altMOD

altMOD is a set of Python modules that enhance the performance of MODELLER, a widely used tool for protein structure prediction through homology modeling. The modules implement two strategies to improve the 3D modeling quality of MODELLER:

1. Improving the accuracy of estimating structural variability between a target protein and its templates using σ values. The authors demonstrate that increasing the correlation between the σ values produced by MODELLER and the true level of structural divergence between target-template pairs improves the program's predictions, particularly in multiple-template modeling.

2. Incorporating statistical potential terms, such as the DOPE potential, into MODELLER's objective function. This addition provides a small but consistent improvement in metrics like GDT-HA and lDDT, as well as a substantial increase in stereochemical quality.