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/
📢 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
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
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!
#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
Thanks to the students, lecturers and guest speakers who attended the 2025 #CCP5 Summer School over the last two weeks in Newcastle!
We hope you had a good stay, and look forward to reading about the fantastic research you'll do with the methods you've learned! #compchem @cosec-ukri.bsky.social
We hope you had a good stay, and look forward to reading about the fantastic research you'll do with the methods you've learned! #compchem @cosec-ukri.bsky.social
July 31, 2025 at 2:04 PM
Thanks to the students, lecturers and guest speakers who attended the 2025 #CCP5 Summer School over the last two weeks in Newcastle!
We hope you had a good stay, and look forward to reading about the fantastic research you'll do with the methods you've learned! #compchem @cosec-ukri.bsky.social
We hope you had a good stay, and look forward to reading about the fantastic research you'll do with the methods you've learned! #compchem @cosec-ukri.bsky.social
And congratulations to the #CCP5 2025 summer school student talk winner, Akanksha Nawani! Well done to everyone that took part in the talk and poster sessions, the standard was extremely high! #compchem @cosec-ukri.bsky.social
July 30, 2025 at 8:34 AM
And congratulations to the #CCP5 2025 summer school student talk winner, Akanksha Nawani! Well done to everyone that took part in the talk and poster sessions, the standard was extremely high! #compchem @cosec-ukri.bsky.social
Many congratulations to the four #CCP5 2025 summer school poster prize winners, Nga Man Cheng, Gustave Szczepan, Sarah Haggenmueller & Matthew Ludwig! @cosec-ukri.bsky.social #compchem
July 30, 2025 at 8:34 AM
Many congratulations to the four #CCP5 2025 summer school poster prize winners, Nga Man Cheng, Gustave Szczepan, Sarah Haggenmueller & Matthew Ludwig! @cosec-ukri.bsky.social #compchem
The advanced bio workshop is in full swing now at the #ccp5 summer school, featuring material from ccpbiosim, @openforcefield.org, mdanalysis & @ppxasjsm.bsky.social. Expertly taught by @matteodegiacomi.bsky.social & @jjguven.bsky.social
July 29, 2025 at 3:29 PM
The advanced bio workshop is in full swing now at the #ccp5 summer school, featuring material from ccpbiosim, @openforcefield.org, mdanalysis & @ppxasjsm.bsky.social. Expertly taught by @matteodegiacomi.bsky.social & @jjguven.bsky.social
The students did a fantastic job presenting their own posters, and it's been great to see scientific discussions taking place all week. Enjoy the upcoming weekend, and week two! @cosec-ukri.bsky.social
July 25, 2025 at 1:30 PM
The students did a fantastic job presenting their own posters, and it's been great to see scientific discussions taking place all week. Enjoy the upcoming weekend, and week two! @cosec-ukri.bsky.social
As we approach the end of the first week of the 2025 #CCP5 Summer School in Newcastle, here are a few highlights! Students have had in-depth seminars and practical sessions on computational methods, and guest research seminars to illustrate their use in modern research.... #compchem
July 25, 2025 at 1:30 PM
July 21, 2025 at 9:53 AM
He's substantially increased the benchmarking datasets, now including hydration free energies, solvation free energies in octanol, and logP calculations for drug-like molecules, all with sub 1 kcal/mol accuracy.
July 1, 2025 at 10:51 AM
He's substantially increased the benchmarking datasets, now including hydration free energies, solvation free energies in octanol, and logP calculations for drug-like molecules, all with sub 1 kcal/mol accuracy.
Harry has augmented the MACE-OFF training data with soft-core dimer energy curves, and also modified the nonlearnable parameters in MACE to enable alchemical scaling of selected nonbonded interactions
July 1, 2025 at 10:51 AM
Harry has augmented the MACE-OFF training data with soft-core dimer energy curves, and also modified the nonlearnable parameters in MACE to enable alchemical scaling of selected nonbonded interactions
"Enhancing Electrostatic Embedding for ML/MM Free Energy Calculations", by Joao Morado et al, is now available on ChemRxiv! doi.org/10.26434/che... #compchem
June 23, 2025 at 11:52 AM
"Enhancing Electrostatic Embedding for ML/MM Free Energy Calculations", by Joao Morado et al, is now available on ChemRxiv! doi.org/10.26434/che... #compchem
Charges can be scaled between the vacuum and solvated charge sets, and combined with Lennard-Jones parameters optimized using the Open Force Field infrastructure, to yield force fields that are suitably polarized for condensed phase modeling.
June 3, 2025 at 2:47 PM
Charges can be scaled between the vacuum and solvated charge sets, and combined with Lennard-Jones parameters optimized using the Open Force Field infrastructure, to yield force fields that are suitably polarized for condensed phase modeling.
📢 New preprint: "A graph neural network charge model targeting accurate electrostatic properties of organic molecules" by @charlie-adams.bsky.social et al out now on @chemrxiv.bsky.social #compchem
doi.org/10.26434/che...
doi.org/10.26434/che...
June 3, 2025 at 2:47 PM
📢 New preprint: "A graph neural network charge model targeting accurate electrostatic properties of organic molecules" by @charlie-adams.bsky.social et al out now on @chemrxiv.bsky.social #compchem
doi.org/10.26434/che...
doi.org/10.26434/che...
The CCPBioSim Annual Conference - Frontiers in Biomolecular Simulations will be taking place in Southampton, 14-16 July 2025. Registration is now open! Details and the registration link can be found at www.ccpbiosim.ac.uk/soton2025 #compchem
May 10, 2025 at 12:42 PM
The CCPBioSim Annual Conference - Frontiers in Biomolecular Simulations will be taking place in Southampton, 14-16 July 2025. Registration is now open! Details and the registration link can be found at www.ccpbiosim.ac.uk/soton2025 #compchem
Great job by @asmaferiel.bsky.social presenting her work on molecular modelling of GALK1 at the @mosmedcdt.bsky.social conference! @wyattyue.bsky.social @matteodegiacomi.bsky.social
April 16, 2025 at 11:39 AM
Great job by @asmaferiel.bsky.social presenting her work on molecular modelling of GALK1 at the @mosmedcdt.bsky.social conference! @wyattyue.bsky.social @matteodegiacomi.bsky.social
And fantastic to hear from @karmencj.bsky.social on the experiences and challenges of building research infrastructure with @omsf.io !
April 7, 2025 at 7:51 PM
And fantastic to hear from @karmencj.bsky.social on the experiences and challenges of building research infrastructure with @omsf.io !
Great overview by @jenkescheen.bsky.social on ASAP and the polaris blind challenges!
April 7, 2025 at 6:27 PM
Great overview by @jenkescheen.bsky.social on ASAP and the polaris blind challenges!
In Montreal ahead of the @conscience-network.bsky.social Symposium on Open Drug Discovery! I'll be speaking about work by @creechem.bsky.social & the Newcastle team in the CACHE challenge participants showcase: cole-group.github.io/2024/09/10/c...
April 5, 2025 at 3:38 PM
In Montreal ahead of the @conscience-network.bsky.social Symposium on Open Drug Discovery! I'll be speaking about work by @creechem.bsky.social & the Newcastle team in the CACHE challenge participants showcase: cole-group.github.io/2024/09/10/c...
Welcome to @finlayclark.bsky.social who joins @chemistryncl.bsky.social from the University of Edinburgh, to work on force field design with the @openforcefield.org ! blogs.ncl.ac.uk/danielcole/a... #compchem
March 5, 2025 at 9:14 AM
Welcome to @finlayclark.bsky.social who joins @chemistryncl.bsky.social from the University of Edinburgh, to work on force field design with the @openforcefield.org ! blogs.ncl.ac.uk/danielcole/a... #compchem
And we purchased and tested a few compounds from Enamine for experimental testing by fantastic collaborators
Siddique Amin & Akane Kawamura. Some (very weak) binding was found for three compounds...
Siddique Amin & Akane Kawamura. Some (very weak) binding was found for three compounds...
January 13, 2025 at 4:01 PM
And we purchased and tested a few compounds from Enamine for experimental testing by fantastic collaborators
Siddique Amin & Akane Kawamura. Some (very weak) binding was found for three compounds...
Siddique Amin & Akane Kawamura. Some (very weak) binding was found for three compounds...
In this paper, we make use of active learning to guide exploration through the chemical space of possible linkers and R-groups to those that are predicted to bind favourably
January 13, 2025 at 4:01 PM
In this paper, we make use of active learning to guide exploration through the chemical space of possible linkers and R-groups to those that are predicted to bind favourably
Looking forward to the start of the @cecamevents.bsky.social workshop on force fields for computational spectroscopy in Paris! #compchem
January 13, 2025 at 8:13 AM
Looking forward to the start of the @cecamevents.bsky.social workshop on force fields for computational spectroscopy in Paris! #compchem