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This chapter discusses differences between two ideal structures versus those involving two similar nonsymmetry‐equivalent surroundings .The symmetry argument predicts nonequivalence of molecular structure whenever its immediate environment is varied. One should always remember that molecular structure is based on an ensemble of atoms that continually vibrate around their well‐defined equilibrium positions...
The Protein Residue Distance & Angle Distribution Database for Secondary Structures (PRDDs) is a dedicated database and structural bioinformatics system for protein analysis and modeling. The database is developed to host and analyze the statistical data for protein residue level distances and angles (called virtual bonds, bond angles, and torsion angles) obtained from their distributions in databases...
This paper refines and introduces a modification to the Marriage in Honey Bee Optimisation algorithm (MBO). The modified algorithm was applied to predict the structure of Met-enkphaline using torsion angles representation and ECEPP/3 energy function. The results showed the significance of the modification. The algorithm was able to find the lowest reported free energy conformation of value -12.43...
Artificial bee colony algorithm (ABC) is a swarm intelligence based algorithm. It is inspired by the foraging behavior of honey bee colony. In this paper, the ABC algorithm was utilized to predict the tertiary structure of C-peptide of ribonuclease A by searching the conformational search space to locate the lowest free energy conformation. Conformations were represented using torsion angles representation...
A protein is characterized by its 3D structure,which defines its biological function. In this paper, we present a scatter search algorithm for predicting 3D structures of proteins based on torsion angles representation. Given the protein??s sequence of amino acids, our algorithm produces a 3D structure that aims to minimize the energy function associated with the structure. Scatter search is an evolutionary...
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