Fig. 3 | Scientific Reports

Fig. 3

From: A comparative study of computational modeling approaches for evaluating structural dynamics and algorithmic suitability of short length peptides

Fig. 3

Plots depicting the structural and essential dynamics of backbone atoms over time for AMP21. The panels represent: (i) RMSD for structures modeled using 4 different algorithms, (ii) RMSF for structures modeled using 4 different algorithms, (iii) Rg for structures modeled using 4 different algorithms, (iv) SASA for structures modeled using 4 different algorithms, (v) PCAfor structures modeled using 4 different algorithms, and (vi) FEL for best modeling algorithm. The gmx rms, gmx rmsf, gmx gyrate and gmx sasa functionalities were used to obtain the RMSD, RMSF, Rg and SASA values, respectively. gmx covar and gmx anaeig were used to obtain values for PC1 and PC2. The Gibbs’ free energy values were extracted using gmx-sham. The values were plotted using the OriginPro 2016 64-bit software.

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