Application of time series analysis on molecular dynamics simulations of proteins: A study of different conformational spaces by principal component analysis
Journal of Chemical Physics, cilt.121, sa.10, ss.4759-4769, 2004 (Scopus)
- Yayın Türü: Makale / Tam Makale
- Cilt numarası: 121 Sayı: 10
- Basım Tarihi: 2004
- Doi Numarası: 10.1063/1.1778377
- Dergi Adı: Journal of Chemical Physics
- Derginin Tarandığı İndeksler: Scopus
- Sayfa Sayıları: ss.4759-4769
- Boğaziçi Üniversitesi Adresli: Evet
Özet
The molecular dynamics simulations of α-amylase inhibitor tendamistat and immunity protein of colicin E7 were analyzed using time series analysis applied on collective coordinates obtained from principal component analysis (PCA). Even though principal component directions obtained for each run were different, the dynamics information obtained from these runs were similar in terms of time series models and parameters. It was observed that cumulative density function of low frequencies in each run conforms to expectations from normal mode analysis. The results show that principal components obtained from certain conformational region of a protein has moderate power in other conformational regions and local minima are similar to certain extent.