From experimental, structural probability distributions to the theoretical causality analysis of molecular changes

• Autorzy: Daniluk, P. , Dziubiński, M. , Lesyng, B. , Hallay-Suszek, M. , Rakowski, F. , Walewski, Ł.
• Języki publikacji: EN

Abstrakty

EN

A brief overview of causality analysis (CA) methods applied to MD simulations data for model biomolecular systems is presented. A CausalMD application for postprocessing of MD data was designed and implemented. MD simulations of two model systems, porphycene (ab initio MD) and HIV-1 protease (coarse-grained MD) were carried out and analyzed. Granger’s causality methodology based on a Multivariate Autoregressive (MVAR) formalism, followed by the Directed Transfer Function (DTF) analysis was applied. A novel approach based on the descriptors of local structure was also presented and prelim- inary results were reported. Casuality analyses are required for a better understanding of biomolecular functioning mechanisms. In particular, such analyses can link physics-based structural dynamics with functions inferred from molecular evolution processes. Current limitations and future developments of the presented methodologies are indicated.

Słowa kluczowe

PL

analiza przyczyn; analiza sygnałów; deskryptory lokalne; wyrównanie; MVAR; dynamika molekularna; porficyny; proteazy HIV-1; funkcja molekularna; ewolucja molekularna

EN

causality analysis; signal analysis; local descriptors; alignment; MVAR; Directed Transfer Function; molecular dynamics; porphycene; HIV-1 protease; molecular function; molecular evolution

• Czasopismo: Computer Assisted Methods in Engineering and Science
• Rocznik: 2012
• Tom: Vol. 19, no. 3
• Strony: 257-276
• Opis fizyczny: Bibliogr. 57 poz., rys., tab., wykr.

Twórcy

autor

Daniluk, P.

autor

Dziubiński, M.

autor

Lesyng, B.

autor

Hallay-Suszek, M.

autor

Rakowski, F.

autor

Walewski, Ł.

• Bioinformatics Laboratory, Mossakowski Medical Research Centre Polish Academy of Sciences Pawińskiego 5, 02-106 Warsaw, Poland,

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