Abstract
Effective prediction of protein tertiary structure from sequence is an important and challenging problem in computational structural biology. Ab initio protein structure prediction is based on amino acid sequence alone, thus, it has a wide application area. With the ab initio method, a large number of candidate protein structures called decoy set can be predicted, however, it is a difficult problem to select a good near-native structure from the predicted decoy set. In this work we propose a new method for selecting the near-native structure from the decoy set based on both contact map overlap (CMO) and graphlets. By generalizing graphlets to ordered graphs, and using a dynamic programming to select the optimal alignment with an introduced gap penalty, a GR_score is defined for calculating the similarity between the three-dimensional (3D) decoy structures. The proposed method was applied to all 54 single-domain targets in CASP11 and all 43 targets in CASP10, and ensemble clustering was used to cluster the protein decoy structures based on the computed CR_scores. The most popular centroid structure was selected as the near-native structure. The experiments showed that compared to the SPICKER method, which is used in I-TASSER, the proposed method can usually select better near-native structures in terms of the similarity between the selected structure and the true native structure.
Highlights
The human genome project was first proposed by American scientists in 1985 and officially launched in 1990 [1]
Since the function of genes can be studied via the study of the corresponding proteins produced through gene expression, the use of bioinformatics to discover the function of a protein product of a gene becomes more and more significant
Since the function of proteins is determined by its tertiary structure, the prediction of tertiary structure based on protein sequences is a very important problem
Summary
The human genome project was first proposed by American scientists in 1985 and officially launched in 1990 [1]. Its purpose is to determine the nucleotide sequence consisting of three billion base pairs contained in a human chromosome, thereby mapping the human genome and identifying the genes and their sequences to decipher humans. With the completion of the program, the gene sequence can be obtained by measuring the obtained map, and the sequence of the corresponding protein can be inferred using the genetic central dogma [2]. Determining protein functions from genomic sequences is a central goal of bioinformatics [3]. Since the function of proteins is determined by its tertiary structure, the prediction of tertiary structure based on protein sequences is a very important problem
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