Mutational effect transfer learning (METL) is a protein language model framework that unites machine learning and biophysical modeling. Transformer-based neural networks are pretrained on biophysical simulation data to capture fundamental relationships between protein sequence, structure and energetics.

Mutational Effect Transfer Learning (METL) framework for pretraining and finetuning biophysics-informed protein language models - gitter-lab/metl

Mutational effect transfer learning (METL) is a protein language model framework that unites machine learning and biophysical modeling. Transformer-based neural networks are pretrained on biophysical ...

The development of large language models and multimodal models has enabled the appealing idea of generating novel molecules from text descriptions. Generative modeling would shift the paradigm from relying on large-scale chemical screening to find molecules with desired properties to directly generating those molecules. However, multimodal models combining text and molecules are often trained from scratch, without leveraging existing high-quality pretrained models. Training from scratch consumes more computational resources and prohibits model scaling. In contrast, we propose a lightweight adapter-based strategy named Chemical Language Model Linker (ChemLML). ChemLML blends the two single domain models and obtains conditional molecular generation from text descriptions while still operating in the specialized embedding spaces of the molecular domain. ChemLML can tailor diverse pretrained text models for molecule generation by training relatively few adapter parameters. We find that the choice of molecular representation used within ChemLML, SMILES versus SELFIES, has a strong influence on conditional molecular generation performance. SMILES is often preferable despite not guaranteeing valid molecules. We raise issues in using the entire PubChem data set of molecules and their associated descriptions for evaluating molecule generation and provide a filtered version of the data set as a generation test set. To demonstrate how ChemLML could be used in practice, we generate candidate protein inhibitors and use docking to assess their quality and also generate candidate membrane permeable molecules.

Scientific databases aggregate vast amounts of quantitative data alongside descriptive text. In biochemistry, molecule screening assays evaluate the functional responses of candidate molecules against...

Focused screening on target-prioritized compound sets can be an efficient alternative to high throughput screening (HTS). For most biomolecular targets, compound prioritization models depend on prior ...

The 20th Machine Learning in Computational Biology (MLCB) meeting will be a two-day hybrid conference, September 10-11, 9am-5pm ET, with the in-person component at the New York Genome Center, NYC. Reg...

Martin Steinegger, who is the only non-DeepMind-affiliated author of the AlphaFold2 Nature paper, offers unique insights and personal reflections.

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