Version 1.1
This web server provides access to a series of tools for ab initio protein structure prediction based on Hydrophobic-Polar (HP) model. To start using it, please select from the listings below, or use the menu on the Top with title ECO (Evolutionary combinatorial optimization) Tools. Select the tool you prefer and download it. If you use our tools for research or education, please cite the article from the 'Publications' section.
MMAH implements a systematic and problem specific design for operators of the evolutionary program which hybrids with local search hill-climbing, a 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 the triangular lattice. This folding implements the modeling method of classic HP model as well as the 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.
HhPN is extended version of basic HP model with inclusion of following physiochemical properties carbon content, disulfide bond, hydrophobicity scale, codon frequency and BLOSUM62 similarity matrix. With which we propose a novel enhanced energy function ‘HhPN’. It takes input in the form of a sequence of 0,1,2,3, highly hydrophobic, partially hydrophobic, polar positive and polar negative respectively. It folds the sequence based on the constituting amino acids propensities towards the secondary structural motif.
Init-Pop calculates initial conformations. They followed the constraint programming such that it generates only valid non-cyclic conformations. The results of this tool can be used by any of the metaheuristics algorithm such as Genetic algorithm, Ant colony optimization, Immune algorithm, Monte Carlo algorithm, etc., where the conformation generated using Init-Pop are subjected for the further optimization.
HP Depiction can be used to visualize the protein conformation on a 2D square lattice. A user needs to pass the HP sequence or binary sequence and movement direction to be followed. Movement direction is from the set of {N, S, E, W} where they represent the movement direction. N for north direction movement (Upward move), S for south direction movement (Downward move), E for east direction movement (Forward move), and W for West direction movement (Backward move), allows for the interactive visualization of lattice protein structures in the HP-model. The program is HP depiction.