BioSimSpace

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

[Julien Michel is also on Mastodon @julienmich80]

@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.

[Antonia Mey @ppxasjsm]

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: https://t.co/9uWZSCe9MG #compchem #MD #Forcefields

[CCPBioSim @ccpbiosim]

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

[BioSimSpace @biosimspace]

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 https://t.co/ZaWl4nL86Z

[CCPBioSim @ccpbiosim]

Training week Thursday : Lots of good sessions - @biosimspace, Force fields with @CCP5UK, Cryo-em @ccp_em, and topoisomerases with Prem Chapagain. #CCPBioSim2020 #CompBio #CompChem

[CCPBioSim @ccpbiosim]

Training week Thursday : Lots of good sessions - @biosimspace, Force fields with @CCP5UK, Cryo-em @ccp_em, and topoisomerases with Prem Chapagain. #CCPBioSim2020 #CompBio #CompChem

[BioSimSpace @biosimspace]

Putting the last finishing touches on the @BioSimSpace material ready for our #CCPBioSim2020 workshop tomorrow morning...

[Antonia Mey @ppxasjsm]

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: https://t.co/Hkq7zjnp0R #compchem 1/🧵

[BioSimSpace @biosimspace]

(BioSimSpace has been used ~7500 times, which is not bad for a newer piece of software)

[BioSimSpace @biosimspace]

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 @julienmich80]

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.

[BioSimSpace @biosimspace]

@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. https://t.co/Qx7lnvZzeN

[JCIM & JCTC Journals @JCIM_JCTC]

Assessment of #Binding Affinity via #Alchemical Free-Energy Calculations
https://t.co/H3eSfVz4Eo
@molecular_cures @ppxasjsm @julienmich80 @cressetgroup
#Current_issue #Computational_biochemistry

[Julien Michel is also on Mastodon @julienmich80]

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 ‘’ https://t.co/taSfxp3Glv

[Cresset @cressetgroup]

#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.

https://t.co/vb4WfzLbn5

#DrugDiscovery

[Julien Michel is also on Mastodon @julienmich80]

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 !
https://t.co/EBeNChdOCR
@chryswoods @davidlmobley @jchodera @ccpbiosim

[BioSimSpace @biosimspace]

@julienmich80 @chryswoods @ppxasjsm @gervasiolab @AdrianMulholla1 Here’s a link to the paper PDF (the proof generated via the review process). The final version will be available once the paper is published. https://t.co/urzRu7yXnf

[Christopher Woods @chryswoods]

@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!)

[Julien Michel is also on Mastodon @julienmich80]

Nice birthday gift, 1st paper in Journal of Open Source Software describing our @biosimspace project. Software and paper available via zenodo https://t.co/MgPknnKaAU . Enjoyed the open peer-review process via github https://t.co/P3kO3wlZux

[BioSimSpace @biosimspace]

@ppxasjsm Yes - the github based review with @JOSS_TheOJ was brilliant. Very much the future of academic publishing today :-)

[Adrian Mulholland @AdrianMulholla1]

BioSimSpace: An interoperable Python framework for biomolecular simulation @BioSimSpace

[Johanna Tiemann @j0kaso]

@MolSSI_NSF @davidlmobley @samplchallenges @Michael_Shirts @livecomsj @julienmich80 on "Reproducible free energy calculations with @biosimspace". How are ΔΔG-hyd calculations across packages (https://t.co/LuMZrERvPp)? To speed up this comparison @biosimspace wraps around all steps along the process of generation, running& analysis (@ProjectJupyter)