BACKGROUND: Protein Language Models (PLMs) are emerging as powerful tools for designing human proteins, including antibodies. These models can predict the effects of mutations in a zero-shot setting-without requiring additional fine-tuning-and suggest plausible amino acid substitutions. RESULTS: We introduce Protein Diversification and Generation through Yielded Mutations (Prodigy) Protein which provides several DirectedEvolution classes that introduce amino acid substitutions in a stepwise manner. Each substitution is evaluated using one of two scoring strategies, and the most promising candidates are sampled accordingly. Users can customize the number of evolution steps, specify target regions within the protein sequence, and set score thresholds to filter out low-quality substitutions during the design process. CONCLUSION: Protein Diversification and Generation through Yielded Mutations (Prodigy) Protein is a fast and flexible tool for in silico protein design. It introduces a consistent and efficient probabilistic framework that leverages any masked language modeling Protein Language Model (PLM) available via Hugging Face. Unlike existing tools, Prodigy Protein can integrate multiple PLMs to design protein variants-an approach not currently supported by other publicly available software.

SUMMARY: InterMine is an open-source data warehouse system that facilitates the building of databases with complex data integration requirements and a need for a fast customizable query facility. Using InterMine, large biological databases can be created from a range of heterogeneous data sources, and the extensible data model allows for easy integration of new data types. The analysis tools include a flexible query builder, genomic region search and a library of 'widgets' performing various statistical analyses. The results can be exported in many commonly used formats. InterMine is a fully extensible framework where developers can add new tools and functionality. Additionally, there is a comprehensive set of web services, for which client libraries are provided in five commonly used programming languages. AVAILABILITY: Freely available from http://www.intermine.org under the LGPL license. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.