|

Fitness landscape for antibodies (Flab2)

Byscientist

There have been many AI models to predict the structure of proteins, especially antibodies. There are several key aspects to developing antibodies as drugs beyond binding to the target of interest. These are : thermostability, expression, aggregation, binding affinity, pharmacokinetics, polyreactivity and immunogenicity. There have been many models available such as IgLM, ProGen2, Chai-1, ESM2, ISM, IgFold among others but there have been severe limitations to the AI model use and this paper helps understand their limitations:

https://pmc.ncbi.nlm.nih.gov/articles/PMC12767642

Similar Posts

  • |

    Open source protein models

    Byscientist

    A company called Profluent (profluent.bio) has been developing protein models that can be used for designing new proteins (https://www.nature.com/articles/s41587-022-01618-2), modeling of new CRISPR-Cas sequences (https://www.nature.com/articles/s41586-025-09298-z) and developing LLM for protein generation (https://www.biorxiv.org/content/10.1101/2025.11.12.688125v1.article-info). What is amazing is that they have open sourced all their models and Profluent-E1 is available in GitHub to download and use. (https://github.com/Profluent-AI/E1)…

  • | |

    TDP43

    Byscientist

    TDP43 (a nuclear DNA-RNA binding protein) is involved in splicing, RNA transport and stability in neurons. It was first identified as a pyrimidine rich TAR DNA sequence in HIV type 1 gene to modulate HIV gene expression. In 95% of the ALS patients, TDP43 is abnormal located within the cell and may also be aggregated,…

  • LoRa in AI image generators

    Byscientist

    This stands for Low Rank adaptation. In AI terms, this is a small add-on to the model that makes it do specific things. It is usually used in the context of stable diffusion. A large model takes very long to train with significant resources. However, sometimes, you need specific details – for example you could…

  • Games can help science – Foldit

    Byscientist

    People spend a significant amount of time playing games and solving puzzles. It has always been argued that there must be some benefit that could be derived from the endeavors. Many man-hours, computer computation and power go into playing games. Obviously, they serve some physiological and psychological functions since so many people continue playing games….