BioMoDes Newsletter -- Issue #05
Here are the latest tools (from last week) for biomolecular modeling and design.
1.0. Intro
Welcome to the 5th 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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STRPsearch: A computational tool for fast identification, classification, and mapping of Structured Tandem Repeats in Proteins. STRPsearch takes as input a protein structure, and then aligns it against structural repeat libraries based on the RepeatsDB to identify repeated structural motifs in the query. Read more...
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PySSA: A GUI application for protein structure prediction, visualization, and analysis, based on ColabFold and PyMOL. Note, however, that PySSA is primarily available for Windows 10 and 11 users. Read more...
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CELL-E 2: A bidirectional text-to-image model that generates images depicting subcellular localization of proteins from amino acid sequences and amino acid sequences from patterns in input localization images. Read more...
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WEDAP: A python package for streamlined plotting of MD simulation data. Read more...
3. Top reads
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GRO Biosciences recently got an oversubscribed $60M Series B Financing and aims to advance its lead gout-targeted program into the clinic. The drug, called ProGly-Uricase, is an engineered uricase linked to glycans on the surface to trick the immune system into reduced negative response against the enzyme. Read more...
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310 AI published a white paper to launch MPM4, its new generative natural language text-to-protein sequence foundation model. Although the model is proprietary, I made two posts about it and the accompanying "MPM4 repository". You can read more here and here...
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