MMAH

MMAH

MMAH implements a systematic and problem specific design for operators of the evolutionary program which hybrids with local search hill-climbing, the namely memetic algorithm (MMAH) to efficiently explore the search space of the PSP. It provides two options to folds the protein primary sequence onto 2D square as well as on the triangular lattice. This folding implements the modeling method of classic HP model as well as a functional model. Input can be either in the form of Fasta sequence or binary sequence where 1 represents the hydrophobic whereas 0 for polar amino acid.

 

Sample Uses:
 

9INS:A|PDBID|CHAIN|SEQUENCE GIVEQCCTSICSLYQLENYCN (Copy and paste the sequence in text box labeled Protein Sequence in the executable file) above is the protein sequence (Fasta format) downloaded from the Protein Databank.

One of the modeled confirmation is presented below: Green encircle bead represents the first residue where last is encircle in blue color. Before folding tool converts the primary sequence into binary sequence {0,1}. 0 for Polar residue shown in blue color and 1 for hydrophobic residue shown in red color. Hydrophobic interaction is shown with a yellow line. S pattern in conformation represents the helix, sheet using a straight line with a minimum of five beads and any other pattern of fold excluding these two considered as a turn.

 
 

Also, a user can pass binary input; in this case program need not perform the conversion, it directly performs the folding.