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To understand how photoactive proteins function, it is necessary to understand the photoresponse of the chromophore. Photoactive yellow protein (PYP) is a prototypical signaling protein. Blue light triggers trans–cis isomerization of the chromophore covalently bound within PYP as the first step in a photocycle that results in the host bacterium moving away from potentially harmful light. At higher...
Prediction of functionally important amino acids in protein structures is challenging problem in the area of protein function prediction. In the quest of looking for better machine learning approaches to address this problem, we have compared a support vector machine and a neural network trained with a particle swarm algorithm (PSO) to nonlinearly combine a subset of features selected from a set of...
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