Vaishali Waman

ContrasTED improves homology classification by using contrastive learning to assign domains to superfamilies with high accuracy, outperforming existing methods.

The paper introduces TEDLH, a library of domain HMMs derived from TED annotations, enabling sensitive detection of remote homologues and expanding coverage of sequence space and CATH superfamily diversity.

The paper introduces TED, a resource that segments and classifies over 370 million domains from the AlphaFold Protein Structure Database, expanding known structural domains and uncovering new structural interactions.

The paper predicts human and viral protein variants that enhance SARS-CoV-2 binding affinity and may increase COVID-19 susceptibility.

The paper characterizes structural and functional motifs of ATP-PPase substrate-specificity groups using structural data to inform antibacterial drug design.

The paper uses AlphaFold2 to analyze protein structures from 21 organisms, identifying 26 novel superfamilies and expanding structural diversity insights.

The paper introduces CATHe, a method using protein language model embeddings to detect remote homologues for CATH superfamilies, achieving high accuracy and validating predictions with AlphaFold structures.

The paper investigates how insertions in the SARS-CoV-2 Spike N-terminal domain may enhance sialic acid binding and contribute to increased transmissibility.

The paper predicts SARS-CoV-2 spike protein interactions with ACE2 orthologues across 215 vertebrates, finds mutations in ACE2 are more detrimental, and shows human strains are present in animals.

The paper compares metabolic pathways in three mycobacteria to identify common drug targets and assess their druggability.