Improved Protocol for the Selection of Structures from Molecular Dynamics of Organic Systems in Solution: The Value of Investigating Different Wavelet Families
Jazyk angličtina Země Spojené státy americké Médium print-electronic
Typ dokumentu časopisecké články
PubMed
36103405
DOI
10.1021/acs.jctc.2c00593
Knihovny.cz E-zdroje
- MeSH
- algoritmy * MeSH
- lidé MeSH
- simulace molekulární dynamiky * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
Wavelets are mathematical tools used to decompose and represent another function described in the time domain, allowing the study of each component of the original function with a scale-compatible resolution. Thus, these transforms have been used to select conformations from molecular dynamics (MD) trajectories in systems of fundamental and technological interest. Recently, our research group has used wavelets to develop and validate a method, meant to select structures from MD trajectories, which we named OWSCA (optimal wavelet signal compression algorithm). Here, we moved forward on this project by demonstrating the efficacy of this method on the study of three different systems (non-flexible organic, flexible organic, and protein). For each system, 93 wavelets were investigated to verify which is the best one for a given organic system. The results show that the best wavelets were different for each system and, also, very close to the experimental values, with the wavelets db1, rbio 3.1, and bior1.1 being selected for the non-flexible, flexible organic, and protein systems, respectively. This reinforces our OWSCA as a very efficient and promising method for the selection of structures from MD trajectories of different classes of compounds. Our findings also point out that additional studies considering wavelet families are needed for defining the best wavelet for representing each system under study.
Chemistry Department Federal University of Lavras 37200 000Lavras MG Brazil
Federal Institute of Education Science and Technology of Espírito Santo Vila Velha29100 000 Brazil
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