Understanding the activity of enzymes in terms of catalyzed reactions and substrate specificity is crucial for engineering purposes. This analysis helps engineers achieve desired features or alter the substrate’s range. The Active Site Modeling and Clustering (ASMC) methodology was initially released in 2010. ASMC uses active site clustering and structural modeling to predict isofunctional clusters from enzyme families. Methods based on structure and sequencing have advanced significantly since then.
Here, the authors have introduced a redesigned ASMC workflow. Recent pocket prediction, structural alignment, and clustering techniques, together with an improved amino acid distance matrix, are all included in this new major version, which increases the relevance of the results and lessens the need for time-consuming human analysis to find pertinent clusters. The authors have also added a script to compare 2D and 3D active sites and introduced multiple sequence alignment as a potential input for the clustering step. To make installation and maintenance easier, the code has finally been consolidated from three different programming languages into one (Python). When tested on a variety of protein families, this updated ASMC version performed better overall than the original.
Linux users can use ASMC, which is publicly accessible at https://github.com/labgem/ASMC and comes with comprehensive documentation (wiki, instructional).Reference:
Thomas Bailly et. al. (2025) ASMC: investigating the amino acid diversity of enzyme active sites. Bioinformatics 41(6): btaf307
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