Workshops & Lectures

Stanford-SLAC CryoEM Center Modeling and Structure Validation Workshop
October 28–30, 2025 | Hybrid (In-person at SLAC + Virtual)

Join us for a three-day hybrid workshop hosted by the Stanford-SLAC CryoEM Center, focused on modeling and structure validation in cryo-electron microscopy (cryoEM). With the growing number of cryoEM structures being solved and deposited, this workshop aims to provide practical guidance and hands-on insights into a variety of tools and approaches. Topics will include model building, refinement and visualization using programs (Coot, Phenix, ModelAngelo, ChimeraX, ISOLDE, and etc) for proteins and nucleic acids, as well as best practices for structure validation and deposition.

The program will feature expert-led lectures, live software demonstrations, and opportunities for interactive learning. Whether you're new to cryoEM modeling or looking to refine your workflows, this workshop is designed to support the structural biology community in generating accurate and reliable models.

Workshop Agenda (Tentative)

Paul Emsley Scientist	MRC -LMB	Model-building, Refinement and Validation using Coot
Lucrezia Catapano Scientist	MRC - LMB	Model-building, Refinement and Validation using Coot
Dari Kimanius, AI/ML Team Leader	Chan Zuckerberg Initiative	Innovations in CryoEM Analysis: Tackling Heterogeneity, Regularization, and Model Building
Rachael Kretsch	Stanford University	Overview of tools for nucleic acid structural modeling and validation

Stephanie Wankowicz Asst. Professor	Vanderbilt	TBA
Tom Goddard	UCSF	Creating Animations with ChimeraX
Tristan Kroll, Principal Scientist	Altos Lab UK	Interactive physics-based model building in ISOLDE
Nigel Moriarty	LBNL/Berkeley	TBA

Oleg Sobolev	LBNL	TBA
Jane Richardson	Duke University	How to get the most out of validation
Greg Pintilie	Stanford University	3DEM Map-Model Validation Using Q-Scores
Stephen Burley, Director, RCSB Protein Data Bank with Justin Flatt	Rutgers, The State University of New Jersey San Diego Supercomputer Center, UCSD	Advancing FAIR and Sustainable 3DEM Data Ingestion, Validation, Management, and Distribution at the Worldwide Protein Data Bank

Workshop Agenda (Tentative)

Day 1: Ab Initio Modeling Methodologies

Paul Emsley Scientist	MRC	Model-building, Refinement and Validation using Coot
Lucrezia Catapano Scientist	MRC Laboratory of Molecular Biology (LMB)	Model-building, Refinement and Validation using Moorhen
Dari Kimanius, AI/ML Team Leader	Chan Zuckerberg Initiative	Innovations in CryoEM Analysis: Tackling Heterogeneity, Regularization, and Model Building
Rachael Kretsch	Stanford University	Overview of tools for nucleic acid structural modeling and validation

Day 2: Model Visualization Refinement

Stephanie Wankowicz Asst. Professor	Vanderbilt	TBA
Tom Goddard	UCSF	Creating Animations with ChimeraX
Tristan Kroll, Principal Scientist	Altos Lab UK	Interactive physics-based model building in ISOLDE
Nigel Moriarty	LBNL/Berkeley	TBA

Day 3: Model Validation and Structure Deposition

Oleg Sobolev	LBNL	TBA
Jane Richardson	Duke University	How to get the most out of validation
Greg Pintilie	Stanford University	3DEM Map-Model Validation Using Q-Scores
Stephen Burley, Director, RCSB Protein Data Bank with Justin Flatt	Rutgers, The State University of New Jersey and San Diego Supercomputer Center, UCSD	Advancing FAIR and Sustainable 3DEM Data Ingestion, Validation, Management, and Distribution at the Worldwide Protein Data Bank