Create interoperable molecular simulation workflow components. Translate molecular file formats. Run biomolecular simulations in a Jupyter notebook.
Joined February 2018
- Tweets 60
- Following 7
- Followers 350
- Likes 42
8 Photos and videos
BioSimSpace retweeted
13 Nov 2020
This was one the motivations for @biosimspace . Though far from perfect users end up running code that combines or compares algorithms in different code bases without having to know all the details.
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BioSimSpace retweeted
20 Oct 2020
And for good news Tuesday find out about how QUBE is now available in Sire/OpenMM and can be readily used to compute binding affinities! Full paper here: bit.ly/37qOJmS #compchem #MD #Forcefields
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BioSimSpace retweeted
9 Oct 2020
Training week Friday : for our final day we are going large and small - DL_MESO with @mikeo_s, QM/MM with @marcvanderkamp and quantum computing with Viv Kendon. #CCPBioSim2020 #CompChem #CompBio
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8 Oct 2020
Great to have the @biosimspace session this morning. Probably the largest number of simultaneous connections to our notebook server ever. Scaled back down now (beauty of cloud) and ready again at notebook.biosimspace.org
8 Oct 2020
Training week Thursday : Lots of good sessions - @biosimspace, Force fields with @CCP5UK, Cryo-em @ccp_em, and topoisomerases with Prem Chapagain. #CCPBioSim2020 #CompBio #CompChem
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BioSimSpace retweeted
8 Oct 2020
Training week Thursday : Lots of good sessions - @biosimspace, Force fields with @CCP5UK, Cryo-em @ccp_em, and topoisomerases with Prem Chapagain. #CCPBioSim2020 #CompBio #CompChem
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7 Oct 2020
Putting the last finishing touches on the @BioSimSpace material ready for our #CCPBioSim2020 workshop tomorrow morning...
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BioSimSpace retweeted
11 Aug 2020
Have you every wondered how to run #alchemical free energy calculations but weren’t sure where to start? This new #BestPractices Guide will help you get started: arxiv.org/abs/2008.03067 #compchem 1/🧵
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20 Jul 2020
somd-freenrg has been used nearly 2 million times! It is built on the same platform as @biosimspace and we have somd-freenrg workflow components to ease setup, running and analysis of these protein-ligand relative FEP binding free energy calculations. Take a look and have a play.
20 Jul 2020
Woah @chryswoods ! Our #FEP code somd-freenrg has been executed nearly 2 million times over the past 12 months. That's a lot of free energies.
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20 Jul 2020
(BioSimSpace has been used ~7500 times, which is not bad for a newer piece of software)
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16 Jul 2020
@biosimspace and Sire are both in the GitHub Arctic Vault and will be stored for 1000 years as part of the GitHub archive program. Future civilisations will be able to gasp at our primitive means of converting Amber topology flies into Gromacs format. archiveprogram.github.com
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BioSimSpace retweeted
13 Jul 2020
Assessment of #Binding Affinity via #Alchemical Free-Energy Calculations
pubs.acs.org/doi/10.1021/acs…
@molecular_cures @ppxasjsm @julienmich80 @cressetgroup
#Current_issue #Computational_biochemistry
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BioSimSpace retweeted
25 May 2020
Glad it’s out ! Very enjoyable collaboration with @cressetgroup to interface our FEP code and @biosimspace with Cresset’s Flare. ‘’Assessment of Binding Affinity via Alchemical Free Energy Calculations ‘’ pubs.acs.org/doi/10.1021/acs…
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BioSimSpace retweeted
5 Dec 2019
#Compchem and #medchem, particularly in the #pharmaceuticalindustry, are always looking for ways to improve productivity at the #hittolead and #leadoptimization stages. We discuss best practice in setting up an #FEP experiment.
bit.ly/2OQ3buU
#DrugDiscovery
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BioSimSpace retweeted
26 Nov 2019
Excited that this implementation interfaces academic open-source software Sire, OpenMM, LOMAP and @biosimspace with the Flare UI from @cressetgroup to make FEP calculations a breeze !
youtube.com/watch?time_conti…
@chryswoods @davidlmobley @jchodera @ccpbiosim
26 Nov 2019
Flare™ V3 release features fully validated and accessible FEP calculations and new workflows
bit.ly/2QQ6CD4
#CompChem #MedChem #CADD #DrugDiscovery #SBDD #MoleculeDesign #FEP
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BioSimSpace retweeted
22 Nov 2019
Happy birthday. Saw an alert on my orcid so suspected it was about to come out. Must say that @JOSS_TheOJ has been my best journal experience ever, and would strongly recommend it as the software journal of choice (i.e. community please use this instead of upstart from elsevier!)
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BioSimSpace retweeted
22 Nov 2019
Nice birthday gift, 1st paper in Journal of Open Source Software describing our @biosimspace project. Software and paper available via zenodo dx.doi.org/10.5281/zenodo.35… . Enjoyed the open peer-review process via github github.com/openjournals/joss…
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BioSimSpace retweeted
22 Nov 2019
BioSimSpace: An interoperable Python framework for biomolecular simulation @BioSimSpace
22 Nov 2019
Nice birthday gift, 1st paper in Journal of Open Source Software describing our @biosimspace project. Software and paper available via zenodo dx.doi.org/10.5281/zenodo.35… . Enjoyed the open peer-review process via github github.com/openjournals/joss…
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BioSimSpace retweeted
5 Nov 2019
@julienmich80 on "Reproducible free energy calculations with @biosimspace". How are ΔΔG-hyd calculations across packages (doi.org/10.1021/acs.jctc.8b0…)? To speed up this comparison @biosimspace wraps around all steps along the process of generation, running& analysis (@ProjectJupyter)
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23 Sep 2019
Thanks for your kind comments about @biosimspace. Really pleased you enjoyed the talk :-)
23 Sep 2019
I really enjoyed the @RSEConUK in Birmingham. I finally manged to get around to write up a blog post on my impressions. #ukrse19
magi.marsupium.org/2019/09/r…
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BioSimSpace retweeted
18 Sep 2019
This workshop will let you use the technology @milliams presented in his #ukrse19 talk (sched.co/QSQk) and shows the serverless that will enable @lesterhedges @biosimspace project (sched.co/OdJ8) to be fully realised. Learn how Bristol is pioneering #CloudRSE
18 Sep 2019
Co-presenting a #ukrse19 workshop tomorrow afternoon. First is #ClusterInTheCloud (create your own personal cluster). Second is super powerful data analytics. Finishes with @fnproject - the o/s serverless project I use to program the #PlanetarySupercomuter sched.co/QT6X
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