DSIMB Lab

DSIMB team is the bioinformatics team of INSERM UMR_S 1134 unit (Université Paris Cité & Université de la Réunion) - Paris.

[Alex TwentySeven @AlexTwentySeve]

The works was done by @RagouRadja , @gabriel_cretin , Julien Diharce and @gellyjc from @DSIMB_Lab @Inserm @EFS_Sante @Univ_Reunion @univ_paris_cite

[Alex TwentySeven @AlexTwentySeve]

Many thanks to the Belbi organizers for the amazing 6th Belgrade Bioinformatics Conference in Belgrade (Serbia) @AlexTwentySeve presented his keynote on " Predicting Variant Pathogenicity by Combining Protein Language Models and Biological Features”.

[DSIMB Lab @DSIMB_Lab]

Many thanks to Vitaly Kurlin and Olga Anosova for the amazing the 7th MACSMIN (https://t.co/f0tTQnNx2l) in Liverpool (UK) few weeks ago! @AlexTwentySeve was overjoyed to have been invited to present: Protein Blocks as a discrete geometric model for protein conformational spaces.

[DSIMB Lab @DSIMB_Lab]

All @DSIMB_Lab (@Inserm_EN, @univ_paris_cite, @Univ_Reunion) servers are currently unreachable. We are currently reconfiguring the servers and this is taking longer than expected, we apologize for the inconvenience.

[DSIMB Lab @DSIMB_Lab]

We thank @mephunguifo and Nourddine Azzaoui from @UCAuvergne for the invitation to present "AlphaFold, the Artificial Intelligence approach (Nobel Prize 2024): a real (r)evolution or not?" by @AlexTwentySeve (@univ_paris_cite, @Inserm_EN, @Univ_Reunion) for LIMOS meeting

[DSIMB Lab @DSIMB_Lab]

An impressive review of "Hierarchical Analysis of Protein Structures: From Secondary Structures to Protein Units and Domains" by C. Perin, @gabrielcreux and @gellyjc https://t.co/OkZCWAJB1j It enhances our comprehension of protein structure, folding, and evolutionary mechanisms

[Tatiana Galochkina @TatianaGalochk1]

Very proud to announce the official release of DIONYSUS, the database of protein-carbohydrate interfaces, accepted for publication in @NAR_Open !

Article: https://t.co/t72TZrR3z7
Web-site: https://t.co/nlX5BuFSEI

Funded by @AgenceRecherche and supported by @diip_upc

[DSIMB Lab @DSIMB_Lab]

Should We Expect a Second Wave of AlphaFold Misuse After the Nobel Prize? ... A title that may seem a bit strong or even strange, but it reflects a recurring problem ... a short editorial by @AlexTwentySeve (@univ_paris_cite, @Inserm_EN, @Univ_Reunion) https://t.co/ZSE9eHgyM0

[DSIMB Lab @DSIMB_Lab]

In Methods Mol Biol (2024), a simple guide to "AlphaFold2 for Protein Structure Prediction: Best Practices and Critical Analyses" by R. Radjasandirane and @AlexTwentySeve (@univ_paris_cite, @Inserm_EN, @Univ_Reunion) https://t.co/mE1OhxEnM7 and in https://t.co/vTZKumOpXW

[DSIMB Lab @DSIMB_Lab]

Impressive work by Carla Martins "A Simple Analysis of the Second (Extra) Disulfide Bridge of VHHs" with F. Gardebien, A Nadaradjane, J. Diharce &
@AlexTwentySeve (@univ_paris_cite, @Inserm_EN, @Univ_Reunion) https://t.co/D4sw8mtacG via @IJMS_MDPI with European #FEDER S3D-VHH

[DSIMB Lab @DSIMB_Lab]

@AlexTwentySeve (@univ_paris_cite, @Inserm_EN, @Univ_Reunion) is happy to share his editorial on Special Issue: "Molecular Dynamics Simulations and Structural Analysis of Protein Domains" https://t.co/9ni69baF3Z
https://t.co/EV5ChErPiy

[Alex TwentySeven @AlexTwentySeve]

Save the date! The 24th GGMM Congress will be held in Normandy from 10 to 12 June 2025. A great conference bringing together the best in molecular modelling. #GGMM https://t.co/Ryc4wH5KBB

[Florent Barbault @BarbaultFlorent]

Save the date! The 24th GGMM Congress will be held in Normandy from 10 to 12 June 2025. A great conference bringing together the best in molecular modelling. #GGMM
https://t.co/wNlzsemk7Z

[DSIMB Lab @DSIMB_Lab]

Save the date! The 24th GGMM Congress will be held in Normandy from 10 to 12 June 2025. A great conference bringing together the best in molecular modelling. #GGMM https://t.co/Uuw8AJU2Eu

[DSIMB Lab @DSIMB_Lab]

@AlexTwentySeve & @gellyjc (@univ_paris_cite, @Inserm_EN, @Univ_Reunion) are very happy to work with our collegue Wei-Chen Lo from @NYCU_official in Hsinchu as part of our #PHC_ORCHID @CampusFrance & Bureau français de Taipei

[Biology+AI Daily @BiologyAIDaily]

Prediction of protein biophysical traits from limited data: a case study on nanobody thermostability through NanoMelt

1/ This paper introduces NanoMelt, a machine learning tool developed to predict nanobody thermostability with high accuracy from limited datasets, addressing a key challenge in protein engineering.

2/ NanoMelt leverages an ensemble learning model combining multiple sequence embeddings and regression techniques, achieving state-of-the-art accuracy on a curated dataset of 640 melting temperature measurements.

3/ The key innovation lies in integrating diverse embeddings, such as ESM-1b and ESM-2, with non-linear models like support vector regression and Gaussian process regression, enabling superior generalization to new nanobody sequences.

4/ A novel contribution is the creation of a robust, curated dataset by adding 129 new experimental thermostability measurements, significantly enhancing the data available for nanobody thermostability prediction.

5/ The tool outperforms existing stability prediction methods like FoldX and DeepSTABp, offering reliable predictions that are valuable for nanobody design and optimization in research and therapeutic applications.

6/ NanoMelt��s predictions are validated through experimental assays, showing close alignment with measured melting temperatures, reinforcing its utility in nanobody development pipelines.

💻Code: https://t.co/EDUg4rSqMv
📜Paper: https://t.co/scX5cDhAMM

[Ragou @RagouRadja]

@gellyjc @AlexTwentySeve @DSIMB_Lab Our findings aim to guide both expert and non-expert users in selecting the most suitable VEP to current advances which also may help in faster and more accurate clinical diagnostics.

#Bioinformatics #Genomics #VEP #AlphaMissense #GeneticVariants #ClinicalDiagnostics #BioRxiv

[Gabriel Cretin @gabriel_cretin]

🎉 I’m thrilled to announce the latest release of SWORD2! Packed with major improvements to enhance your bioinformatics workflows. Let’s dive into what’s new! 👇
💾 Github: https://t.co/mdKPC8NkPs
🌐Webserver: https://t.co/UQDbADS3zb
@DSIMB_Lab
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[National Centre for Biological Sciences @NCBS_Bangalore]

🏆We are honoured to share that Professor R. Sowdhamini has been awarded the Dr Raja Ramanna Award by the Govt of Karnataka!
🎉Congratulations Prof Sowdhamini!
Know more about her work in Computational approaches to Protein Science here https://t.co/Xky3ATyvk2

[DSIMB Lab @DSIMB_Lab]

@AlexTwentySeve (@univ_paris_cite, @Inserm_EN, @Univ_Reunion) is happy to present the work of R. Radjasandirane, N. El Jahrani & @gabrielcreux "How bioinformatics can cast doubt on sequencing results (in the context of ET)" at @SFBBM #SFBBM2024