Marina Gorostiola González

Another one of my PhD chapters got published! 🎉🎉 In this chapter, @CDDLeiden we looked at the possibility of creating dynamic protein descriptors (3DDPDs) for bioactivity modeling from MD data. jcheminf.biomedcentral.com/articles/10.11… github.com/CDDLeiden/3ddpd

The highest impact factor is when your paper reaches your mom’s fridge❤️

Great to see published this great collaborative effort that I contributed to! Have a look! 🎉✨

Amazing achievement by my PhD supervisor @GJPvWesten !! Stoked to be part of your group! ✨🎉

The longer people are in academia, the more they realize that when reading papers it's best to ignore Intro, Discussion etc. and just look at Methods and Results journals.plos.org/plosone/articl…

me on my 20th supplementary figure

"Chatbots in Drug Discovery: A Case Study on Anti-Cocaine Addiction Drug Development with ChatGPT" arxiv.org/abs/2308.06920

Introducing PINNACLE, a contextual graph AI model for comprehensive protein understanding PINNACLE dynamically adjusts its outputs based on molecular contexts in which it operates Providing outputs tailored to molecular contexts is essential for broader use of foundational models in biology and medicine Leveraging #single-cell atlas, PINNACLE is trained on contextualized protein networks to generate context-aware representations split across 156 cell type contexts from 24 tissues Pretrained PINNACLE protein representations can be adapted for broad array of tasks 🧪enhance 3D structural representations 💊study genomic drug effects across cell type contexts 🎯nominate #therapeutic targets 🌲zero-shot retrieval of the tissue hierarchy Led by a superstar PhD student @_michellemli! Grateful for wonderful collaborators @harvardmed @HarvardDBMI @BrighamWomens @MassGeneralNews @MassGenBrigham @Roche @harvard_data Y Huang @YepHuang, M Sumathipala @marissa_sumathi, MQ Liang, A Valdeolivas, A Ananthakrishnan, K Liao, and D Marbach #AI4Science #SingleCell #AI #Proteins [1/4]

Getting started!! #shef2023

New preprint alert! Our work @CDDLeiden on dynamic protein descriptors for PCM modelling is now available on ChemRvix and all the code on our group GitHub. Looking forward to the feedback on our newly developed 3DDPDs 🥳 chemrxiv.org/engage/chemrxi…

Work by @OlivierBeqgn , @BongersBrandon , @Willemjespers , @GJPvWesten et al. :” Papyrus: a large-scale curated dataset aimed at bioactivity predictions” Get the data here: doi.org/10.5281/zenodo… Scripts to adapt your own data: github.com/CDDLeiden/Papy… jcheminf.biomedcentral.com/articles/10.11…

Some pretty cool collaborative work on somatic mutations in GPCRs!

Probably the best @CDDLeiden tradition: Computational cheese day!!

Too many studies that apply machine learning to science & medicine employ incorrect methodologies. Many make very basic mistakes, such as not having separate training & test sets, using the test set (not a separate validation set) for feature selection, hyperparameter tuning, etc

College completely failed to teach me data analysis. So I spent over 10,000 hours learning Python. Then, I picked the 13 best libraries for machine learning and data analysis. But unlike college, these won't cost you $120,000. Here they are for free:

The amazing #2022ICCS is over. The @cddleiden delegation also had posters from: @BournezC , @martin_sicho , @ManuelG81702324 , @sohvi_luukkonen , @DavidAraripe , @1inde1 , @BolaK_DDD , @BongersBrandon , Helle vd Maagdenberg, Rosan Kuin. CC @LeidenScienceEN , @LACDR #2022ICCS

@yew_mun Not yet, but hopefully before the end of the year!

@m_gorostiola The title interests me! Is that a published article for it? 😃

Today I presented our work on 3D protein dynamic descriptors (3DDPDs) at #2022ICCS . Great ideas during the Q&A session and room for collaboration with other tools presented these days!

Great presence of @CDDLeiden at the @intconfchemstr. Talks by @OlivierBeqgn and @m_gorostiola. Posters by many group members. CC @sails_Leiden @LACDR #2022iccs

@m_gorostiola presenting her work about 3DDPDs. Used a preliminary version of Papyrus for collecting data. Super nice presentation (though, once again, I am very biased). #2022ICCS