Category: Past Talks

Although cryo-EM has been drastically improved to generate high-resolution three-dimensional (3D) maps that contain detailed structural information about macromolecules, the computational methods for using the data to automatically build structure models are lagging far behind. The traditional cryo-EM model building approach is template-based homology modeling. Manual de novo modeling is very time-consuming when no template model is found in the database. In recent years, de novo cryo-EM modeling using machine learning (ML) and deep learning (DL) has ranked among the top-performing methods in macromolecular structure modeling. Deep-learning-based de novo cryo-EM modeling is an important application of artificial intelligence, with impressive results and great potential for the next generation of molecular biomedicine. Accordingly, I will talk about the representative ML/DL-based de novo cryo-EM modeling methods that we developed.

Cryo electron tomograms (cryo-ET) are nothing short of amazing. There is so much to see, but wouldn’t it be nice if we could identify all those structural features in terms of their molecular identity? The combination of cryo-single molecule localization microscopy (cryo-SMLM) and cryo-ET should provide a pathway to making such identification. What are the challenges to realizing the combination’s full potential? Why the fish tank?

HEMNMA is a method to analyze continuous conformational variability of purified macromolecular complexes (in vitro), introduced in 2014 (Jin et al., Structure 22:496-506, 2014). Its software with user friendly graphical interface is part of the open-source ContinuousFlex plugin of Scipion 2 and Scipion 3 (Harastani et al., Protein Science 29:223–236, 2020). HEMNMA combines single particle image analysis, normal mode analysis, and dimension reduction techniques to visualize the full distribution of states (conformational landscape) in a low-dimensional space (usually 2D or 3D space), from which one can obtain 3D reconstructions and movies of molecular motions along desired directions. After a brief reminder on HEMNMA, I will present current developments, including combining HEMNMA with deep learning to accelerate the conformational landscape determination and an extension of HEMNMA to analyze continuous conformational variability of macromolecular complexes in cells from in situ cryo electron tomography data.     

We are delighted to announce that we will be hosting a pilot virtual One World Cryo-EM Poster Session on March 10-11, 2021. This poster session, held on gather.town, will be a chance to discuss research with colleagues, share your own work, and socialize with others in the community.

A list of posters, presenters, and their availability can be found below or at the following link.

We have 3 live poster sessions on: March 10 11am-1pm EST, March 10 8-10pm EST, March 11 8am-10am EST. 

If you are interested in presenting, please submit your poster on this application form. With your poster, you may optionally submit a 3-5 minute video to be displayed alongside your poster for visitors outside of live poster sessions. More information and details are provided in the form.

Please make sure that you are on our mailing list. This is the only place where the links to the gather.town poster session will be posted. As always, you can find more information at https://cryoem.world. 

We are excited to host this poster session, and hope that you will join us.

Important Rules and Policies

As a participant, you agree that any information presented in the One World Cryo-EM poster session, whether in a poster, talk, video, or discussion, is private communication and that the information is not for public use.

You agree not to record the information by any means and not to quote or publish it without the written permission of the presenter. This includes posting information on social media, in publications, and on blogs. 

You understand that the posters are not peer-reviewed and not archivable.

You understand that it is up to each participant to follow these restrictions. The organizers are not responsible for enforcing these restrictions. 

Note that the list of poster titles and authors will be available on the OWCryo-EM website. Therefore, you may tweet a recommendation to visit poster #123 titled x by y (#OWCryoEMPosters) without referencing the content.

As a presenter, you may post your own poster on Twitter and invite people to retweet it and meet you at your poster #OWCryoEMPosters.

FAQ

Q: What is gather.town? What do posters there look like?
A: This is what a poster looks like on gather.town: https://gather.town/app/5Qb5FSmPM0wtDvpd/sample_poster (the actual session is expected to have a slightly larger number of posters).

Q: How do I view the gather.town session?
A: Please make sure that you are on our mailing list. This is the only place where the links to the gather.town poster session will be posted.

Q: What is the poster selection process?
A: In this pilot poster session, we expect to accept all novel work that satisfies the topic, quality, and form requirements.

Q: How do I submit a poster?
A: Please submit your completed poster on this application form. You are not required to submit a title and abstract before submitting the full poster.

Q: What are the requirements for the poster?
A: Posters should be in an image format (eg .png, .jpg, but not .pdf), and should be at least 4000×6000 pixels. You may resubmit posters up to 10 times until February 22nd. These will be collectively posted in gather.town, and we will let you know your poster ID number. Here is a poster size example.

Q: What are the requirements for the video?
A: Videos are optional, and should be between 3-5 minutes long and provide viewers a brief description of your poster. These will be posted next to your poster for visitors that cannot make the live session, or to provide visitors context about your poster.

Three-dimensional reconstruction of the electron-scattering potential of biological macromolecules from electron cryo-microscopy (cryo-EM) projection images is an ill-posed problem. The most popular cryo-EM software solutions to date rely on a regularization approach that is based on the prior assumption that the scattering potential varies smoothly over three-dimensional space. Although this approach has been hugely successful in recent years, the amount of prior knowledge that it exploits compares unfavorably with the knowledge about biological structures that has been accumulated over decades of research in structural biology. Here, a regularization framework for cryo-EM structure determination is presented that exploits prior knowledge about biological structures through a convolutional neural network that is trained on known macromolecular structures. This neural network is inserted into the iterative cryo-EM structure-determination process through an approach that is inspired by regularization by denoising. It is shown that the new regularization approach yields better reconstructions than the current state of the art for simulated data, and options to extend this work for application to experimental cryo-EM data are discussed.

Advance registration is required: https://yale.zoom.us/meeting/register/tJApcu6grD4iGdFaQsDVdpJEaGD1oE-3VOjB

Single particle cryoEM projects are often hampered by low SNR particle views, which are missed by most particle pickers or severely de-prioritized causing junk to be preferentially picked. Moreover, for non-globular, small, asymmetric, and aggregated proteins, picking and centering such particles becomes critical. To solve these issues and more, we present Topaz particle picking using a novel positive-unlabelled framework and Topaz-Denoise using the Noise2Noise framework. We show that Topaz and Topaz-Denoise significantly increase the number of real particles picked, enable conventionally difficult projects, significantly decrease classification bias, and increase collection efficiency. We show the first in-depth analysis of pre-trained 2D and 3D denoising models for cryoEM and cryoET, which remove the characteristic sheets of noise in cryoEM micrographs of proteins and cryoET cellular tomograms. We also will highlight Topaz pre-trained picking models. In the past several months, Topaz has been used by numerous labs around the world to enable and optimize single particle cryoEM projects, including several SARS-CoV2 projects. These recent projects and more will be highlighted to show the unique and timely power of Topaz. We will also highlight Topaz integration into the most popular cryoEM suites: Relion, CryoSPARC, Scipion, and Appion.