@biosimspace

Create interoperable molecular simulation workflow components. Translate molecular file formats. Run biomolecular simulations in a Jupyter notebook.

biosimspace.org
Joined February 2018
  • Tweets60
  • Following7
  • Followers347
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Replying to @eriklindahl @davidlmobley
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
Antonia Mey@ppxasjsm20 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
CCPBioSim@ccpbiosim9 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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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
CCPBioSim@ccpbiosim8 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
CCPBioSim@ccpbiosim8 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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Putting the last finishing touches on the @BioSimSpace material ready for our #CCPBioSim2020 workshop tomorrow morning...
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BioSimSpace retweeted
Antonia Mey@ppxasjsm11 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/🧵

Best Practices for Alchemical Free Energy Calculations

Alchemical free energy calculations are a useful tool for predicting free energy differences associated with the transfer of molecules from one environment to another. The hallmark of these...

arxiv.org
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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.
Julien Michel is also on Mastodon@julienmich8020 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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(BioSimSpace has been used ~7500 times, which is not bad for a newer piece of software)
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@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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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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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…

Assessment of Binding Affinity via Alchemical Free-Energy Calculations

Abstract. Free-energy calculations have seen increased usage in structure-based drug design. Despite the rising interest, automation of the complex calcula

pubs.acs.org
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BioSimSpace retweeted
Cresset@cressetgroup5 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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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

Flare V3 new science and improved results

Flare V3 enables computational and medicinal chemists to access new...

youtube.com
Cresset@cressetgroup26 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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Replying to @julienmich80 @biosimspace @ppxasjsm @gervasiolab @AdrianMulholla1
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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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: An interoperable Python framework for biomolecular simulation @BioSimSpace
Julien Michel is also on Mastodon@julienmich8022 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
Johanna Tiemann@j0kaso5 Nov 2019
Replying to @j0kaso @MolSSI_NSF @davidlmobley @samplchallenges @Michael_Shirts @livecomsj
@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)

Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages

Abstract. Alchemical free energy calculations are an increasingly important modern simulation technique to calculate free energy changes on binding or solv

pubs.acs.org
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Thanks for your kind comments about @biosimspace. Really pleased you enjoyed the talk :-)
Magnus Hagdorn 🌍@mhagdorn23 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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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
Christopher Woods@chryswoods18 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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