 Introduction HYDRA is a multi-objective optimization-based de novo protein design method, which is implemented in a new quantified and continuous sequence space.We use two different energy functions to evaluate the decoy sequences simultaneously, and aided by the prior information collected from DSSP and PDB data base, a space transformation procedure is conducted in each iteration.In the new ordered sequence space, the searching process will be boosted dramatically. When the algorithm converges, final solutions will be selected from the pareto set(undominated solutions).Flowchart of HYDRA is shown in figure1
Fig. 1. Flow chart of HYDRA. Code The data and code are contained in the following compressed files: Click here to download the HYDRA stand alone version package,here to download the database. Unzip the "database.zip" and copy two folders "pdbbase" and "dsspbase" into folder "HYDRA". Hydra runs on Linux, matlab and python numpy should be installed 1UBQ protein designed by Hydra is expressed and purified,its structure file solved using NMR can be downloaded here Click here to download the file. Reference to be continued |
