Dear All,

Here is a short update on the HCMD project:

- We improved the MAXDO code (this is the program running on the grid). The MAXDO code has been improved so that the receptor and ligand proteins are now treated symmetrically during the energy minimization process. As a consequence, the docking of two proteins is about 4 to 5 times faster than in the previous version of the program.

- We finished the implementation and optimization of JET (this is the program which will predict the positions of the protein interfaces) for interfacing it with MAXDO. Running JET predictions before MAXDO is crucial because of the large computational time that docking is taking. By predicting in advance the protein interfaces, we are able to reduce greatly the surface region to be investigated with MAXDO on your machines.

- Right now, we are working on the interface between the two programs, JET and MAXDO. There are two problems that we are dealing with right now: 1) We want to estimate the surface of a protein that we need to dock, based on JET predition, to be sure to have enough information to discriminate correct partners. 2) We want to develop a numerical criteria that, based on JET predictions and MAXDO analysis, discriminates correct partners. This criteria will follow the one that we have developed during phase 1 and that was based on real interface information.

- As soon as the interface problems are done, we shall make the last refinements to the MAXDO code. This will take about a week of testing and then we will deliver the code to World Community Grid.

- Last but not least, we are collecting from French scientists interested in the project a set of proteins important for muscular dystrophy which will be tested on phase 2. In phase 2 we shall look for protein partners for our target proteins within a very large dataset of potential candidates.

Looking forward to working with you very soon on the project.

Very best regards to All,

Alessandra