ReviewCurrent opinion in structural biology2024
Using residue interaction networks to understand protein function and evolution and to engineer new proteins.
Review in Current opinion in structural biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
15 citing papers in PubMed.
- Exploring proteins and protein-ligand complexes through residue interaction networks.Nature protocols · 2026Review
- Surface electrostatic networks control hydrophobic core remodeling in a pH-dependent switching protein.bioRxiv : the preprint server for biology · 2026Article
- i-gRINN: a next-generation web server for protein energy network analysis of heterogeneous biomolecular systems with natural language-based data exploration.Nucleic acids research · 2026Article
- Structural Features of a Tiny Viral Protein, ORF7b of SARS-CoV-2.International journal of molecular sciences · 2026Article
- Untangling the Complexity of Binding Across Biomolecular Interfaces with Interaction Network Models.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A Robust Ensemble Machine Learning Approach for Inhibitor Discovery: Case Study of HIV-1 NNRTI and Validation Using MD Simulation.Chemistry, an Asian journal · 2026Article
- WatCon: A Python Tool for Analysis of Conserved Water Networks Across Protein Families.JACS Au · 2025Article
- Clustering and Analyzing Ensembles of Residue Interaction Networks from Molecular Dynamics Simulations.Journal of chemical information and modeling · 2025Article
- Identification and understanding of allostery hotspots in proteins: Integration of deep mutational scanning and multi-faceted computational analyses.Journal of molecular biology · 2025Review
- The Evolving Landscape of Protein Allostery: From Computational and Experimental Perspectives.Journal of molecular biology · 2025Review
- Approaches for regulating enzyme activities: Recent advances in experiment and computation.Current opinion in structural biology · 2025Review
- Network Dynamics as Fingerprints of Thermostability in an In Silico-Engineered DyP-Type Peroxidase.ACS catalysis · 2025Article
- 'Intelligent' proteins.Cellular and molecular life sciences : CMLS · 2025Review
- Enzyme Enhancement Through Computational Stability Design Targeting NMR-Determined Catalytic Hotspots.Journal of the American Chemical Society · 2025Article
- The more we learn, the more diverse it gets: structures, functions and evolution in the Phosphofructokinase Superfamily.The Biochemical journal · 2025Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Residue interaction networks (RINs) provide graph-based representations of interaction networks within proteins, providing important insight into the factors driving protein structure, function, and stability relationships. There exists a wide range of tools with which to perform RIN analysis, taking into account different types of interactions, input (crystal structures, simulation trajectories, single proteins, or comparative analysis across proteins), as well as formats, including standalone software, web server, and a web application programming interface (API). In particular, the ability to perform comparative RIN analysis across protein families using "metaRINs" provides a valuable tool with which to dissect protein evolution. This, in turn, highlights hotspots to avoid (or target) for in vitro evolutionary studies, providing a powerful framework that can be exploited to engineer new proteins.
Indexed as
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.