protein-protein – BioExcel – Centre of Excellence for Computation Biomolecular Research

Using machine-learning-driven approaches to boost hot-spot’s knowledge

February 18, 2022November 3, 2022Stian Soiland-Reyes

This review aims to present the current knowledge on PPIs, providing a detailed understanding of the microspecifications of the residues involved in those interactions and the characteristics of those defined as HS through a thorough assessment of related field-specific methodologies. [...]

DeepRank: A deep learning framework for data mining 3D protein-protein interfaces

December 3, 2021November 3, 2022Stian Soiland-Reyes

Three-dimensional (3D) structures of protein complexes provide fundamental information to decipher biological processes at the molecular scale. The vast amount of experimentally and [...]

MetaScore: A novel machine-learning based approach to improve traditional scoring functions for scoring protein-protein docking conformations

October 9, 2021November 3, 2022Stian Soiland-Reyes

We present here MetaScore, a new machine-learning based approach to improve the scoring of docked conformations. MetaScore utilizes a random forest (RF) classifier trained to distinguish near-native from non-native conformations using a rich set of features extracted from the respective protein-protein interfaces. These include physico-chemical properties, energy terms, interaction propensity-based features, geometric properties, interface topology features, evolutionary conservation and also scores produced by traditional scoring functions (SFs). [...]

Information-Driven Modeling of Biomolecular Complexes

October 5, 2021November 3, 2022Stian Soiland-Reyes

Proteins play crucial roles in every cellular process by interacting with each other, nucleic acids, metabolites, and other molecules. The resulting assemblies can [...]

Native or Non-Native Protein–Protein Docking Models? Molecular Dynamics to the Rescue

August 3, 2021November 3, 2022Stian Soiland-Reyes

Molecular docking excels at creating a plethora of potential models of protein–protein complexes. To correctly distinguish the favorable, native-like models from the remaining [...]