Alexander van Teijlingen

20 posts

Alexander van Teijlingen

@AlexandervanTe1

Postdoc at the University of Strathclyde

Sumali Mart 2020

56 Sinusundan32 Mga Tagasunod

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TuttleLab@TuttleLab·3 Mar

@AlexandervanTe1 account on how changes in Martini have affected the modelling of short peptide self assembly in water is out now in Acc. Chem. Res. excellent input from an undergrad project students who is also an author… @scotch_research @StrathChem pubs.acs.org/doi/10.1021/ac…

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TuttleLab@TuttleLab·2 Şub

Our collaborative review (@UlijnGroup @maithreyirtea @AlexandervanTe1) on the collaborative design of peptide-based materials and complex systems is out now... onlinelibrary.wiley.com/doi/10.1002/an… @StrathChem @asrc_gc @ASRCnanoscience

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Alexander van Teijlingen@AlexandervanTe1·15 Eki

Check out this account on OpenSea opensea.io/assets/0x495f9… via @opensea

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Alexander van Teijlingen@AlexandervanTe1·5 Tem

.@ChrisStephens as my MP, please oppose the #PolicingBill It will give police more powers to shut down protest, stop and search without suspicion, and criminalise Gypsy and Traveller communities. #PoliceCrackdownBill pic.twitter.com/cr1tCOlq92

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TuttleLab@TuttleLab·28 Nis

Hot off the press... being able to search for peptides longer than 3 amino acids has always been a goal - our new ML approach now makes that possible! pubs.acs.org/doi/abs/10.102… @AlexandervanTe1 #MachineLearning #CoarseGraining #MLCG

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Alon Aviram@AlAviram·24 Mar

Commander steps into remind officer that it’s not advisable to manhandle journalists after this incident #bristol

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Elizabeth Sankey@sankles·13 Mar

I feel sick

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Karla Adam@karlaadam·13 Mar

Scuffles break out at Clapham Common memorial for Sarah Everard as people chant “arrest your own.”

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Thing Bad@Merman_Melville·23 Şub

kind of a bummer to have been born at the very end of the Fuck Around century just to live the rest of my life in the Find Out century

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Alexander van Teijlingen@AlexandervanTe1·24 Eyl

Resubmission for #AIChem20posters with the correct hashtag this time.

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Alexander van Teijlingen@AlexandervanTe1·26 Ağu

@sudarshanb259 Yes. We restrict the dataset (ie. remove all peptides with log P > 0) then run the algorithm in order to find the interesting cases of peptides that do aggregate but at least less due to the hydrophobic effect.

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Sudarshan@sudarshanb259·25 Ağu

@AlexandervanTe1 So, your ML model is able to predict peptides of high AP, and surprisingly, for some of these peptides have log P < 0. And enthalpy (intermolecular interaction) plays a major role in the aggregation rather than entropy (hydrophobicity). Have I understood it properly?

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Alexander van Teijlingen@AlexandervanTe1·25 Ağu

3. This is the interesting part, that it does aggregate despite being soluble (at least as far as log P < 0 = soluble) means the molecules are interacting in an attractive fashion in the way we would expect for a self-assembling nanomaterial.

Sudarshan@sudarshanb259

@AlexandervanTe1 @scotch_research 3. A basic question. When you write "a soluble hexapeptide that aggregates in water" in Figure 2, is it soluble in water? If so, how can it still form aggregates?

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Alexander van Teijlingen@AlexandervanTe1·26 Ağu

Ahh sorry i misunderstood. During the CGMD simulation there are 300 peptides in the simulation box. The datasets are 8000 (20^3) for tripeptides, up to 64,000,000 (20^6) for hexapeptides.

Sudarshan@sudarshanb259

@AlexandervanTe1 Thanks. With a dataset of 300, you are able to capture the feature-target relationship to a good extend. Great!

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Alexander van Teijlingen@AlexandervanTe1·25 Ağu

2. sum(SP2) is the total number of SP2 carbon atoms, max ASA and Bulkiness are described in the references listed, twitter character limit ties my hands a bit here. Briefly, maxASA is the highest ASA for an amino acid in the tripeptide Gly-X-Gly in all biophysical conformations.

Sudarshan@sudarshanb259

@AlexandervanTe1 @scotch_research 2. In the Judred parameters, what does sum(SP2) means? Is it the total number of SP2 hybridized atoms? What is Max SASA and how do you define bulkiness?

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Alexander van Teijlingen@AlexandervanTe1·25 Ağu

1. 300

Sudarshan@sudarshanb259

@AlexandervanTe1 @scotch_research Interesting work. I want some clarifications to understand the work better. 1. How many peptides, in total, have you considered for 50ns CGMD run?

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Alexander van Teijlingen@AlexandervanTe1·22 Ağu

My poster submission for #ScotCHEM2020, Beyond tripeptides - how machine learning can help to reduce computational search spaces, particularly in the field of peptide self-assembly. PDF version with clickable links: strathcloud.sharefile.eu/d-see45fd85944… @scotch_research