Analysis and prediction of protein local structure based on

. For each sequence segment, these substructures are its “specific structural alphabet”. The smaller these candidate lists are, the faster the protein structure can be constructed; the more accurate these candidate lists are, the more accurate the final protein structure will be. A major obstacle in protein

Abstract not found

Motivation: The 3D structure of a protein sequence can be assembled from the substructures corresponding to small segments of this sequence. For each small sequence segment, there are only a few more likely substructures. We call them the ‘structural alphabet ’ for this segment. Classical

key words: secondary structure, structure-sequence relationship, ab initio.

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GSATools: analysis of allosteric communication and functional

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alphabet. Such a model learns simultaneously the shape of representative structural letters describing the local conformation and the logic of their connections, i.e. the transition matrix between the letters. Here, we move one step further and report some evidence that such a model of protein local

Loops connect regular secondary structures. In many instances, they are known to play crucial biological roles. To bypass the limitation of secondary structure description, we previously defined a structural alphabet composed of 16 structural prototypes, called Protein Blocks (PBs). It leads