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Search ID: vanNoort_et_al_MSB_2012.all

Data given:

  • 241 sequences
  • 883 variations/modifications
  • sites added from other sources

Information used for this search:

  • 3,117 three-dimensional structures
  • 10,461 alignments
  • protein-protein interaction structures
  • 884 experimentally identified interactions

Sequence identity thresholds: 0% for structure matches, 0% / 0% for homo-/hetero-dimeric prot-prot interactions, 0% for prot-chem and 0% for prot-DNA/RNA interactions. Proteins in experimental protein interactions were grouped using none, and interactions were also considered to be reliable if both proteins had at least 90% seq identity to an interaction of 3D structure. Protein-protein interactions were considered to be reliable if they had a STRING score >= or both proteins had at least 90% sequence identity to a 3D structure of an interaction.

Protein Summary

Site Summary

The panel above left provides information about this job, including the various thresholds determining which interactions were included. The bar charts centre and right show percentages (numbers in mouseover) of proteins and sites known/predicted to be in various categories. The network below shows all proteins and their known or predicted interaction partners. Thicker links show where sites are at the intermolecular interface. Mouseover for more information.

Results per protein/gene

The table below gives various details for each gene/protein as a whole. n = number of changes, n! = number of mismatches, nP = number of sites and protein-protein interfaces, nC = number of sites and protein-chemical interfaces, nD = number of sites and DNA/RNA interfaces. Mechismo Score measures the overall impact of all changes on biomolecular interactions predicted. Mousing over on the column header gives more information.

Results per site

The table below gives various details for each change. ! = whether or not the original amino acid matched our sequence, nP = number of proteins this site interacts with, Prot = the most confident protein interactors, nC = the number of chemicals the site interacts with, Chem = list of all chemical classes, DNA = details of DNA/RNA binding sites. Mechismo score measures the overall functional impact of this change on biomolecular interactions predicted. T, I, and A links take you to pages detailing the particular structure showing This change only, all changes at the Interface, or All changes respectively. The first square in Prot/Chem/DNA columns gives the confidence (High, Medium, or Low) and the second denotes the predicted effect (Enabling, Disabling or Neutral). Mousing over the column header gives more information.