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Scaffolding protein functional sites using deep learning

Publications associées (103)

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On the use of direct-coupling analysis with a reduced alphabet of amino acids combined with super-secondary structure motifs for protein fold prediction

Jaume Bonet Martinez

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

Fast end-to-end learning on protein surfaces

Bruno Emanuel Ferreira De Sousa Correia, Freyr Sverrisson

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 ...

IEEE COMPUTER SOC2021

Continuous assessment of transferable forcefields for molecular simulations is essential to identify their weaknesses and direct improvement efforts. The latest efforts focused on better describing disordered proteins while retaining proper description of ...

2021

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Imaging of proteins at the single-molecule level can reveal conformational variability, which is essential for the understanding of biomolecules. To this end, a biologically relevant state of the sample must be retained during both sample preparation and i ...

NATL ACAD SCIENCES2021

In-silico behavior of dissolved prolamins under electric field effect applied by electrospinning process using molecular dynamics simulation

Niloufar Sharif

This paper describes processing of alpha-zeins (Z19 and Z22) and alpha-gliadin (G) dissolved in aqueous ethanol under an electric field from a molecular viewpoint using molecular dynamics simulation. From the results, it was found that zeins dominated in h ...

ELSEVIER2021

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Correlating the structures and properties of a polymer to its monomer sequence is key to understanding how its higher hierarchy structures are formed and how its macroscopic material properties emerge. Carbohydrate polymers, such as cellulose and chitin, a ...

NATL ACAD SCIENCES2021

Bottom-up de novo design of functional proteins with complex structural features

Luciano Andres Abriata, Bruno Emanuel Ferreira De Sousa Correia, Sandrine Madeleine Suzanne Georgeon, Leo Scheller, Jaume Bonet Martinez, Fabian Sesterhenn, Stéphane Rosset, Che Yang, Eva Anna van Aalen

De novo protein design has enabled the creation of new protein structures. However, the design of functional proteins has proved challenging, in part due to the difficulty of transplanting structurally complex functional sites to available protein structur ...

NATURE RESEARCH2021

Communication across membranes controls critical cellular processes and is achieved by receptors translating extracellular signals into selective cytoplasmic responses. While receptor tertiary structures can now be readily characterized, receptor associati ...

2021

Divalent Cation Dependence Enhances Dopamine Aptamer Biosensing

Nako Nakatsuka

Oligonucleotide receptors (aptamers), which change conformation upon target recognition, enable electronic biosensing under high ionic-strength conditions when coupled to field-effect transistors (FETs). Because highly negatively charged aptamer backbones ...

2021

Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design

Bruno Emanuel Ferreira De Sousa Correia, Jaume Bonet Martinez

Structure-based antibody and antigen design has advanced greatly in recent years, due not only to the increasing availability of experimentally determined structures but also to improved computational methods for both prediction and design. Constant improv ...

AMER CHEMICAL SOC2021