7th – 9th January 2025
Diamond User meeting
Themes:
- Existing and maturing user modalities
- I04 updates and developments of dose aware data collection
- VMXi user programme and developments
- XFEL hub: upcoming projects for time-resolved serial crystallography
- An update on I24, KMX, and serial crystallography
- VMXm – microfocus and sub-microfocus MX
- Future user modalities
- HeXI (a new instrument for electron diffraction)
- K04 (a new ultra-high throughput beamline for MX and XChem)
- Fast forward fragment screening
- Opportunities with DLS-II
- Science and infrastructure
- PhD and PostDoc research at Diamond
- Visiting scientists, RCaH
- Software (xia2 multiplex, Fragalysis, PanDDA2)
11:00-11:05
Welcome by DUC representatives
David Briggs and Colin Levy
The Francis Crick Institute, University of Manchester
11:05 – 11:20
Diamond MX group – capabilities and news for 2025
Dave Hall
Diamond Light Source Ltd
11:20 – 11:40
I04 Beamline: An Update on Dose-Aware Data Collection Strategies
David Aragao
Diamond Light Source Ltd
11:40 – 12:00
Exploiting automated high throughput room temperature crystallography at VMXi
Mike Hough
Diamond Light Source Ltd
12:00 – 12:55
Lunch
12:55 – 13:15
The XFEL Hub at Diamond: creating tools for time-resolved crystallography and spectroscopy
Allen Orville
Diamond Light Source Ltd
13:15 – 13:35
Taking your samples further: opportunities for microfocus and serial MX at I24
Robin Owen
Diamond Light Source Ltd
13:35 – 13:55
VMXm and HeXI
Gwyndaf Evans
Diamond Light Source Ltd
13:55 – 14:10
Investigating the use of Cyclic peptides as inhibitors and substrates for the SARS-CoV-2 Main Protease
Taylah Andrews-Clark
Diamond Light Source Ltd/University of Oxford
14:10 – 14:40
Coffee Break
14:40 – 14:55
Room-temperature fragment-based screening at Diamond: towards the optimisation of a high-throughput experiment
Megan Lambert
Diamond Light Source Ltd
14:55 – 15:10
Let’s polish the Diamond: Enhancing user experiences together
Neeli Katti
Diamond Light Source Ltd
15:10 – 15:30
Faster, Larger, Better XChem: Fast Forward Fragments for progressing fragment hits
Frank von Delft and Warren Thompson
Diamond Light Source Ltd
15:30-16:00
DUC Discussion
David Briggs, Colin Levy
The Francis Crick Institute / University of Manchester
16:00 – 17:30
Break
16:00 – 17:30
CCP4 WG1 meeting
Session 1
17:30 – 18:15
Structure-function relationships of metalloproteins and assembly of their metallocofactors.
Yvain Nicolet
Institut de Biologie Structurale, FRANCE
18:15 – 19:00
"Skill Mismatch: Are We Training Structural Biologists for Jobs That Won’t Exist?" – round table discussion
Robbie Joosten (Chair), Tom Davies, Alisia Fadini, Julie Menetrey
Netherlands Cancer Institute (Netherlands), Astex Pharmaceuticals (UK), University of Cambridge (UK), Universite Paris-Saclay, FRANCE
19:00 – 21:00
Networking event including street food and poster session
What's new in CCP4?
09:00 – 09:10
What's new in CCP4?
Ville Uski
UKRI-STFC CCP4, UK
09:10 – 09:45
What's New in the Land of Coot: Demo of Moorhen and for the newly updated/available ligand tools
Lucrezia Catapano
UKRI-MRC LMB, UK
09:45 – 10:00
New approaches for structure refinement in CCP4i2
Martin Maly
UKRI-MRC LMB, UK
10:00 – 10:15
Linking data sources with CCP4 Cloud: a fully online setup for structure determination
Jools Wills
UKRI-STFC CCP4, UK
10:15 – 10:30
What’s New in CCP4 Cloud?
Maria Fando
UKRI-STFC CCP4, UK
10:30 – 11:00
Break
Session 2
Demystifying the black box – new features and old tricks to use software efficiently.
11:00 – 11:30
Approaches to processing and selecting data in multi-crystal collection strategies
James Beilsten-Edmands
Diamond Light Source, UK
11:30 – 12:00
Solve your structure with MR at warp speed.
Airlie McCoy
Cambridge Institute for Medical Research, UK
12:00 – 12:30
Some considerations on diffraction data quality, diffraction limits, and refinement approaches and outcomes.
Gerard Bricogne
Global Phasing, UK
12:30 – 14:00
Lunch
Lunchtime Bytes – In person only
13:00 – 14:00
Preparing and using predicted models
Adam Simpkin
University of Liverpool, UK
13:00 – 14:00
Glycan Validation With Privateer
Lou Holland
University of York, UK
13:00 – 14:00
Moorhen: Refinement and Depictions
Lucrezia Catapano
UKRI-MRC LMB, UK
13:00 – 14:00
CCP4i2
Paul Bond
University of York, UK
13:00 – 14:00
High Throughput Structure Solution in CCP4 Cloud
Eugene Krissinel
UKRI-STFC CCP4, UK
13:00 – 14:00
AlphaBridge and AlphaFill: assisting in the biological interpretation of AlphaFold models
Daniel Alvarez
Netherlands Cancer Institute, NETHERLANDS
13:00 – 14:00
ARCIMBOLDO at Low Resolution: Verification
Elisabet Jiménez
Molecular Biology Institute of Barcelona (IBMB-CSIC), SPAIN
13:00 – 14:00
New ways to find the data you are interested in
Genevieve Evans and Deborah Harrus
PDB EBI, UK
Session 3
Using prior knowledge to improve and validate models.
14:00 – 14:30
Untangling models reveals hidden information in structural data
James Holton
University of California at San Francisco (UCSF), USA
14:30 – 15:00
Leveraging Large-Scale Data to Refine and Validate Metalloprotein Structures: Insights into Metal Coordination and Carboxylate Interactions
Milana Bazayeva
Cleveland Clinic, USA
15:00 – 15:30
Reconstructing Biological Molecules with Help from Video Gamers
Robbie Joosten, Scott Horowitz
Netherlands Cancer Institute, NETHERLANDS / University of Denver, USA
Session 4
AI in structural biology I: Predicted models and how to use them.
16:00 – 16:30
AI for molecular modeling and protein design
Eva Smorodina
University of Oslo, Norway
16:30 – 17:00
Accelerating biological research using AlphaFold
Oleg Kovalevskiy
Google Deepmind, UK
17:00 – 17:30
Recent advances and limitations of RNA 3D structure prediction
Clement Bernard
Université Paris Saclay, FRANCE
17:30 – 19:00
Break
19:00 – 00:00
Conference Dinner + social including Ceilidh and Board Games café
Session 5
AI in structural biology II: Other applications.
09:00 – 09:30
Artificial Intelligence in Structural Biology – The Good, The Bad and The Ugly
Wladek Minor
University of Virginia School of Medicine, USA
09:30 – 10:00
Integrating Machine Learning Frameworks in Scientific Workflows
Piero Gasparotto
Paul Scherrer Institute / Microsoft Quantum, SWITZERLAND
10:00 – 10:30
Exploring deep learning approaches to solving the phase problem
Mitchell Miller
Rice University, USA
10:30 – 11:00
Break
Session 6
Dynamics
11:00 – 11:30
Molecular-Dynamics Simulations of Protein Crystals to Enhance Conventional Modeling and Refinement
Michael Wall
Los Alamos National Laboratory, USA
11:30 – 12:00
Explaining Conformational Diversity in Protein Families through Molecular Motions and Predicting them with Unsupervised and Supervised Learning Approaches
Sergei Grudinin
Université Grenoble-Alpes, FRANCE
12:00 – 12:30
Mathematically deriving protein flexibility for single protein structures
Virginia Apostolopoulou
Center for free electron lasers, GERMANY
12:30 – 13:00
Lunch
Lunchtime Bytes – In person only
13:00 – 14:00
Coot 1: Ligands and Depictions
Lucrezia Catapano and Paul Emsley
UKRI-MRC LMB, UK
13:00 – 14:00
ModelCraft and NucleoFind
Jordan Dialpuri and Paul Bond
University of York, UK
13:00 – 14:00
LUNUS jupyter notebooks for preparation and analysis of protein crystal molecular-dynamics simulations
Michael Wall
Los Alamos National Laboratory, USA
13:00 – 14:00
Latest developments on Dials User Interface (Dui)
Luis Fuentes-Montero
Diamond Light Source, UK
13:00 – 14:00
Processing and visualising diffraction data with multiple software packages in the browser using DiffraView
David McDonagh
UKRI-STFC CCP4, UK
13:00 – 14:00
An overview of CCP-EM for cryoEM & ET
Agnel Joseph
UKRI-STFC CCP-EM, UK
13:00 – 14:00
Servalcat and MetalCoord: refinement of structures with metal sites
Martin Maly
University of Southampton, UK
Session 7
More ways to characterize your sample.
14:00 – 14:25
Kinetic cryocrystallography vs time-resolved crystallography: when to trap reaction intermediates and when to observe them in real-time.
Nicolas Caramello
European Synchrotron Radiation Facility (ESRF), FRANCE
14:25 – 14:50
Placing low-occupancy fragments using the anomalous signal of sulfur and halogen atoms
Shumeng Ma
Yale University, USA
14:50 – 15:15
Joint neutron and X-ray protein crystallography: complementary tools in the detailed analysis of enzyme structures
Zoe Fisher
European Spallation Source, SWEDEN
15:15 – 15:40
Improved protein structures by quantum refinement
Ulf Ryde
Lund University, SWEDEN
