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- W4214882158 abstract "Protein aggregation is a common and complex phenomenon in biological processes, yet a robust analysis of this aggregation process remains elusive. The commonly used methods such as center-of-mass to center-of-mass (COM-COM) distance, the radius of gyration (Rg), hydrogen bonding (HB), and solvent accessible surface area do not quantify the aggregation accurately. Herein, a new and robust method that uses an aggregation matrix (AM) approach to investigate peptide aggregation in a MD simulation trajectory is presented. An nxn two-dimensional AM is created by using the interpeptide Cα-Cα cutoff distances, which are binarily encoded (0 or 1). These aggregation matrices are analyzed to enumerate, hierarchically order, and structurally classify the aggregates. Comparison of the present AM method suggests that it is superior to the HB method since it can incorporate nonspecific interactions and the Rg and COM-COM methods since the cutoff distance is independent of the length of the peptide. More importantly, the present method can structurally classify the peptide aggregates, which the conventional Rg, COM-COM, and HB methods fail to do. The unique selling point of this method is its ability to structurally classify peptide aggregates using two-dimensional matrices." @default.
- W4214882158 created "2022-03-05" @default.
- W4214882158 creator A5017847638 @default.
- W4214882158 creator A5065435920 @default.
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- W4214882158 date "2022-03-01" @default.
- W4214882158 modified "2023-09-24" @default.
- W4214882158 title "Binary Matrix Method to Enumerate, Hierarchically Order, and Structurally Classify Peptide Aggregation" @default.
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- W4214882158 doi "https://doi.org/10.1021/acs.jcim.2c00069" @default.
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- W4214882158 hasPublicationYear "2022" @default.
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