BioMoDes Newsletter -- Issue #04
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Here are the latest tools (from last week) for biomolecular modeling and design.
1.0. Intro
Welcome to the 4th 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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AllergenAI: A neural network for predicting and quantifying protein allergenicity using amino acid sequence as input. Read more...
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ProBASS: A protein language model for predicting mutational effect on protein-protein binding affinity using sequence and structural information. ProBASS (Protein Binding Affinity from Structure and Sequence) is a fine-tuned model based on the general purpose protein language model ESM-2 and the inverse folding model ESM-IF1. Read more...
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ProteStar: A method for compressing protein structure files. ProteStAr (Protein Structures Archiver), supports PDB, mmCIF, PAE (JSON) files, and offers up to 4X compression ratio than gzip. Read more...
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NRIMD: An online server for analyzing long-range, allosteric interactions in proteins from MD simulation data. The NRIMD server accepts C-alpha MD simulation trajectories from common MD engines like GROMACS, AMBER, NAMD, OpenMM, LAMMPS, CHARMM, and Desmond. Read more...
3. Top read
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A paper published in Bioinformatics describes a curated set of side chain rotamers for the most common post-translational modifications (PTMs). The PTMs available in the rotamer library include those found in PDB structures such as phosphorylation, methylation, and acetylation. The authors created and analyzed both backbone-dependent and backbone-independent rotamer libraries. Read more...
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