75 citations · 408 across the 27 of their papers we have counts for
11 papers · 1 filter
Out-of-equilibrium selection pressure enhances inference from protein sequence data
Nicola Dietler, Cyril Malbranke, Anne-Florence Bitbol
Homologous proteins have similar three-dimensional structures and biological functions that shape their sequences. The resulting coevolution-driven correlations underlie methods fr…
DiffPaSS -- High-performance differentiable pairing of protein sequences using soft scores
Umberto Lupo, Damiano Sgarbossa, Martina Milighetti +1
Identifying interacting partners from two sets of protein sequences has important applications in computational biology. Interacting partners share similarities across species due…
Pairing interacting protein sequences using masked language modeling
Umberto Lupo, Damiano Sgarbossa, Anne-Florence Bitbol
Predicting which proteins interact together from amino-acid sequences is an important task. We develop a method to pair interacting protein sequences which leverages the power of p…
Impact of phylogeny on structural contact inference from protein sequence data
Nicola Dietler, Umberto Lupo, Anne-Florence Bitbol
Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino-aci…
Combining phylogeny and coevolution improves the inference of interaction partners among paralogous proteins
Carlos A. Gandarilla-Perez, Sergio Pinilla, Anne-Florence Bitbol +1
Predicting protein-protein interactions from sequences is an important goal of computational biology. Various sources of information can be used to this end. Starting from the sequ…
Generative power of a protein language model trained on multiple sequence alignments
Damiano Sgarbossa, Umberto Lupo, Anne-Florence Bitbol
Computational models starting from large ensembles of evolutionarily related protein sequences capture a representation of protein families and learn constraints associated to prot…