Protein Hotspot Prediction Using S-Transform

Kasparek, Jan; Maderankova, Denisa; Tkacz, Ewaryst

doi:10.1007/978-3-319-06593-9_29

Cited by 6 publications

(3 citation statements)

References 26 publications

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“…As a consequence, cavity search performed on a static GPCR structure may miss a potent allosteric site. On the other hand, lack of a cavity in a putative allosteric site location, e.g., resulting from hot-spot calculation [ 13 ] doesn’t mean that such location should be rejected.…”

Section: Introductionmentioning

confidence: 99%

Signaling within Allosteric Machines: Signal Transmission Pathways Inside G Protein-Coupled Receptors

2017

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In recent years, our understanding of function of G protein-coupled receptors (GPCRs) has changed from a picture of simple signal relays, transmitting only a particular signal to a particular G protein heterotrimer, to versatile machines, capable of various responses to different stimuli and being modulated by various factors. Some recent reports provide not only the data on ligands/modulators and resultant signals induced by them, but also deeper insights into exact pathways of signal migration and mechanisms of signal transmission through receptor structure. Combination of these computational and experimental data sheds more light on underlying mechanisms of signal transmission and signaling bias in GPCRs. In this review we focus on available clues on allosteric pathways responsible for complex signal processing within GPCRs structures, with particular emphasis on linking compatible in silico- and in vitro-derived data on the most probable allosteric connections.

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Section: Introductionmentioning

confidence: 99%

Signaling within Allosteric Machines: Signal Transmission Pathways Inside G Protein-Coupled Receptors

2017

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“…Finally, the power spectrum values obtained were assigned to each amino acid and the amino acids were mapped. EIIP method is one of the most frequently used methods in the literature [ 27 , 28 ]. The CPNR method was first proposed in the comparison of protein functions [ 29 ].…”

Section: Data and The Proposed Methodsmentioning

confidence: 99%

A Novel Protein Mapping Method for Predicting the Protein Interactions in COVID-19 Disease by Deep Learning

Alakuş

Türkoğlu

2021

Interdiscip Sci Comput Life Sci

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“…A more accurate method of hot spot detection was presented in a study by applying modified Gabor wavelet transform [30]. Other methods of hot spot analysis use short-time Fourier transform (STFT) [31] and S transform [32,33], which allow for signal analysis in the time-frequency plane. An algorithm employing digital filtering was also presented [34].…”

Section: Methods Of Hot Spot Identificationmentioning

confidence: 99%

Hot spot identification by means of classification methods employing wavelet transform-based features

Tamulewicz¹,

Tkacz²,

Provazník³

2020

Preprint

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Background: Proteins can interact with one another by an interface composed of two proteins. Some of the interface residues - called hot spots - have the greatest impact on binding energy in a protein complex. This paper introduces the application of continuous wavelet transform based on the fast Fourier transform (CWTFT) to the analysis of hot spots in proteins.Results: The algorithm was evaluated by using data sets containing 30 proteins. From the number of tested classifiers the best 10 models were preferred. The classifiers achieved sensitivity of 52% - 71%, specificity of 70% - 83% and accuracy of 70% - 74%.Conclusion: The analyses show that the method combining CWTFT and classification algorithms is able to identify hot spot residues with valuable results.Methods: The basis of the algorithm is extraction of features from spectra obtained by using CWTFT with different wavelet functions including Morlet, m^th order derivative of Gaussian, Paul and Bump wavelets. Then, the classifiers that are able to separate hot spot from non-hot spot residues according to these features are applied.

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Protein Hotspot Prediction Using S-Transform

Cited by 6 publications

References 26 publications

Signaling within Allosteric Machines: Signal Transmission Pathways Inside G Protein-Coupled Receptors

Signaling within Allosteric Machines: Signal Transmission Pathways Inside G Protein-Coupled Receptors

A Novel Protein Mapping Method for Predicting the Protein Interactions in COVID-19 Disease by Deep Learning

Hot spot identification by means of classification methods employing wavelet transform-based features

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