ArticleMolecular physics2021
Subsets of adjacent nodes (SOAN): A fast method for computing suboptimal paths in protein dynamic networks.
Article in Molecular physics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- Untangling the Complexity of Binding Across Biomolecular Interfaces with Interaction Network Models.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Impact of Replicas and Simulation Length on In Silico Behaviors of a Protein Domain.Chemphyschem : a European journal of chemical physics and physical chemistry · 2025Article
- Disease mutations and phosphorylation alter the allosteric pathways involved in autoinhibition of protein phosphatase 2A.The Journal of chemical physics · 2023Article
- Mechanism of Rad26-assisted rescue of stalled RNA polymerase II in transcription-coupled repair.Nature communications · 2021Article
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4 authors.
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Abstract
Suboptimal path analysis in a protein structural or dynamical network becomes increasingly popular for identifying critical residues involved in allosteric communication and regulation. Several software packages have been developed for calculating suboptimal paths, including NetworkView, WISP, and CNAPATH (Bio3D). Although these packages work well for biological systems of moderate sizes, they either dramatically slow down or are subjected to accuracy issues when applied to large systems such as supramolecular complexes. In this work, we develop a new method called SOAN, which implements a modified version of Yen's algorithm for finding loopless
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