Abstract
Protein 3-dimensional structure prediction is determination of the 3-dimensional structure of a protein from its amino acid sequence by using protein structure prediction software. By understanding protein’s 3-dimensional structure, we should be able to figure out the function of the said protein. We already have several protein prediction software, but the purpose of this study is to determine how accurate they are, and if the results presented are true and to what extent. To determine how accurate protein 3-dimensional structure prediction software are, we compared x-ray crystallography determined protein structures to software predicted 3-dimensonal protein structures. All of the software used showed good accuracy, and according to our results, “i-Tasser” software was the most accurate, closely followed by RaptorX.
Highlights
Proteins 3-dimensional structure prediction is a process of determining the 3-dimensonal folded structure of the protein based on its amino acid composition and interaction between those amino acids
SuperPose results are given as RMSD value or Root Mean Square Deviation, the measure of the average distance between the atoms of superimposed proteins
The accuracy was lower than expected, but it happened in one software but two or more which leads me to think that the protein structure was too complex for a 3-dimensional prediction software to process
Summary
Proteins 3-dimensional structure prediction is a process of determining the 3-dimensonal folded structure of the protein based on its amino acid composition and interaction between those amino acids. Product of translation process in the cell is a linear chain of amino acids which is not yet functional but it becomes functional only when it is assumes its fully folded conformation. This linear chain will have to pass through several folds, to become fully functional. We got new insights into protein folding and we are able to harness all the processing power of the computers and programming to develop structure prediction software, right after learning more about how amino acids interacted with one another. It’s much cheaper and faster using computers, and once the prediction becomes reliable enough it may reduce the time spent in the laboratory
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