Investigating an efficient and accurate protocol for sampling structures from molecular dynamics simulations: a close look by different wavelet families

Gonçalves, Mateus A.; Júnior, Arismar Morais Gonçalves; Cunha, Elaine F. F. da; Ramalho, Teodorico C.

doi:10.1007/s00214-021-02816-y

Cited by 4 publications

(3 citation statements)

References 53 publications

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“…For compounds containing transition metals, the most suitable wavelet is bior1.3. 35 Figure 3a shows the original signal (blue signal) and the signal treated with the bior 1.3 wavelet (red signal), figure 3b shows only the treated signal. Analyzing the signals in Figure 2, it is possible to observe that each step of the signal corresponds to a conformation (interaction calls as can be seen in the X axis legend of Figure 2), in real numbers the number of initial structures was 6000 and the number of treated structures was 100, thus; it is noted that the number of treated structures (number of steps of the red signal) are much smaller than the number of initial structures (number of steps of the blue signal), this signal compression and consequently the number of conformations is very important for further calculations to be performed.…”

Section: Selection Of Structures From Molecular Dynamics Simulationsmentioning

confidence: 99%

Wavepress is a user-friendly toolkit for computational chemistry, drug design and data analysis

Gonçalves

Nunes

Sáfadi

et al. 2023

Preprint

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Wavepress is a signal processing software that has a simple and friendly interface that can be used by researchers, professors and students. The program uses the wavelet transform, which is a signal processing tool, being used to handle a signal in the time-scale space. In this way, the program can be used for signal processing capable of reducing, without losing important information, the amount of information. Thus, it is possible to obtain graphs and tables to explore the results in a comprehensive and satisfying way. In this work, the main features of Wavepress are explored with applications in computational chemistry, drug design and stock market, all examples are illustrated with graphs and tables got with Wavepress.

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Section: Selection Of Structures From Molecular Dynamics Simulationsmentioning

confidence: 99%

Wavepress is a user-friendly toolkit for computational chemistry, drug design and data analysis

Gonçalves

Nunes

Sáfadi

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…In this line, in the current work, we have employed the wavelet bior 1.3 to select the main conformations obtained by molecular dynamics calculations. Wavelet bior 1.3 is used successfully for the selection of MD configurations for coordination compounds containing transition metals [28].…”

Section: 2-molecular Quantum Simulations Structure Selection (Owsca) ...mentioning

confidence: 99%

Exploring 129Xe NMR parameters for structural investigation of biomolecules: relativistic, solvent, and thermal Effects

Gonçalves

Andolpho

Cunha

et al. 2022

Preprint

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In recent years, the study of new probes has aroused great interest in the scientific community around the world. Therefore, in the present work, we present a potential candidate for a new spectroscopic probe, the Xe(CO)3(NNO) conjugated to 2-(4’-Aminophenyl) Benzothiazole complex, XeABT. For this proposal, chemical shift calculations at the DFT level were performed, thus, a factorial design was carried out in order to choose the best computational method. The best combination was the base function ZORA-def2-TZVP, with the functional PBE0 and considering the relativistic effects with the ZORA implementation. Our findings reveal that the 129Xe chemical shifts is affected by thermal and solvent effects and considering an enzymatic environment a significant decrease in δ(129Xe) values are observed, suggesting with the XeABT complex it may be a promising spectroscopic probe.

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“…In addition to simultaneous quantitative determination of a multi-component mixtures [36,37], CWT has been used for periodic error compensation [38], electrochemical signals [39], spectrophotometric determination of drugs using high performance liquid chromatography [40], solvent effect on MRI probe and [41] sampling structures from molecular dynamics simulations [42]. This approach has the advantages of removing the Fourier transform restriction, increasing the signal-to-noise ratio in comparison to previous approaches, and reducing spectral interference.…”

Section: Introductionmentioning

confidence: 99%

Mean Centered Kinetic—Spectrophotometric Data—Continuous Wavelet Transform for Simultaneous Determination of Dopamine and Uric Acid in Presence of Ascorbic Acid at Biological Samples

et al. 2022

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In the present study, a rapid, practical, selective and sensitive method was proposed for simultaneous determination of dopamine (DA) and uric acid (UA). Kinetic profiles of analytes were recorded and transformed by different mother wavelets. The contribution of ascorbic acid was neglected using mean centering of data before transformation. The concentrations range were 1.0–60.0 μmol L−1 and 7–40.0 μmol L−1, with detection limit of 0.06 and 0.30 μmol L−1 for uric acid and dopamine, respectively. The results of sym8 and db4 mother wavelets showed that proposed method creates a most selective and sensitive determination without using initial separation steps. The obtained results by CWT-sym8 and CWT-db4 were compared with partial least squares (PLS) results. The simultaneous quantitation of DA and UA with the proposed method was successfully applied in different urine and serum samples.

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Investigating an efficient and accurate protocol for sampling structures from molecular dynamics simulations: a close look by different wavelet families

Cited by 4 publications

References 53 publications

Wavepress is a user-friendly toolkit for computational chemistry, drug design and data analysis

Wavepress is a user-friendly toolkit for computational chemistry, drug design and data analysis

Exploring 129Xe NMR parameters for structural investigation of biomolecules: relativistic, solvent, and thermal Effects

Mean Centered Kinetic—Spectrophotometric Data—Continuous Wavelet Transform for Simultaneous Determination of Dopamine and Uric Acid in Presence of Ascorbic Acid at Biological Samples

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