ReviewBioinformatics (Oxford, England)2016
Understanding the fabric of protein crystals: computational classification of biological interfaces and crystal contacts.
Review in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- ESpma: A method for assessing biological/non-biological interfaces using point-clouds-based structural features and protein language models.Protein science : a publication of the Protein Society · 2026Article
- Statistical analysis of sequential motifs at biologically relevant protein-protein interfaces.Computational and structural biotechnology journal · 2024Article
- Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data.Scientific data · 2023Article
- AHoJ: rapid, tailored search and retrieval of apo and holo protein structures for user-defined ligands.Bioinformatics (Oxford, England) · 2022Article
- Antibody interfaces revealed through structural mining.Computational and structural biotechnology journal · 2022Article
- PDB-wide identification of physiological hetero-oligomeric assemblies based on conserved quaternary structure geometry.Structure (London, England : 1993) · 2021Article
- MCDB: A comprehensive curated mitotic catastrophe database for retrieval, protein sequence alignment, and target prediction.Acta pharmaceutica Sinica. B · 2021Article
- Trop2 Forms a Stable Dimer with Significant Structural Differences within the Membrane-Distal Region as Compared to EpCAM.International journal of molecular sciences · 2021Article
- Modeling and Structure Determination of Homo-Oligomeric Proteins: An Overview of Challenges and Current Approaches.International journal of molecular sciences · 2021Review
- CAVIAR: a method for automatic cavity detection, description and decomposition into subcavities.Journal of computer-aided molecular design · 2021Article
- Getting to know each other: PPIMem, a novel approach for predicting transmembrane protein-protein complexes.Computational and structural biotechnology journal · 2021Article
- QSalignWeb: A Server to Predict and Analyze Protein Quaternary Structure.Frontiers in molecular biosciences · 2021Review
- Quaternary Structure of the Tryptophan Synthase α-Subunit Homolog BX1 fromJournal of the American Society for Mass Spectrometry · 2020Article
- Assessment of protein assembly prediction in CASP13.Proteins · 2019Article
- Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm.PLoS computational biology · 2019Article
- Distinguishing crystallographic from biological interfaces in protein complexes: role of intermolecular contacts and energetics for classification.BMC bioinformatics · 2018Article
- Integrating co-evolutionary signals and other properties of residue pairs to distinguish biological interfaces from crystal contacts.Protein science : a publication of the Protein Society · 2018Article
- Automated evaluation of quaternary structures from protein crystals.PLoS computational biology · 2018Article
- Assessment of protein assembly prediction in CASP12.Proteins · 2018Article
- Investigation of protein quaternary structure via stoichiometry and symmetry information.PloS one · 2018Article
Corrections and comments
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5 authors.
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Abstract
Modern structural biology still draws the vast majority of information from crystallography, a technique where the objects being investigated are embedded in a crystal lattice. Given the complexity and variety of those objects, it becomes fundamental to computationally assess which of the interfaces in the lattice are biologically relevant and which are simply crystal contacts. Since the mid-1990s, several approaches have been applied to obtain high-accuracy classification of crystal contacts and biological protein-protein interfaces. This review provides an overview of the concepts and main approaches to protein interface classification: thermodynamic estimation of interface stability, evolutionary approaches based on conservation of interface residues, and co-occurrence of the interface across different crystal forms. Among the three categories, evolutionary approaches offer the strongest promise for improvement, thanks to the incessant growth in sequence knowledge. Importantly, protein interface classification algorithms can also be used on multimeric structures obtained using other high-resolution techniques or for protein assembly design or validation purposes. A key issue linked to protein interface classification is the identification of the biological assembly of a crystal structure and the analysis of its symmetry. Here, we highlight the most important concepts and problems to be overcome in assembly prediction. Over the next few years, tools and concepts of interface classification will probably become more frequently used and integrated in several areas of structural biology and structural bioinformatics. Among the main challenges for the future are better addressing of weak interfaces and the application of interface classification concepts to prediction problems like protein-protein docking.
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