PRENbase is an annotated database of known and predicted prenylated proteins. Homologous proteins are merged into clusters. This search interface is designed to allow sophisticated queries for the experimental status of the modification (known/predicted...), exclusive or shared types of modifying enzymes (FT, GGT1, GGT2) as well as for evolutionary conservation by constraining the taxonomic distribution within these clusters or for single sequences.

We have also created a HumanPRENbase with clusters centered around individual prenylated human proteins and their true orthologues (splitting up larger families into paralogous subclusters; e.g. H-Ras, N-Ras, K-Ras are individual clusters rather than merged in the Ras superfamily cluster). Click here for the HumanPRENbase!

To start with, the default settings will give access to the collection of both known and predicted eukaryotic and viral prenylated proteins, which can then be browsed. Below we have listed a series of standard queries that you might find useful or are particularly biologically important:

• Review of previous knowledge of prenylated proteins:

List the clusters including KNOWN eukaryotic and viral prenylated proteins.

• Likely candidates for prenylation due to already verified prenylation of homologues:

List the clusters including LIKELY eukaryotic and viral prenylated proteins.

• Targets for experimental validation of NEW predicted prenylation:

List the clusters including NEWLY PREDICTED eukaryotic prenylated proteins.

As above but require conservation between Mammalia and Insecta.
As above but require conservation between Mammalia and Nematoda.
As above but require conservation between Mammalia and Fungi.
As above but require conservation between Mammalia and Plants.

• Possible targets for FTI (FT inhibition, see accompanying publications for details and HumanPRENbase for focus on human FTI targets):

List only proteins that are unique substrates to FT and not GGT1 or GGT2.

List the clusters of proteins containing unique substrates to FT and not GGT1 or GGT2 and conserved between Mammalia and Insecta.

List the clusters of proteins containing unique substrates to FT and not GGT1 or GGT2 and conserved between Mammalia and Nematoda.

List the clusters of proteins containing unique substrates to FT and not GGT1 or GGT2 and conserved between Mammalia and Fungi.

List the clusters of proteins containing unique substrates to FT and not GGT1 or GGT2 and conserved between Mammalia and Plants.

• FT substrates less affected by FT inhibition or with altered anchor type under FTI:

List FT substrates that can be alternatively prenylated by GGT1 or GGT2.

• Predicted prenylation in Viruses:

List the number of viral proteins with capacity to be prenylated if the biological context would allow processing by eukaryotic host enzymes.

• Possible importance of specific farnesyl anchor length:

List clusters that only include FT but not GGT1 or GGT2 substrates.

• Evolutionary exchangeability of different prenyl anchors:

List clusters that include both FT and GGT1 substrates.