Publication
Supplementary dataset for Enzyme promiscuous profiles for protein sequence and reaction annotation
Publications associées (32)
Opportunities and challenges in design and optimization of protein function
Bruno Emanuel Ferreira De Sousa Correia, Casper Alexander Goverde
The field of protein design has made remarkable progress over the past decade. Historically, the low reliability of purely structure-based design methods limited their application, but recent strategies that combine structure-based and sequence-based calcu ...
Nature Portfolio2024Impact of phylogeny on structural contact inference from protein sequence data
Anne-Florence Raphaëlle Bitbol, Nicola Dietler, Umberto Lupo
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 acid usage at contacting sites. Because homologous proteins share a common ance ...
ROYAL SOC2023Generative power of a protein language model trained on multiple sequence alignments
Anne-Florence Raphaëlle Bitbol, Damiano Sgarbossa, Umberto Lupo
Computational models starting from large ensembles of evolutionarily related protein sequences capture a representation of protein families and learn constraints associated to protein structure and function. They thus open the possibility for generating no ...
eLIFE SCIENCES PUBL LTD2023De novo designed proteins: a study in engineering novel folds and functions
Alexandra Krina Van Hall-Beauvais
Proteins control nearly every facet of life on a molecular level. Proteins are formed from linear strings of amino acids, which fold into three-dimensional structures that can enact functions. Evolution has created highly efficient proteins in diverse fold ...
EPFL2023First paleoproteome study of fossil fish otoliths and the pristine preservation of the biomineral crystal host
Anders Meibom, Jaroslaw Hubert Stolarski, Jinming Guo
Otoliths are calcium carbonate components of the stato-acoustical organ responsible for hearing and maintenance of the body balance in teleost fish. During their formation, control over, e.g., morphology and carbonate polymorph is influenced by complex ins ...
NATURE PORTFOLIO2023Extracting phylogenetic dimensions of coevolution reveals hidden functional signals
Anne-Florence Raphaëlle Bitbol
Despite the structural and functional information contained in the statistical coupling between pairs of residues in a protein, coevolution associated with function is often obscured by artifactual signals such as genetic drift, which shapes a protein's ph ...
NATURE PORTFOLIO2022Towards automating de novo protein design for novel functionalities: controlling protein folds and protein-protein interactions
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 ...
EPFL2022Revealing evolutionary constraints on proteins through sequence analysis
Anne-Florence Raphaëlle Bitbol
Statistical analysis of alignments of large numbers of protein sequences has revealed sectors of collectively coevolving amino acids in several protein families. Here, we show that selection acting on any functional property of a protein, represented by an ...
2019IMPACT: Interval-based Multi-pass Proteomic Alignment with Constant Traceback
James Richard Larus, Sahand Kashani, Stuart Anthony Byma
Darwin is a genomics co-processor that achieved a 15000x acceleration on long read assembly through innovative hardware and algorithm co-design. Darwins algorithms and hardware implementation were specifically designed for DNA analysis pipelines. This pape ...
2019Evaluating the similarity of biochemical reactions and its uses for mapping novel and orphan reactions to protein sequences
Recent advances in synthetic biochemistry have resulted in a wealth of de novo hypothetical enzymatic reactions that are not matched to protein-encoding genes, deeming them “orphan”. Nearly half of known metabolic enzymes are also orphan, leaving important ...
2018