Learning from 3D protein structures has gained wide interest in protein modeling and
structural bioinformatics. Unfortunately, the number of available structures is orders of …

Protein structure alignment algorithms are often time-consuming, resulting in challenges for
large-scale protein structure similarity-based retrieval. There is an urgent need for more …

Fast identification of protein structures that are similar to a specified query structure in the
entire Protein Data Bank (PDB) is fundamental in structure and function prediction. We …

Motivation Given a protein of unknown function, fast identification of similar protein structures
from the Protein Data Bank (PDB) is a critical step for inferring its biological function. Such …

Mutations in amino acid sequences can provoke changes in protein function. Accurate and
unsupervised prediction of mutation effects is critical in biotechnology and biomedicine, but …

Motivation: With rapidly expanding protein structure databases, efficiently retrieving
structures similar to a given protein is an important problem. It involves two major issues:(i) …

As protein databases continue to grow in size, exhaustive search methods that compare a
query structure against every database structure can no longer provide satisfactory …

Motivation: Many evolutionarily distant, but functionally meaningful links between proteins
come to light through comparison of spatial structures. Most programs that assess structural …

Abstract Changes that occur in proteins over time provide a phylogenetic signal that can be
used to decipher their evolutionary history and the relationships between organisms …

Assessing structural similarity and defining common regions through comparison of protein
spatial structures is an important task in functional and evolutionary studies of proteins …