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Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server

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Generative 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 LTD2023

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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 SOC2023

Proteins, the central building blocks of life, play pivotal roles in nearly every biological function. To do so, these macromolecular structures interact with their surrounding environment in complex ways, leading to diverse functional behaviors. The predi ...

EPFL2023

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The data and scripts used to produce, analyze, and visualize the results of the manuscript Enzyme promiscuous profiles for protein sequence and reaction annotation by Homa MohammadiPeyhani, Anastasia Sveshnikova, Ljubisa Miskovic, and Vassily Hatzimanikati ...

Zenodo2023

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Self-supervised neural language models with attention have recently been applied to biological sequence data, advancing structure, function and mutational effect prediction. Some protein language models, including MSA Transformer and AlphaFold's EvoFormer, ...

NATURE PORTFOLIO2022

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 PORTFOLIO2022

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 ...

OXFORD UNIV PRESS2021

A Rosetta-based protein design protocol converging to natural sequences

Bruno Emanuel Ferreira De Sousa Correia, Zander Harteveld, Stéphane Rosset, Giulia Sormani

Computational protein design has emerged as a powerful tool capable of identifying sequences compatible with pre-defined protein structures. The sequence design protocols, implemented in the Rosetta suite, have become widely used in the protein engineering ...

AMER INST PHYSICS2021

MPGM: Scalable and Accurate Multiple Network Alignment

Matthias Grossglauser, Ehsan Kazemi

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 ...

IEEE COMPUTER SOC2020

IMPACT: 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 ...

2019