Igor Tolstoy

ProTrek introduces a tri-modal contrastive learning model for protein sequence, structure, and function, achieving significant improvements in speed and accuracy over existing tools.

The paper presents a structure-based classification framework for Caudoviricetes using whole-proteome structural clustering to resolve distant viral relationships.

Muscle-3D is a scalable multiple structure alignment method that combines structural context with advanced alignment techniques, showing strong performance on benchmark datasets.

The paper identifies instances of DNA polymerase (DNAP) swapping among bacteriophages, showing gene replacements between families and subfamilies without altering surrounding gene organization.