ArticleACS omega2022
Entropies Derived from the Packing Geometries within a Single Protein Structure.
Article in ACS omega, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- Computational design of α-amylase fromComputational and structural biotechnology journal · 2024Article
- Glycosylation and Crowded Membrane Effects on Influenza Neuraminidase Stability and Dynamics.The journal of physical chemistry letters · 2023Article
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Authors and funding
2 authors.
Funding
Abstract
A fast, simple, yet robust method to calculate protein entropy from a single protein structure is presented here. The focus is on the atomic packing details, which are calculated by combining Voronoi diagrams and Delaunay tessellations. Even though the method is simple, the entropies computed exhibit an extremely high correlation with the entropies previously derived by other methods based on quasi-harmonic motions, quantum mechanics, and molecular dynamics simulations. These packing-based entropies account directly for the local freedom and provide entropy for any individual protein structure that could be used to compute free energies directly during simulations for the generation of more reliable trajectories and also for better evaluations of modeled protein structures. Physico-chemical properties of amino acids are compared with these packing entropies to uncover the relationships with the entropies of different residue types. A public packing entropy web server is provided at packing-entropy.bb.iastate.edu, and the application programing interface is available within the PACKMAN (https://github.com/Pranavkhade/PACKMAN) package.
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