Cole Group
@colegroupncl.bsky.social
We are a computational research group at Newcastle University led by #UKRIFLF Dr Danny Cole specialising in atomistic simulations in medicinal chemistry and biology https://blogs.ncl.ac.uk/danielcole/
Reposted by Cole Group
Delighted to announce that I've been awarded a #Marsden Fast-Start grant and will be moving back to New Zealand 🇳🇿 to start a position in my hometown at the University of Canterbury!
A list of all successful 2025 #MarsdenFund projects can be found below. Congratulations to all of the funded researchers!
www.royalsociety.org.nz/what-we-do/f...
www.royalsociety.org.nz/what-we-do/f...
Marsden Fund Awards 2025
Published on 6 Whiringa-ā-rangi November 2025
You can download an Excel spreadsheet of these results here: 2025-Marsden Fund Supplement
The definitions of the 8 Marsden Fund panels can be found here...
www.royalsociety.org.nz
November 24, 2025 at 12:46 PM
Delighted to announce that I've been awarded a #Marsden Fast-Start grant and will be moving back to New Zealand 🇳🇿 to start a position in my hometown at the University of Canterbury!
Reposted by Cole Group
The latest article in our Lessons Learned category is out now!
"The Journey of Data: Lessons Learned in Modeling Kinase Affinity, Selectivity, and Resistance" by López-Ríos de Castro et al helps guide the development of platforms for structure-enabled ML for drug discovery: doi.org/10.33011/liv...
"The Journey of Data: Lessons Learned in Modeling Kinase Affinity, Selectivity, and Resistance" by López-Ríos de Castro et al helps guide the development of platforms for structure-enabled ML for drug discovery: doi.org/10.33011/liv...
November 21, 2025 at 2:50 PM
The latest article in our Lessons Learned category is out now!
"The Journey of Data: Lessons Learned in Modeling Kinase Affinity, Selectivity, and Resistance" by López-Ríos de Castro et al helps guide the development of platforms for structure-enabled ML for drug discovery: doi.org/10.33011/liv...
"The Journey of Data: Lessons Learned in Modeling Kinase Affinity, Selectivity, and Resistance" by López-Ríos de Castro et al helps guide the development of platforms for structure-enabled ML for drug discovery: doi.org/10.33011/liv...
📢 We have a fully funded PhD studentship available for Oct 2026 start on "Training force fields for computer-aided drug design with machine learning", in collaboration with Ioan Magdau and SandboxAQ.
Full details and how to apply: www.ncl.ac.uk/postgraduate...
Closing date: 18 Jan 2026
#compchem
Full details and how to apply: www.ncl.ac.uk/postgraduate...
Closing date: 18 Jan 2026
#compchem
November 19, 2025 at 3:15 PM
📢 We have a fully funded PhD studentship available for Oct 2026 start on "Training force fields for computer-aided drug design with machine learning", in collaboration with Ioan Magdau and SandboxAQ.
Full details and how to apply: www.ncl.ac.uk/postgraduate...
Closing date: 18 Jan 2026
#compchem
Full details and how to apply: www.ncl.ac.uk/postgraduate...
Closing date: 18 Jan 2026
#compchem
"Enhancing Electrostatic Embedding for ML/MM Free Energy Calculations" is now out in #JCTC: pubs.acs.org/doi/10.1021/...
Great job by João and team! #compchem
Great job by João and team! #compchem
November 14, 2025 at 6:36 PM
"Enhancing Electrostatic Embedding for ML/MM Free Energy Calculations" is now out in #JCTC: pubs.acs.org/doi/10.1021/...
Great job by João and team! #compchem
Great job by João and team! #compchem
If you're at #ukqsar today, be sure to check out posters by @finlayclark.bsky.social, on work with @openforcefield.org, and @asmaferiel.bsky.social & @chikitng.bsky.social on computer-aided drug design methods! #compchem
November 13, 2025 at 10:34 AM
If you're at #ukqsar today, be sure to check out posters by @finlayclark.bsky.social, on work with @openforcefield.org, and @asmaferiel.bsky.social & @chikitng.bsky.social on computer-aided drug design methods! #compchem
📢 Looking for a PhD in computational drug discovery? Check out this funded opportunity with @agnesnoy.bsky.social at York, in collaboration with researchers at Newcastle, Oxford & Inspiralis! ⬇️
Would you like to fight against antimicrobial resistance (AMR) developing antibiotics? Apply to the PhD opportunity below and come to York. Collaboration with colegroupncl.bsky.social, @dghilarov.bsky.social and Inspiralis Ltd.
Fully funded via DiMeN DTP 💡
www.findaphd.com/phds/project...
Fully funded via DiMeN DTP 💡
www.findaphd.com/phds/project...
MRC DiMeN Doctoral Training Partnership: Computational Drug Discovery Targeting DNA Gyrase to Tackle Antimicrobial Resistance at University of York on FindAPhD.com
PhD Project - MRC DiMeN Doctoral Training Partnership: Computational Drug Discovery Targeting DNA Gyrase to Tackle Antimicrobial Resistance at University of York, listed on FindAPhD.com
www.findaphd.com
November 3, 2025 at 9:31 AM
📢 Looking for a PhD in computational drug discovery? Check out this funded opportunity with @agnesnoy.bsky.social at York, in collaboration with researchers at Newcastle, Oxford & Inspiralis! ⬇️
Reposted by Cole Group
OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇
October 28, 2025 at 6:30 PM
OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇
Reposted by Cole Group
Chapin Cavendar's paper, Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields, is out now in LiveCoMS. Read it for a detailed look at the great work he has been doing toward an OpenFF protein force field, and stay tuned!
livecomsjournal.org/index.php/li...
livecomsjournal.org/index.php/li...
Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v1.0]
| Living Journal of Computational Molecular Science
livecomsjournal.org
October 28, 2025 at 3:19 PM
Chapin Cavendar's paper, Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields, is out now in LiveCoMS. Read it for a detailed look at the great work he has been doing toward an OpenFF protein force field, and stay tuned!
livecomsjournal.org/index.php/li...
livecomsjournal.org/index.php/li...
Reposted by Cole Group
In the latest @livecomsjournal.bsky.social
perpetual review, Cavender et al overview NMR and crystallographic experimental datasets that can be used to benchmark protein force fields, including best practices for setup and analysis of simulations!:
livecomsjournal.org/index.php/li...
#compchem
perpetual review, Cavender et al overview NMR and crystallographic experimental datasets that can be used to benchmark protein force fields, including best practices for setup and analysis of simulations!:
livecomsjournal.org/index.php/li...
#compchem
October 28, 2025 at 3:36 PM
In the latest @livecomsjournal.bsky.social
perpetual review, Cavender et al overview NMR and crystallographic experimental datasets that can be used to benchmark protein force fields, including best practices for setup and analysis of simulations!:
livecomsjournal.org/index.php/li...
#compchem
perpetual review, Cavender et al overview NMR and crystallographic experimental datasets that can be used to benchmark protein force fields, including best practices for setup and analysis of simulations!:
livecomsjournal.org/index.php/li...
#compchem
It's ligand-focussed day at the #CCPBioSim training week, and we've been using @openforcefield.org & @openmm.org to parameterise and run protein-ligand MD, and @mdanalysis.bsky.social & ProLIF for analysis! #compchem
October 15, 2025 at 4:29 PM
It's ligand-focussed day at the #CCPBioSim training week, and we've been using @openforcefield.org & @openmm.org to parameterise and run protein-ligand MD, and @mdanalysis.bsky.social & ProLIF for analysis! #compchem
Reposted by Cole Group
We’re pleased to announce Sage 2.3.0 Release Candidate 2 (rc2)! Sage 2.3.0 will be the first OpenFF force field to use the AshGC neural network charge model, which was trained to AM1BCC ELF10 charges, and allows for rapid charge assignment for molecules with hundreds or thousands of heavy atoms.
October 10, 2025 at 3:02 PM
We’re pleased to announce Sage 2.3.0 Release Candidate 2 (rc2)! Sage 2.3.0 will be the first OpenFF force field to use the AshGC neural network charge model, which was trained to AM1BCC ELF10 charges, and allows for rapid charge assignment for molecules with hundreds or thousands of heavy atoms.
📣 Pleased to share that the second part of Rachael Pirie's PhD work on 3D shape similarity methods is now available in the Proceedings of the Royal Society A!
@chemistryncl.bsky.social
@mosmedcdt.bsky.social
Code: github.com/RPirie96/KQM...
Article: royalsocietypublishing.org/doi/10.1098/...
@chemistryncl.bsky.social
@mosmedcdt.bsky.social
Code: github.com/RPirie96/KQM...
Article: royalsocietypublishing.org/doi/10.1098/...
Riemannian geometry and molecular similarity II: Kähler quantization | Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences
Shape similarity between molecules is a concept used by chemists for virtual screening,
with the goal of reducing the cost and duration of drug discovery campaigns. This
paper reports an entirely nove...
royalsocietypublishing.org
October 10, 2025 at 1:46 PM
📣 Pleased to share that the second part of Rachael Pirie's PhD work on 3D shape similarity methods is now available in the Proceedings of the Royal Society A!
@chemistryncl.bsky.social
@mosmedcdt.bsky.social
Code: github.com/RPirie96/KQM...
Article: royalsocietypublishing.org/doi/10.1098/...
@chemistryncl.bsky.social
@mosmedcdt.bsky.social
Code: github.com/RPirie96/KQM...
Article: royalsocietypublishing.org/doi/10.1098/...
Reposted by Cole Group
Here's why we think this is still important today:
livecomsjournal.org/index.php/li...
But we'd love to continue that debate! What do you like about LiveCoMS, what made you publish with us or read an article? Or what can we do better, what is holding you off submitting your first manuscript?
livecomsjournal.org/index.php/li...
But we'd love to continue that debate! What do you like about LiveCoMS, what made you publish with us or read an article? Or what can we do better, what is holding you off submitting your first manuscript?
Why LiveCoMS matters
| Living Journal of Computational Molecular Science
livecomsjournal.org
October 6, 2025 at 3:21 PM
Here's why we think this is still important today:
livecomsjournal.org/index.php/li...
But we'd love to continue that debate! What do you like about LiveCoMS, what made you publish with us or read an article? Or what can we do better, what is holding you off submitting your first manuscript?
livecomsjournal.org/index.php/li...
But we'd love to continue that debate! What do you like about LiveCoMS, what made you publish with us or read an article? Or what can we do better, what is holding you off submitting your first manuscript?
Reposted by Cole Group
"Scientists are well aware that they seem to be getting a bad deal." www.theguardian.com/science/2017...
8 years ago, in response to this article, we wrote about the need for LiveCoMS, a diamond open access journal with no charge for submissions or for libraries: livecomsjournal.org/index.php/li...
8 years ago, in response to this article, we wrote about the need for LiveCoMS, a diamond open access journal with no charge for submissions or for libraries: livecomsjournal.org/index.php/li...
Is the staggeringly profitable business of scientific publishing bad for science?
The long read: It is an industry like no other, with profit margins to rival Google – and it was created by one of Britain’s most notorious tycoons: Robert Maxwell
www.theguardian.com
October 6, 2025 at 3:21 PM
"Scientists are well aware that they seem to be getting a bad deal." www.theguardian.com/science/2017...
8 years ago, in response to this article, we wrote about the need for LiveCoMS, a diamond open access journal with no charge for submissions or for libraries: livecomsjournal.org/index.php/li...
8 years ago, in response to this article, we wrote about the need for LiveCoMS, a diamond open access journal with no charge for submissions or for libraries: livecomsjournal.org/index.php/li...
Reposted by Cole Group
📢 New software tutorial alert!
Gravelle et al introduce a suite of tutorials for new users of the LAMMPS simulation package, including molecular simulation basics, reactive force fields, GCMC and enhanced sampling #compchem
doi.org/10.33011/liv...
Gravelle et al introduce a suite of tutorials for new users of the LAMMPS simulation package, including molecular simulation basics, reactive force fields, GCMC and enhanced sampling #compchem
doi.org/10.33011/liv...
October 2, 2025 at 2:35 PM
📢 New software tutorial alert!
Gravelle et al introduce a suite of tutorials for new users of the LAMMPS simulation package, including molecular simulation basics, reactive force fields, GCMC and enhanced sampling #compchem
doi.org/10.33011/liv...
Gravelle et al introduce a suite of tutorials for new users of the LAMMPS simulation package, including molecular simulation basics, reactive force fields, GCMC and enhanced sampling #compchem
doi.org/10.33011/liv...
Reposted by Cole Group
Interested in biomolecular simulation?
The latest article by Lier et al describes advanced tutorials for the GROMOS software, including free energy calculations, enhanced sampling and neural network potentials with SchNetPack! #compchem
livecomsjournal.org/index.php/li...
The latest article by Lier et al describes advanced tutorials for the GROMOS software, including free energy calculations, enhanced sampling and neural network potentials with SchNetPack! #compchem
livecomsjournal.org/index.php/li...
September 30, 2025 at 5:06 PM
Interested in biomolecular simulation?
The latest article by Lier et al describes advanced tutorials for the GROMOS software, including free energy calculations, enhanced sampling and neural network potentials with SchNetPack! #compchem
livecomsjournal.org/index.php/li...
The latest article by Lier et al describes advanced tutorials for the GROMOS software, including free energy calculations, enhanced sampling and neural network potentials with SchNetPack! #compchem
livecomsjournal.org/index.php/li...
Reposted by Cole Group
Save the date, my fellow computational alchemists! The upcoming '26 Workshop on Free Energy Methods in Drug Design will be held in Barcelona, Spain, on May 4-6, 2026. The registration link will be sent soon!
September 23, 2025 at 5:36 PM
Save the date, my fellow computational alchemists! The upcoming '26 Workshop on Free Energy Methods in Drug Design will be held in Barcelona, Spain, on May 4-6, 2026. The registration link will be sent soon!
Congrats to @asmaferiel.bsky.social who was part of the winning team for the @mosmedcdt.bsky.social Ideation Training event!
September 16, 2025 at 12:24 PM
Congrats to @asmaferiel.bsky.social who was part of the winning team for the @mosmedcdt.bsky.social Ideation Training event!
Reposted by Cole Group
The latest @livecomsjournal.bsky.social tutorial "Molecular Dynamics: From Basics to Application" by Vollmers, Chen et al is out now! doi.org/10.33011/liv...
It includes comprehensive MD tutorials in GROMACS, covering forcefields, thermodynamic ensembles, long-range electrostatics and much more!
It includes comprehensive MD tutorials in GROMACS, covering forcefields, thermodynamic ensembles, long-range electrostatics and much more!
September 9, 2025 at 12:19 PM
The latest @livecomsjournal.bsky.social tutorial "Molecular Dynamics: From Basics to Application" by Vollmers, Chen et al is out now! doi.org/10.33011/liv...
It includes comprehensive MD tutorials in GROMACS, covering forcefields, thermodynamic ensembles, long-range electrostatics and much more!
It includes comprehensive MD tutorials in GROMACS, covering forcefields, thermodynamic ensembles, long-range electrostatics and much more!
Registration is now open, deadline 26 Sept! ⬇️
#CCPBioSim will be running their annual training week of hands-on workshops in basic biomolecular simulation techniques from the 13th-17th October, in Sheffield.
For more details, visit www.ccpbiosim.ac.uk/training2025
The registration link there will open shortly! #compchem
For more details, visit www.ccpbiosim.ac.uk/training2025
The registration link there will open shortly! #compchem
September 9, 2025 at 9:19 AM
Registration is now open, deadline 26 Sept! ⬇️
#CCPBioSim will be running their annual training week of hands-on workshops in basic biomolecular simulation techniques from the 13th-17th October, in Sheffield.
For more details, visit www.ccpbiosim.ac.uk/training2025
The registration link there will open shortly! #compchem
For more details, visit www.ccpbiosim.ac.uk/training2025
The registration link there will open shortly! #compchem
August 29, 2025 at 7:46 AM
#CCPBioSim will be running their annual training week of hands-on workshops in basic biomolecular simulation techniques from the 13th-17th October, in Sheffield.
For more details, visit www.ccpbiosim.ac.uk/training2025
The registration link there will open shortly! #compchem
For more details, visit www.ccpbiosim.ac.uk/training2025
The registration link there will open shortly! #compchem
Reposted by Cole Group
Did you know you can use custom force field parameters in OpenFE? Try out this cookbook to learn more! docs.openfree.energy/en/latest/co... #compchem
BespokeFit: Using bespoke force field parameters with OpenFE protocols — OpenFE documentation
docs.openfree.energy
August 27, 2025 at 7:25 PM
Did you know you can use custom force field parameters in OpenFE? Try out this cookbook to learn more! docs.openfree.energy/en/latest/co... #compchem
Reposted by Cole Group
CACHE 7 is launched with support from the @gatesfoundation.bsky.social and unpublished data from Damian Young at @bcmhouston.bsky.social, Tim Willson @thesgc.bsky.social and Neelagandan Kamaria InSTEM. Design selective PGK2 inhibitors. We'll test them experimentally.
bit.ly/4lnVYOs
bit.ly/4lnVYOs
August 12, 2025 at 7:07 PM
CACHE 7 is launched with support from the @gatesfoundation.bsky.social and unpublished data from Damian Young at @bcmhouston.bsky.social, Tim Willson @thesgc.bsky.social and Neelagandan Kamaria InSTEM. Design selective PGK2 inhibitors. We'll test them experimentally.
bit.ly/4lnVYOs
bit.ly/4lnVYOs
Reposted by Cole Group
Interested in solvation free energies of small molecules and proteins?
The latest @livecomsjournal.bsky.social tutorial by Egger-Hoerschinger et al provides a guide to quantifying hydration thermodynamics using Grid Inhomogeneous Solvation Theory (GIST):
doi.org/10.33011/liv...
#compchem
The latest @livecomsjournal.bsky.social tutorial by Egger-Hoerschinger et al provides a guide to quantifying hydration thermodynamics using Grid Inhomogeneous Solvation Theory (GIST):
doi.org/10.33011/liv...
#compchem
August 14, 2025 at 4:45 PM
Interested in solvation free energies of small molecules and proteins?
The latest @livecomsjournal.bsky.social tutorial by Egger-Hoerschinger et al provides a guide to quantifying hydration thermodynamics using Grid Inhomogeneous Solvation Theory (GIST):
doi.org/10.33011/liv...
#compchem
The latest @livecomsjournal.bsky.social tutorial by Egger-Hoerschinger et al provides a guide to quantifying hydration thermodynamics using Grid Inhomogeneous Solvation Theory (GIST):
doi.org/10.33011/liv...
#compchem