Publications related to From Reinforcement to High-Performance Damping

Scaffolding protein functional sites using deep learning

Bruno Emanuel Ferreira De Sousa Correia, Karla Montserrat Castro Gilabert, Basile Isidore Martin Wicky, Jue Wang

The binding and catalytic functions of proteins are generally mediated by a small number of functional residues held in place by the overall protein structure. Here, we describe deep learning approaches for scaffolding such functional sites without needing ...

AMER ASSOC ADVANCEMENT SCIENCE2022

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

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

Reversible and Broad-Range Oxygen Sensing Based on Purely Organic Long-Lived Photoemitters

Esther Amstad, René M. Rossi, Efe Armagan

The detection of oxygen (O-2) by optical sensors is of growing importance, for example, in biology, life science, environmental science, and aerodynamics, where the composition of gases is crucial for many applications. Purely organic optical O-2 sensors a ...

2021

Kinetic Euclidean Distance Matrices

Martin Vetterli, Ivan Dokmanic, Puoya Tabaghi

Euclidean distance matrices (EDMs) are a major tool for localization from distances, with applications ranging from protein structure determination to global positioning and manifold learning. They are, however, static objects which serve to localize point ...

IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC2020

Stabilization strategies in biomass depolymerization using chemical functionalization

Jeremy Luterbacher, Ydna Marie Questell-Santiago

A central feature of most lignocellulosic-biomass-valorization strategies is the depolymerization of all its three major constituents: cellulose and hemicellulose to simple sugars, and lignin to phenolic monomers. However, reactive intermediates, generally ...

NATURE PUBLISHING GROUP2020

Atomic Motif Recognition in (Bio)Polymers: Benchmarks From the Protein Data Bank

Michele Ceriotti, Piero Gasparotto, Benjamin Aaron Helfrecht, Federico Giberti

Rationalizing the structure and structure–property relations for complex materials such as polymers or biomolecules relies heavily on the identification of local atomic motifs, e.g., hydrogen bonds and secondary structure patterns, that are seen as buildin ...

2019

Active Site-Induced Evolutionary Constraints Follow Fold Polarity Principles in Soluble Globular Enzymes

Matteo Dal Peraro, Luciano Andres Abriata, Alexander Mayorov

A recent analysis of evolutionary rates in >500 globular soluble enzymes revealed pervasive conservation gradients toward catalytic residues. By looking at amino acid preference profiles rather than evolutionary rates in the same data set, we quantified th ...

OXFORD UNIV PRESS2019

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From Reinforcement to High-Performance Damping

Investigating the intra-molecular and inter-molecular effects of post-translational modifications on intrinsically disordered protein regions and structured protein regions

Scaffolding protein functional sites using deep learning

Fast end-to-end learning on protein surfaces

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

SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions

Reversible and Broad-Range Oxygen Sensing Based on Purely Organic Long-Lived Photoemitters

Kinetic Euclidean Distance Matrices

Stabilization strategies in biomass depolymerization using chemical functionalization

Atomic Motif Recognition in (Bio)Polymers: Benchmarks From the Protein Data Bank

Active Site-Induced Evolutionary Constraints Follow Fold Polarity Principles in Soluble Globular Enzymes

Graph Chatbot

Chat with Graph Search

Kinetic Euclidean Distance Matrices

Reversible and Broad-Range Oxygen Sensing Based on Purely Organic Long-Lived Photoemitters

Investigating the intra-molecular and inter-molecular effects of post-translational modifications on intrinsically disordered protein regions and structured protein regions

Scaffolding protein functional sites using deep learning

Fast end-to-end learning on protein surfaces

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

SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions

Stabilization strategies in biomass depolymerization using chemical functionalization

Atomic Motif Recognition in (Bio)Polymers: Benchmarks From the Protein Data Bank

Active Site-Induced Evolutionary Constraints Follow Fold Polarity Principles in Soluble Globular Enzymes