D. Elastic Network Models and ProDy for Bimolecular Systems Dynamics |
| July 26, 2016 | Christian Olsen, Ph.D. Geneious (Custom BLAST, workflow builder, annotation tools, CRISPER tools) |
| Sept 13, 2016 | Daniel Cappell, Ph.D. Communicating your research results using PyMOL |
| Oct 4, 2016 | Prof. Willy Wriggers Combining Structures from Different Biophysical Origins with Situs |
| Oct 11, 2016 | Ishita Aloni, Ph.D. Protein Ligand Database |
| Nov 1, 2016 | Prof. Willy Wriggers Multiscale Computational Modeling and Visualization with Sculptor |
| Dec 6, 2016 | Abhishek Singharoy,Ph.D. Structure Determination of a Cell Organelle with a Computational Microscope |
| Date | Name, Institution Title |
| Date | Name, Institution Title |