Download Computational Methods for Protein Structure Prediction and by Ying Xu, Dong Xu, Jie Liang PDF

By Ying Xu, Dong Xu, Jie Liang

Quantity of this two-volume series provides a accomplished evaluate of protein constitution prediction equipment and comprises protein threading, De novo tools, purposes to membrane proteins and protein complexes, structure-based drug layout, in addition to constitution prediction as a platforms challenge. a chain of appendices evaluate the organic and chemical fundamentals concerning protein constitution, computing device technology for structural informatics, and prerequisite arithmetic and facts.

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Additional info for Computational Methods for Protein Structure Prediction and Modeling: Volume 2: Structure Prediction (Biological and Medical Physics, Biomedical Engineering)

Sample text

To make prediction more accurate, some threading programs employ a two-stage strategy: (a) thread a query sequence against a representative structure database and to identify a few possible native-like structures, and (b) thread the query sequence against all family/superfamily members of the identified structures in (a). Certain preprocessing of the template database might be needed for some threading programs. 4, protein structure needs to be represented as structure graphs as required by the threading algorithm.

For simplicity of discussion, we can regard the length of the longer one to be infinite. It is not hard to convince ourselves that for a randomly selected DNA sequence, its best (local) alignment with the longer sequence will have a higher probability to have a better score than with the shorter sequence. The reason is that the longer sequence, by chance, should have a higher probability to have portions of its sequence similar to the query sequence, compared to the shorter sequence. This indicates that the background alignment-score distributions for the two "template" sequences are different.

2 depicts schematically the situation where each of the two substructures has a number ofstructural positions, which are close enough to structural positions in the other substructure so that their alignments with amino acids need to be considered when calculating the interaction energy in the other substructure. These structural positions can be considered as extended parts of the other substructure (shown as extended arms for each substructure in Fig. 2). The difference between these extended parts and the original positions ofa substructure is that when doing alignment 12.

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