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Pipeline publication

[…] protein interaction networks and to calculate the number of interactions of each human and yeast Mediator subunit. For the purpose of the current study, Mediator subunit with 10 or more direct interactions was considered as ‘Hub’ (). For subunit-subunit interactions five or more direct interactions were considered as threshold., Four major types of PTMs such as phosphorylation of Ser, Thr and Tyr, N-linked Asn and O-linked proline glycosylation, Lys/Arg methylation and Lys acetylation were analyzed in Mediator subunits of S. cereviseae, A. thaliana, O. saitva subsp. japonica, C. elegans, D. melanogaster, D. rerio, G. gallus and H. sapiens. PTMs were predicted with freely available web tools NetPhos 2.0 (), NetNGlyc 1.0 (), PMeS () and PAIL () with default parameters. A stretch of 30 residues in Mediator complex subunits was considered as PTM hotspot if the fraction of predicted PTM sites in this stretch was between 0.1 and 0.3., The protein–protein recognition and interaction sites were predicted in Mediator subunits of 30 organisms using MoRFpred (). A stretch of at least five amino acids with a score greater than or equal to 0.5 was considered as a potential recognition and binding site. Such stretches were highlighted on multiple sequence alignments constructed using MAFFT () and ALSCRIPT (). MoRF was called ‘conserved’ if it is aligned in the multiple sequence alignment for at least four organisms., Homology models of […]

Pipeline specifications

Software tools NetPhos, NetNGlyc, PMes, PAIL