Concept

Protein function prediction

Publications associées (202)

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The Square Kilometre Array Observatory (SKAO) will explore the radio sky to new depths in order to conduct transformational science. SKAO data products made available to astronomers will be correspondingly large and complex, requiring the application of ad ...

OXFORD UNIV PRESS2023

Combining phylogeny and coevolution improves the inference of interaction partners among paralogous proteins

Anne-Florence Raphaëlle Bitbol

Author summaryWhen two protein families interact, their sequences feature statistical dependencies. First, interacting proteins tend to share a common evolutionary history. Second, maintaining structure and interactions through the course of evolution yiel ...

PUBLIC LIBRARY SCIENCE2023

De Novo Crystal Structure Determination from Machine Learned Chemical Shifts

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Determination of the three-dimensional atomic-level structure of powdered solids is one of the key goals in current chemistry. Solid-state NMR chemical shifts can be used to solve this problem, but they are limited by the high computational cost associated ...

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Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences

Anne-Florence Raphaëlle Bitbol, Nicola Dietler, Andonis Samuel Rene Gerardos

Inferring protein-protein interactions from sequences is an important task in computational biology. Recent methods based on Direct Coupling Analysis (DCA) or Mutual Information (MI) allow to find interaction partners among paralogs of two protein families ...

San Francisco2022

Pre-bcc: A novel integrated machine learning framework for predicting mechanical and durability properties of blended cement concrete

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Partially replacing ordinary Portland cement (OPC) with low-carbon supplementary cementitious materials (SCMs) in blended cement concrete (BCC) is perceived as the most promising route for sustainable concrete production. Despite having a lower environment ...

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Deep learning approaches for conformational flexibility and switching properties in protein design

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Following the hugely successful application of deep learning methods to protein structure prediction, an increasing number of design methods seek to leverage generative models to design proteins with improved functionality over native proteins or novel str ...

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Towards automating de novo protein design for novel functionalities: controlling protein folds and protein-protein interactions

Zander Harteveld

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 ...

EPFL2022

Extracting 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 PORTFOLIO2022

Beyond potentials: Integrated machine learning models for materials

Michele Ceriotti

Over the past decade, interatomic potentials based on machine learning (ML) techniques have become an indispensable tool in the atomic-scale modeling of materials. Trained on energies and forces obtained from electronic-structure calculations, they inherit ...

SPRINGER HEIDELBERG2022

Exploring quantum perceptron and quantum neural network structures with a teacher-student scheme

Near-term quantum devices can be used to build quantum machine learning models, such as quantum kernel methods and quantum neural networks (QNN), to perform classification tasks. There have been many proposals on how to use variational quantum circuits as ...

2022

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