ArticleJournal of bioinformatics and computational biology2012
A chemical group graph representation for efficient high-throughput analysis of atomistic protein simulations.
Article in Journal of bioinformatics and computational biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Comparative analysis of thermal adaptations of extremophilic prolyl oligopeptidases.Biophysical journal · 2024Article
- Comparative Modeling and Analysis of Extremophilic D-Ala-D-Ala Carboxypeptidases.Biomolecules · 2023Article
- Mutation Effects on Structure and Dynamics: Adaptive Evolution of the SARS-CoV-2 Main Protease.Biochemistry · 2023Article
- Network Hamiltonian Models for Unstructured Protein Aggregates, with Application to γD-Crystallin.The journal of physical chemistry. B · 2023Article
- Conformational sampling of CMT-2D associated GlyRS mutations.Brain multiphysics · 2022Article
- Neural Upscaling from Residue-Level Protein Structure Networks to Atomistic Structures.Biomolecules · 2021Article
- Conserved patterns and interactions in the unfolding transition state across SH3 domain structural homologues.Protein science : a publication of the Protein Society · 2021Article
- Sequence Characterization and Molecular Modeling of Clinically Relevant Variants of the SARS-CoV-2 Main Protease.Biochemistry · 2020Article
- Comparative Exploratory Analysis of Intrinsically Disordered Protein Dynamics Using Machine Learning and Network Analytic Methods.Frontiers in molecular biosciences · 2019Article
- Protein structure networks provide insight into active site flexibility in esterase/lipases from the carnivorous plant Drosera capensis.Integrative biology : quantitative biosciences from nano to macro · 2018Article
- Structure prediction and network analysis of chitinases from the Cape sundew, Drosera capensis.Biochimica et biophysica acta. General subjects · 2017Article
- Calmodulin Gates Aquaporin 0 Permeability through a Positively Charged Cytoplasmic Loop.The Journal of biological chemistry · 2017Article
- Sequence comparison, molecular modeling, and network analysis predict structural diversity in cysteine proteases from the Cape sundew, Drosera capensis.Computational and structural biotechnology journal · 2016Article
- Analyzing disease-associated protein structures with visual analytics.AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science · 2013Article
- A comparison of multiscale methods for the analysis of molecular dynamics simulations.The journal of physical chemistry. B · 2012Article
Corrections and comments
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Authors and funding
2 authors.
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Abstract
Graphs are rapidly becoming a powerful and ubiquitous tool for the analysis of protein structure and for event detection in dynamical protein systems. Despite their rise in popularity, however, the graph representations employed to date have shared certain features and parameters that have not been thoroughly investigated. Here, we examine and compare variations on the construction of graph nodes and graph edges. We propose a graph representation based on chemical groups of similar atoms within a protein rather than residues or secondary structure and find that even very simple analyses using this representation form a powerful event detection system with significant advantages over residue-based graph representations. We additionally compare graph edges based on probability of contact to graph edges based on contact strength and analyses of the entire graph structure to an alternative and more computationally tractable node-based analysis. We develop the simplest useful technique for analyzing protein simulations based on these comparisons and use it to shed light on the speed with which static protein structures adjust to a solvated environment at room temperature in simulation.
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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.