Phosphorylation prediction

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PhosphoPredictis a novel bioinformatics approach to predict kinase-specific phosphorylation substrates and sites in the human proteome by combining informative protein sequence and functional features to build the prediction models using random forest (RF).

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Answer

How useful is computational prediction of phosphorylation sites with cognate protein kinases?

Computational prediction of phosphorylation sites (p-sites) with their cognate protein kinases (PKs) is greatly helpful for further experimental design. Previously, our group developed and maintained a series of PK-specific p-site predictors.

How does NetPhos predict phosphorylation sites in proteins?

The NetPhos 3.1 server predicts serine, threonine or tyrosine phosphorylation sites in eukaryotic proteins using ensembles of neural networks. Both generic and kinase specific predictions are performed. The generic predictions are identical to the predictions performed by NetPhos 2.0 .

What is the GPS algorithm for phosphorylation site prediction and scoring?

In 2004, we developed a novel algorithm of group-based phosphorylation site predicting and scoring ( GPS) 1.0, based on a hypothesis of short similar peptides exhibiting similar biological functions. We considerably refined the algorithm and constructed an online service of GPS 1.1, which could predict p-sites for 71 PK clusters.

What is the best way to predict phosphorylation sites for peptides?

In 2004, we developed a novel algorithm, group-based phosphorylation site predicting and scoring (GPS) 1.0, based on the hypothesis that similar short peptides exhibit similar biological functions. Accordingly, we refined the algorithm and constructed an online service of GPS 1.1, which can predict p-sites for 71 PK clusters.

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How do you confirm phosphorylation?

Methods for Detecting Protein PhosphorylationIntroduction. … Kinase Activity Assays. … Phospho-Specific Antibody Development. … Western Blot. … Enzyme-Linked Immunosorbent Assay (ELISA) … Cell-Based ELISA. … Intracellular Flow Cytometry and ICC/IHC. … Mass Spectrometry.More items…


What triggers phosphorylation?

For example, phosphorylation is activated by stimuli such as epigenetic modifications, cytogenetic alterations, genetic mutations or the tumor micro-environment. Consequently, the protein receives a phosphate group by adenosine triphosphate (ATP) hydrolysis and due to enzymatic activity of kinase.


What happens when proteins get phosphorylated?

Phosphorylation alters the structural conformation of a protein, causing it to become either activated or deactivated, or otherwise modifying its function. Approximately 13000 human proteins have sites that are phosphorylated.


What is phosphorylation and why is it important?

Explanation: Phosphorylation is an important mechanism by which the activity of proteins can be altered after they are formed. A phosphate group ( PO3−4 ) is added to a protein by specific enzymes called kinases. This phosphate group is usually provided by ATP, the energy carrier of the cell.


Where does phosphorylation occur?

Substrate-level phosphorylation occurs in the cytoplasm of cells (glycolysis) and in the mitochondria (Krebs cycle). It can occur under both aerobic and anaerobic conditions and provides a quicker, but less efficient source of ATP compared to oxidative phosphorylation.


How does phosphorylation affect gene expression?

In addition to recruitment of histone demethylase(s), histone phosphorylation is thought to facilitate gene expression by structural relaxation of chromatin via neutralization of positive charge on histone proteins, reducing their affinity for DNA and generating a DNA structure permissive for transcription.


What happens when you phosphorylate an enzyme?

The phosphorylation of a protein can make it active or inactive. Phosphorylation can either activate a protein (orange) or inactivate it (green). Kinase is an enzyme that phosphorylates proteins. Phosphatase is an enzyme that dephosphorylates proteins, effectively undoing the action of kinase.


What happens when a molecule is phosphorylated?

In biology, phosphorylation is the transfer of phosphate molecules to a protein. This transfer prepares the proteins for specialized tasks in a living being.


How does phosphorylation affect enzyme activity?

Protein phosphorylation alters the structural conformation of a protein, causing it to become activated, deactivated, or modifying its function. For example, phosphorylation of the enzyme glycogen synthetase changes the enzyme’s shape and reduces its activity.


What is the meaning of phosphorylation?

Listen to pronunciation. (fos-FOR-ih-LAY-shun) A process in which a phosphate group is added to a molecule, such as a sugar or a protein.


What is phosphorylation in physiology?

Phosphorylation: A biochemical process that involves the addition of phosphate to an organic compound. Examples include the addition of phosphate to glucose to produce glucose monophosphate and the addition of phosphate to adenosine diphosphate (ADP) to form adenosine triphosphate (ATP).


What is the significance of phosphorylation in glycolysis?

The cascade effect of phosphorylation eventually causes instability and allows enzymes to open the carbon bonds in glucose. Phosphorylation functions as an extremely vital component of glycolysis, for it helps in transport, control and efficiency.


What is post translational modification?

The post-translational modification (PTM) of proteins plays an extremely important role in numerous cellular functions and biological processes [ 1 ], including altering proteins’ physiochemical properties, conformation, localization, and enzymatic activity; it also plays an important role in several other processes, such as cell signaling, regulation of gene expression, and cellular metabolism, to name a few [ 2 ]. Over 200 diverse PTMs have been recognized [ 3 ], of which phosphorylation is the most abundant and well-established PTM in eukaryotes and is crucial to almost all aspects of cell life.


What is the role of PTM in cellular regulation?

Post-translational modification (PTM) is a biological process that alters proteins and is therefore involved in the regulation of various cellular activities and pathogenesis. Protein phosphorylation is an essential process and one of the most-studied PTMs: it occurs when a phosphate group is added to serine (Ser, S), threonine (Thr, T), or tyrosine (Tyr, Y) residue. Dysregulation of protein phosphorylation can lead to various diseases—most commonly neurological disorders, Alzheimer’s disease, and Parkinson’s disease—thus necessitating the prediction of S/T/Y residues that can be phosphorylated in an uncharacterized amino acid sequence. Despite a surplus of sequencing data, current experimental methods of PTM prediction are time-consuming, costly, and error-prone, so a number of computational methods have been proposed to replace them. However, phosphorylation prediction remains limited, owing to substrate specificity, performance, and the diversity of its features.


What is RF in ML?

RF is broadly used ML algorithm used for solving classification problems and making predictions [ 42, 43, 44 ]. This algorithm is based on the ensemble of decision-making trees which yield individual outputs and the most common output of the model is considered as final RF prediction. The node of the tree and the subset of features used for generating trees is chosen randomly [ 45 ]. RF has many advantages which made it suitable for use in the present study. It is considered as a highly accurate learning classifier which can efficiently handle large dimensional datasets, deals with overfitting and does not consume a lot of time for training and prediction amongst many others [ 42, 46 ]. In this study, the RF models were trained using RandomForest package available from Weka [ 41 ].


Can computational methodology be used for predicting putative phosphorylation sites?

The results obtained in the present work indicate that the proposed computational methodology can be effectively used for predicting putative phosphory lation sites further facilitating discovery of various biological processes mechanisms.

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