Edoardo Sarti

The paper identifies and characterizes orphan genes in eight root-knot nematode species, finding they contribute to parasitism and are expressed during the infective juvenile stage.

The paper evaluates AlphaFold predictions using a new scoring function and identifies three structural populations in proteomes.

The paper evaluates transformer-based models' ability to predict structural features of orphan proteins and finds they perform poorly on these sequences compared to homologous proteins.

The paper introduces new quantitative measures to assess AlphaFold predictions by analyzing pLDDT values along protein sequences.

The paper introduces SPECTRALDOM, an improved method for protein domain identification that outperforms existing approaches without using evolutionary information.

The paper analyzes AlphaFold predictions across whole genomes, examining packing properties, pLDDT scores, and disordered regions to improve confidence assessment.

EncoMPASS provides a database of membrane proteins analyzed through structure, sequence, and symmetry, enabling study of their properties and evolution.

This paper introduces position anchoring in AlignMe to improve pairwise sequence alignment of membrane proteins by incorporating functional or structural information, enhancing accuracy while maintaining reproducibility.

FilterDCA predicts inter-domain and inter-protein contacts using coevolutionary analysis and interpretable filters, achieving comparable accuracy to deep learning methods while being fully transparent.

The paper introduces MemSTATS, a benchmark set for membrane protein symmetries, and evaluates four symmetry detection algorithms on it.