Biological vs. Crystallographic Protein Interfaces: An Overview of Computational Approaches for Their Classification

Crystals

AlexandreM. J. J. Bonvin¹  Katarina Elez¹  Anna Vangone² 

[1] Bijvoet Center for Biomolecular Research, Faculty of Science – Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands;Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Nonnenwald 2, 82377 Penzberg, Germany;

关键词: protein-protein interface;    biological interface;    crystallographic interface;    classification;    webserver;    x-ray crystallography;    protein structure;    machine learning;   

DOI  :  10.3390/cryst10020114

来源: DOAJ

【 摘 要 】

Complexes between proteins are at the basis of almost every process in cells. Their study, from a structural perspective, has a pivotal role in understanding biological functions and, importantly, in drug development. X-ray crystallography represents the broadest source for the experimental structural characterization of protein-protein complexes. Correctly identifying the biologically relevant interface from the crystallographic ones is, however, not trivial and can be prone to errors. Over the past two decades, computational methodologies have been developed to study the differences of those interfaces and automatically classify them as biological or crystallographic. Overall, protein-protein interfaces show differences in terms of composition, energetics and evolutionary conservation between biological and crystallographic ones. Based on those observations, a number of computational methods have been developed for this classification problem, which can be grouped into three main categories: Energy-, empirical knowledge- and machine learning-based approaches. In this review, we give a comprehensive overview of the training datasets and methods so far implemented, providing useful links and a brief description of each method.

【 授权许可】

Unknown