Chemical cross-linking combined with mass spectrometry has proven useful for studying
protein-protein interactions and protein structure, however the low density of cross-link data …

The extant complex proteins must have evolved from ancient short and simple ancestors.
The double-ψ β-barrel (DPBB) is one of the oldest protein folds and conserved in various …

The dedicator of cytokinesis (DOCK) family of guanine nucleotide exchange factors (GEFs)
promotes cell motility, phagocytosis, and cancer metastasis through activation of Rho …

Computational protein design (CPD) is a powerful technique to engineer existing proteins or
to design novel ones that display desired properties. Rosetta is a software suite including …

Despite advances in sampling and scoring strategies, Monte Carlo modeling methods still
struggle to accurately predict de novo the structures of large proteins, membrane proteins, or …

Motivation Structure-based computational protein design (CPD) plays a critical role in
advancing the field of protein engineering. Using an all-atom energy function, CPD tries to …

Background The development, optimization and validation of protein modeling methods
require efficient tools for structural comparison. Frequently, a large number of models need …

Seed plants express cellulose synthase (CESA) protein isoforms with non-redundant
functions, but how the isoforms function differently is unknown. Compared to bacterial …

Conformational search space exploration remains a major bottleneck for protein structure
prediction methods. Population‐based meta‐heuristics typically enable the possibility to …

Residue contact map is essential for protein three‐dimensional structure determination. But
most of the current contact prediction methods based on residue co‐evolution suffer from …