Artificial intelligence-based protein structure prediction methods such as AlphaFold2 have emerged as powerful tools for characterizing proteins sequence-structure relationship offering unprecedented opportunities for the molecular interpretation of biological and biochemical phenomena. While initially confined to providing a static representation of proteins through their global free-energy minimum, AlphaFold2 has demonstrated the ability to partially sample conformational landscapes, providing insights into protein dynamics, which is fundamental for interpreting and potentially tuning the function of natural and artificial proteins. In this study, we show that targeted column masking of AlphaFold2's multiple sequence alignment enables the characterization and estimation of the population ratio of the two main conformations of engineered green fluorescent proteins with alternative β-strands. The possibility of quickly estimating relative populations through AlphaFold2 predictions is expected to speed-up the computational design of related systems for sensing applications.