Project progress:

June 2011

Paper published: Environment Specific Substitution Tables Improve Membrane Protein Alignment

January 2011

We have submitted a paper about SToMP.

With the paper, we are releasing JSUBST and a set of SToMP tables to the public. These tables are, so far, proof-of-concept tables. Given a lot of time, these could potentially become much better still.

October 2010

SToMP tables can be generated from any set of PDB files within one day. Generating the tables themselves from the data is actually a matter of seconds/minutes. It is thus a simple matter to customise the structural environments for which one needs substitution tables.

October 2008

Statistical analysis of the tables show the expected behaviour, in most cases.

One example: “Lipid-exposed residues in transmembrane helices are very different from water-exposed residues in soluble or even membrane proteins.”

Another example: “Residues in contact with the polar head groups of the membrane lipids are less different from water-exposed residues than are the residues in contact with the hydrophobic lipid tail groups.”

I have presented a poster about this project at the ISMB 2008 conference and the associated 3Dsig satellite meeting in Toronto, Canada.


  1. -Pipeline to generate the data needed to make substitution tables (uses iMembrane)

  2. -JSUBST, the Java programme which generates the tables themselves from the above data (modified re-implementation of SUBST by Kenji Mizuguchi)

  3. -Analysis pipeline, which runs some simple statistical analyses on a set of substitution tables

  4. -Created membrane-specific modelling software MEDELLER, using the SToMP tables

  5. -More detailed analysis of the substitution tables, in collaboration with Jamie R. Hill

  6. -Proof-of-concept sequence-to-structure alignment (threading) using SToMP

  7. -Structure prediction with MEDELLER based on SToMP/FUGUE alignments

Web links:

  1. -Paper

  2. -JSUBST source code repository

  3. -Paper supplementary material and software download links

  4. -Software and Resources at the Oxford Protein Informatics Group

  5. -Oxford Protein Informatics Group

  6. -University of Oxford, UK