# Prediction of native contacts in proteins from an out--of--equilibrium coevolutionary process

Source: [Prediction of native contacts in proteins from an out--of--equilibrium coevolutionary process](<https://www.sota2.com/research/paper/68fa5ef21e209131ce9e6720>)

Collection index: [llms.txt](<https://www.sota2.com/research/llms.txt>)

Data updated: 2025-10-25T19:04:52.118Z

Authors: D. Oriani, M. Cagiada, G. Tiana

Published: 2020-02-09T15:40:23.000Z

## Abstract

The analysis of coevolution of residues in homologous proteins is a powerful tool to predict their native conformation. The standard framework in which coevolutionary analysis is usually worked out is that of equilibrium Potts models, assuming that proteins have evolved for enough time to reach thermodynamic equilibrium in sequence space. Here we propose a model to describe correlations in sequences based on an explicit description of the evolutionary kinetics of proteins. We show that this procedure improves the correct prediction of native contacts with respect to equilibrium--based models.

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## Original sources and implementation

[Original paper](<https://arxiv.org/abs/2002.03383>)

[PDF](<https://arxiv.org/pdf/2002.03383.pdf>)