Publications related to Threading (protein sequence)

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 Portfolio2024

Supplementary dataset for Enzyme promiscuous profiles for protein sequence and reaction annotation

Vassily Hatzimanikatis, Ljubisa Miskovic, Homa Mohammadi Peyhani, Anastasia Sveshnikova

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

Impact 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 SOC2023

A generic framework for hierarchical de novo protein design

Bruno Emanuel Ferreira De Sousa Correia, Zander Harteveld, Jaume Bonet Martinez, Fabian Sesterhenn, Stéphane Rosset, Che Yang

De novo protein design enables the exploration of novel sequences and structures absent from the natural protein universe. De novo design also stands as a stringent test for our understanding of the underlying physical principles of protein folding and may ...

NATL ACAD SCIENCES2022

Statistical potentials from the Gaussian scaling behaviour of chain fragments buried within protein globules

Stefano Zamuner

Knowledge-based approaches use the statistics collected from protein data-bank structures to estimate effective interaction potentials between amino acid pairs. Empirical relations are typically employed that are based on the crucial choice of a reference ...

PUBLIC LIBRARY SCIENCE2022

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

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

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Threading (protein sequence)

Prolamins' 3D structure: A new insight into protein modeling using the language of numbers and shapes

Opportunities and challenges in design and optimization of protein function

Supplementary dataset for Enzyme promiscuous profiles for protein sequence and reaction annotation

Impact of phylogeny on structural contact inference from protein sequence data

A generic framework for hierarchical de novo protein design

Statistical potentials from the Gaussian scaling behaviour of chain fragments buried within protein globules

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

Fast end-to-end learning on protein surfaces

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

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

Graph Chatbot

Chat with Graph Search

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

Opportunities and challenges in design and optimization of protein function

Impact of phylogeny on structural contact inference from protein sequence data

A generic framework for hierarchical de novo protein design

Prolamins' 3D structure: A new insight into protein modeling using the language of numbers and shapes

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

Statistical potentials from the Gaussian scaling behaviour of chain fragments buried within protein globules

Supplementary dataset for Enzyme promiscuous profiles for protein sequence and reaction annotation

Fast end-to-end learning on protein surfaces

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