A Simple Definition of Structural Regions in Proteins and Its Use in Analyzing Interface Evolution

2010/09/23 by Emmanuel D. Levy · 272 citations
Biochemistry, Genetics and Molecular Biology · Chemistry · Mathematics · #Amino acid #Biochemistry #Bioinformatics and Genomic Networks #Biological system #Biology #Chemistry #Combinatorics #Computational biology #Computer science #Core (optical fiber) #Crystallography #Fungal and yeast genetics research #Genetics #Geometry #Interface (matter) #Mathematics #Partition (number theory) #Protein Structure and Dynamics #Protein structure #Saccharomyces cerevisiae #Simple (philosophy) #Surface (topology) #Yeast

paper · doi:10.1016/j.jmb.2010.09.028

published in Journal of Molecular Biology 403(4), 660-670 (Elsevier BV)

openalex publication_date 2010/09/23 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/06

Citations

• Interior and surface of monomeric proteins

Cited by

• Structural comparison of homologous protein-RNA interfaces reveals widespread overall conservation contrasted with versatility in polar contacts
• DynaPIN: A Tool for Characterizing Dynamic Protein Interfaces
• Decrypting protein surfaces by combining evolution, geometry, and molecular docking
• Commutative algebra neural network reveals genetic origins of diseases
• An atlas of protein homo-oligomerization across domains of life
• Why variant effect predictors and multiplexed assays agree and disagree
• Topological Machine Learning for Protein-Nucleic Acid Binding Affinity Changes Upon Mutation
• Atom-level Protein Representation Learning Improves Protein Structure Prediction
• Functional specialization in nucleotide sugar transporters occurred through differentiation of the gene cluster EamA (DUF6) before the radiation of Viridiplantae. [europepmc]
• Rationalization and design of the complementarity determining region sequences in an antibody-antigen recognition interface. [europepmc]
• Protein interface classification by evolutionary analysis. [europepmc]
• Evolutionary, physicochemical, and functional mechanisms of protein homooligomerization. [europepmc]
• Biophysics of protein evolution and evolutionary protein biophysics. [europepmc]
• On human disease-causing amino acid variants: statistical study of sequence and structural patterns. [europepmc]
• An integrated map of HIV genome-wide variation from a population perspective. [europepmc]
• Universal distribution of mutational effects on protein stability, uncoupling of protein robustness from sequence evolution and distinct evolutionary modes of prokaryotic and eukaryotic proteins. [europepmc]
• Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method. [europepmc]
• Globular and disordered-the non-identical twins in protein-protein interactions. [europepmc]
• Predicting the Effect of Mutations on Protein-Protein Binding Interactions through Structure-Based Interface Profiles. [europepmc]
• Local Geometry and Evolutionary Conservation of Protein Surfaces Reveal the Multiple Recognition Patches in Protein-Protein Interactions. [europepmc]
• Coupling between Protein Stability and Catalytic Activity Determines Pathogenicity of G6PD Variants. [europepmc]
• Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology. [europepmc]
• Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation. [europepmc]
• SKEMPI 2.0: an updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation. [europepmc]
• Infinite Assembly of Folded Proteins in Evolution, Disease, and Engineering. [europepmc]
• iSEE: Interface structure, evolution, and energy-based machine learning predictor of binding affinity changes upon mutations. [europepmc]
• Protein Abundance Biases the Amino Acid Composition of Disordered Regions to Minimize Non-functional Interactions. [europepmc]
• A topology-based network tree for the prediction of protein-protein binding affinity changes following mutation. [europepmc]
• Mutant libraries reveal negative design shielding proteins from supramolecular self-assembly and relocalization in cells. [europepmc]
• The properties of human disease mutations at protein interfaces. [europepmc]
• Loss-of-function, gain-of-function and dominant-negative mutations have profoundly different effects on protein structure. [europepmc]
• Simple mechanisms for the evolution of protein complexity. [europepmc]
• A dynamical view of protein-protein complexes: Studies by molecular dynamics simulations. [europepmc]