BioMoDes Newsletter -- Issue #04
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.
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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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