Conrado Pedebos

a robot says hey guys in a purple light ALT: a robot says hey guys in a purple light

🚀 Making it Rain ☁️💦 just got an AI-powered upgrade! 🚀

First, we made MD simulations rain down from the cloud. Now, we’re bringing deep learning into the mix! 🌩️🤖

AlphaFold can predict protein, DNA, or RNA complexes.. BUT is it easy to determine the reliable interactions?🤔

➡️ AlphaBridge will identify the most confident interactions, making your analysis easier!

🌐Try it here: alpha-bridge.eu
👀Read more: www.biorxiv.org/content/10.1...

Systematic Approach to Parametrization of Disaccharides for the Martini 3 Coarse-Grained Force Field Sugars are ubiquitous in biology; they occur in all kingdoms of life. Despite their prevalence, they have often been somewhat neglected in studies of structure–dynamics–function relationships of macro...

So seems like the group is on a roll this month!
Here’s our latest work on parametrising coarse-grained models of sugars (disaccharides) by Astrid Brandner & in collaboration with Iain Smith, @pauloctsouza.bsky.social and @cg-martini.bsky.social pubs.acs.org/doi/10.1021/... #glycotime

Diacylation of Peptides Enables the Construction of Functional Vesicles for Drug‐Carrying Liposomes Membrane-forming phospholipids are generated in cells by enzymatic diacylation of non-amphiphilic polar head groups. Analogous non-enzymatic processes may have been relevant at the origin of life and....

Charged peptides instead of phospholipids? Another multidisciplinary study - a collaboration led by Neal Devaraj at UCSD. Sims done in my lab by @conradopedebos.bsky.social
Out now in Angew Chemie

onlinelibrary.wiley.com/doi/10.1002/...

In a multidisciplinary study led by Georgina Benn and Tom Silhavy we show the role of OmpA in controlling the organisation of the outer membrane and in sharing the mechanical load. www.pnas.org/doi/10.1073/....

Who remembers running away from the ref on FIFA? 😂

Huge accomplishment! Congrats, bro!

Cookiecutter for Computational Molecular Sciences: A Best Practices Ready Python Project Generator Scientific software development takes far more than good programming abilities and scientific reasoning. Concepts such as version control, continuous integration, packaging, deployment, automatic documentation compiling, licensing, and even file structure are not traditionally taught to scientific programmers. The skill gap leads to inconsistent code quality and difficulty deploying products to the broader audience. Most of the implementation of these skills however can be constructed at project inception. The Cookiecutter for Computational Molecular Sciences generates ready-to-go Python projects that incorporate all of the concepts above from a single command. The final product is then a software project which lets developers focus on the science and minimizes worries about nonscientific and nonprogramming concepts because the best practices, as established by the Molecular Sciences Software Institute, have already been incorporated for them. This is a community driven project with widespread adoption across the computational molecular sciences. The Molecular Sciences Software Institute and Computational Molecular Sciences community also continually contribute and update the Cookiecutter for Computational Molecular Science, ensuring that the project is responsive to community needs and tool updates. All are welcome to suggest changes and contribute to making this the best starting point for Python-based scientific code.

If you want to help your students move from just writing code and scripts to actually developing scientific software that is useable and maintainable in the long-term, check out our latest paper in JCE. pubs.acs.org/doi/10.1021/...

Google Colab

Accessing GPU clusters or high-performance computers can be a challenge in Brazil, so I created a Colab notebook for NetSci to perform GC analysis. It works seamlessly, even with Colab’s free tier! Check it out here:

colab.research.google.com/drive/1GGJKr...

Paper: t.co/evNxaX2omW

Super happy to see this one out!