BioMoDes Newsletter -- Issue #03
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Here are the latest tools (from last week) for biomolecular modeling and design.
1. Intro
Welcome to the 3rd Issue of the BioMoDes Newsletter and Top Reads, a newsletter where I share with you the latest tools and my top-reads in Biomolecular Modeling and Design, focusing on computational structural biology and drug design.
If you are a new subscriber, you can read the previous issues of the newsletter here. You can also access the BioMoDes repository here. Thank you for subscribing!
Let's get straight into new tools and some of my top reads of the past week.
2. New tools over the last couple of weeks
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DiffPALM: A method for pairing interacting protein sequences based on protein language models trained on MSAs. Read more...
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PepFlow: A method to predict structures of peptides, including single-state and ensembles of conformations. PepFlow is also capable of generating structures of macrocycles. Read more...
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AutoRNA: A method for the prediction of RNA 3D structure using VAE. Read more...
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DDAffinity: A neural network for predicting changes in binding affinity upon multiple mutations. Read more...
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MolSnapper: A diffusion model for molecule generation that integrates expert knowledge based on 3D pharmacophores (reference points). Read more...
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GCDM (Geometry-Complete Diffusion Model): A diffusion model for 3D molecule generation and optimization. Read more...
3. Top reads
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The Open Protein Modeling Consortium (OPMC) published a preprint that introduces SaprotHub, user-friendly platform for training, implementation, and sharing of protein modeling models. Read more...
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A preprint introduced AlphaFastPPi, a Python package that streamlines large-scale protein-protein interaction analysis. AlphaFastPPi is based on AlphaFold-Multimer and AlphaPulldown, perform similar tasks as AlphaPulldown but much faster. Read more...
4. Bonus
Oleg Trott (the guy that originally developed AutoDock Vina) expressed some concerns about the benchmarking results (and methodology) reported in the AF3 paper. Read more about Oleg’s post...
That's it for this week. Feel free to reach out by replying to this email if you have any suggestions or would like to have other discussions.
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