parallel code search algorithm
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Objective is a joint primary and secondary code (SC) acquisition estimator of tiered Global Navigation Satellite Systems (GNSS) signals. The estimator is based on the Parallel Code Search algorithm (PCS) combined with the Single-Block-Zero-Padding (SBZP) and the Pre-correlation Coherent Accumulation (PCA). The PCA realizes the extension of the coherent integration time in front of the PCS. However, the PCS with the SBZP and the PCA is affected by a navigation/SC bit transition problem due to its cyclic property of a computed Cross-Ambiguity Function (CAF). This CAF is degraded by diverse parasitic fragments and is not directly applicable for an acquisition. A novel analysis of this mechanism and its impact is presented. Then, the proposed modified SBZP (mSBZP) modified PCA (mPCA) PCS estimator is constructed, which does not degrade the CAF. The mSBZP allows the use of the PCS algorithm in the presence of SC bit transition, while the mPCA decreases the number of PCS algorithm calculations by a factor of SC chip count due to SC pre-correlation processing. The algorithm has the same detection performance in comparison with conventional Double-Block-Zero-Padding (DBZP). However, it allows using the PCS of half-length with longer latency up to a factor of SC chip count.
MOTIVATION: Protein tunnels and channels are key transport pathways that allow ligands to pass between proteins' external and internal environments. These functionally important structural features warrant detailed attention. It is difficult to study the ligand binding and unbinding processes experimentally, while molecular dynamics simulations can be time-consuming and computationally demanding. RESULTS: CaverDock is a new software tool for analysing the ligand passage through the biomolecules. The method uses the optimized docking algorithm of AutoDock Vina for ligand placement docking and implements a parallel heuristic algorithm to search the space of possible trajectories. The duration of the simulations takes from minutes to a few hours. Here we describe the implementation of the method and demonstrate CaverDock's usability by: (i) comparison of the results with other available tools, (ii) determination of the robustness with large ensembles of ligands and (iii) the analysis and comparison of the ligand trajectories in engineered tunnels. Thorough testing confirms that CaverDock is applicable for the fast analysis of ligand binding and unbinding in fundamental enzymology and protein engineering. AVAILABILITY AND IMPLEMENTATION: User guide and binaries for Ubuntu are freely available for non-commercial use at https://loschmidt.chemi.muni.cz/caverdock/. The web implementation is available at https://loschmidt.chemi.muni.cz/caverweb/. The source code is available upon request. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
- MeSH
- algoritmy MeSH
- ligandy MeSH
- proteiny MeSH
- simulace molekulového dockingu MeSH
- software * MeSH
- vazebná místa MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- ligandy MeSH
- proteiny MeSH
