In the course of evolution, proteins undergo important changes in their amino acid
sequences, while their three-dimensional folded structure and their biological function …

Potts Hamiltonian models of protein sequence co-variation are statistical models constructed
from the pair correlations observed in a multiple sequence alignment (MSA) of a protein …

HIV-1 infection depends on the integration of viral DNA into host chromatin. Integration is
mediated by the viral enzyme integrase and is blocked by integrase strand transfer inhibitors …

Global coevolutionary models of homologous protein families, as constructed by direct
coupling analysis (DCA), have recently gained popularity in particular due to their capacity …

Protein kinases are dynamic, adopting different conformational states that are critical for their
catalytic activity. We assess a range of structural features derived from the conserved αC …

Potts models and variational autoencoders (VAEs) have recently gained popularity as
generative protein sequence models (GPSMs) to explore fitness landscapes and predict …

Inactive conformations of protein kinase catalytic domains where the DFG motif has a “DFG-
out” orientation and the activation loop is folded present a druggable binding pocket that is …

Conspectus Protein kinases are enzymes that catalyze the covalent transfer of the γ-
phosphate of an adenosine triphosphate (ATP) molecule onto a tyrosine, serine, threonine …

Understanding protein conformational variability remains a challenge in drug discovery. The
issue arises in protein kinases, whose multiple conformational states can affect the binding …

Background Boltzmann machines are energy-based models that have been shown to
provide an accurate statistical description of domains of evolutionary-related protein and …