Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences
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Direct-coupling analysis (DCA) for studying the coevolution of residues in proteins has been widely used to predict the three-dimensional structure of a protein from its sequence. We present RADI/raDIMod, a variation of the original DCA algorithm that grou ...
Proteins are fundamental components in biological systems and crucial for a variety of biological functions. Over the last decades, significant progress in structural biology has facilitated the study of proteins and their interactions with molecular partn ...
BackgroundStatistical potentials, also named knowledge-based potentials, are scoring functions derived from empirical data that can be used to evaluate the quality of protein folds and protein-protein interaction (PPI) structures. In previous works we deco ...
Proteins' biological functions are defined by the geometric and chemical structure of their 3D molecular surfaces. Recent works have shown that geometric deep learning can be used on mesh-based representations of proteins to identify potential functional s ...
The sheer size of the protein sequence space is massive: a protein of 100 residues can have 20^100 possible sequence combinations; and knowing that this exceeds the number of atoms in the universe, the chance of randomly discovering a stable new sequence w ...
Protein dynamics is undoubtedly a pervasive ingredient in all biological functions. However, structural biology has been strongly driven by a static-centered view of protein architecture. We argue that the recent advances of cryo-electron microscopy (EM) h ...
Protein structure is tightly intertwined with function according to the laws of evolution. Understanding how structure determines function has been the aim of structural biology for decades. Here, we have wondered instead whether it is possible to exploit ...
Protein-protein interaction (PPI) network alignment is a canonical operation to transfer biological knowledge among species. The alignment of PPI-networks has many applications, such as the prediction of protein function, detection of conserved network mot ...
Recent developments in high-throughput reverse genetics1,2 have revolutionized our ability to map gene function and interactions3,4,5,6. The power of these approaches depends on their ability to identify functionally associated genes, which elicit similar ...
Identifying protein-protein interactions is crucial for a systems-level understanding of the cell. Recently, algorithms based on inverse statistical physics, e.g., direct coupling analysis (DCA), have allowed to use evolutionarily related sequences to addr ...
