The protein folding problem is a critical puzzle in biology, focusing on unraveling how a linear sequence of amino acids organizes into its functional,three-dimensional structure. Proteins are vital molecules in living organisms, carrying out essential biological functions, and their precise folding is crucial for proper functionality. The process involves intricate interactions between amino acids, influenced by physicochemical properties and environmental conditions. Predicting the final folded structure accurately is challenging due to the vast conformational space proteins can explore. Understanding protein folding has broad implications for drug development, structural biology, and disease research, as misfolded proteins can lead to various disorders. Experimental and computational methods are employed to study protein folding, but accurately predicting structures from sequences remains a complex and unsolved problem with significant implications for biology and medicine.
Here it is a list of important amino-acids in this link , choose the amino-acids you want to use and download its jason from this link and put jasons in this directory
for solving this problem we used genetic algorithm, having 3 population (HowSulfurCombined,HowTheyCombined,HowRotationAndDeltaOccured) we used linear multi-population optimization.
to find your optimized molecule download files in this link https://drive.google.com/file/d/1pYKXACVMCKPd5nOSfTGSqNLNgEauYnuh/view?usp=sharing and together with files in this repository put them in a directory then load the docker image
sudo docker load < HW2Image
sudo docker run -it -v ./:/Libraries --entrypoint bash chargefw2
cd Libraries/
cd Help/
and run main.py
python3 main.py
your molecule would be saved as a .pdb file in this directory if you want to see how does your molecule look like upload your .pdb file in this jupyter notebook and run it!
