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With the explosion of protein sequences generated in the Post-Genomic Age, it is urgent to develop an automated method to predict protein quaternary structure. To explore this problem, we adopted an approach based on a sequence encoding descriptor by fusing PseAA (Pseudo Amino Acid) and DC (Dipeptide Composition) representing a protein sample. Here, a completely different approach, manifold learning...
This paper presents a novel priority based data mining algorithm using improved K-means clustering for detecting proteins sequence from dataset of frequent item set. The priorities are set depending on the number of hits (counts) from the dataset concurrently using the concept of multiprocessing. Which dynamically changing for a period of time series, a novel algorithm is used for classification and...
MicroRNAs are one type of noncoding RNA that regulate their target mRNAs before mRNAs are translated into proteins. Although it has been demonstrated that the regulation is through partial binding of the seed region of a miRNA and its targets, the mechanism of this process is not fully discovered. Some biological experiments have shown that even perfect base pairing in the seed region does not always...
We propose a binary matrix factorization (BMF) algorithm under the Bayesian Ying-Yang (BYY) harmony learning, to detect protein complexes by clustering the proteins which share similar interactions through factorizing the binary adjacent matrix of the protein-protein interaction (PPI) network. The proposed BYY-BMF algorithm automatically determines the cluster number while this number is usually specified...
Abstract-Prediction of protein-proteininteraction sites is very important to the function of a protein and drug design. In this paper, we adequately utilize the characters of ensemble learning, which can improve the accuracy of individual classifier and generalization ability of the system, and propose a new prediction method of protein-protein interaction sites: ensemble learning method based on...
Studies of intrinsically disordered proteins that lack a stable tertiary structure but still have important biological functions critically rely on computational methods that predict this property based on sequence information. Although a number of fairly successful models for prediction of protein disorder were developed over the last decade, the quality of their predictions is limited by available...
Recent studies showed that protein-protein interaction network based features can significantly improve the prediction of protein subcellular localization. However, it is unclear whether network prediction models or other types of protein-protein correlation networks would also improve localization prediction. We present NetLoc, a novel diffusion kernel-based logistic regression (KLR) algorithm for...
In this paper, we present a method based on mining maximal frequent patterns for core-attachment complexes identification in yeast protein-protein interaction networks (PINs). Our method contains of two stages. Firstly, it finds all the protein-complex cores by mining maximal frequent patterns in PIN using FP-growth method. Then it filters the redundant cores and adds the attachment proteins for each...
Understanding the metabolism of new species (e.g. endophytic fungi that produce fuel) have tremendous impact on human lives. Based on predicted proteins and existing reaction databases, one can construct the metabolic network for the species. Next is to identify critical metabolic pathways from the network. Existing computational techniques identify conserved pathways based on multiple networks of...
Protein complexes are important entities to organize various biological systems. However, they are still limited in availability. Thus, it is a challenging problem to predict protein complexes computationally from existing genome-wide data sets, like protein-protein interaction (PPI) networks. In this paper, we propose an efficient algorithm for predicting protein complexes by random walking on a...
Recent high-throughput experimental methods have generated protein-protein interaction data in the genome scale, called interactome. Various graph clustering algorithms have been applied to the protein interactome networks for identifying protein complexes and predicting functional modules. Although the previous algorithms are scalable and robust, their accuracy is still limited because of complex...
New technological advances in large-scale protein-protein interaction (PPI) detection provide researchers a valuable source for elucidating the bimolecular mechanism in the cell. In this paper, we investigate the problem of protein complex detection from noisy protein interaction data, i.e., finding the subsets of proteins that are closely coupled via protein interactions. Many people try to solve...
Protein structure prediction is one of the most important problems in bioinformatics and structural biology. This work proposes a novel and suitable methodology to model protein structure prediction with atomic-level detail by using a parallel multi-objective ab initio approach. In the proposed model, i) A trigonometric representation is used to compute backbone and side-chain torsion angles of protein...
High throughput experimental methods which detect protein-protein interactions have generated large datasets offering a first estimation and representation of an organism's protein interaction network. However, there is still lack of information concerning protein complexes, although many automated methods have been applied to this problem. In this paper, a new hierarchical clustering algorithm, called...
Protein secondary structure prediction is a fundamental and important component in the analytical study of protein structure and functions. Using the pseudo amino acid (PseAA) composition to represent the sample of a protein can incorporate a considerable amount of sequence pattern information so as to improve the prediction quality for its structural or functional classification. In this paper, the...
The identification of protein-protein interface residues is essential for drug design, understanding cell activity of organism. In this paper, a couple of covering algorithms are presented to predict protein-protein interaction sites by using several protein features, such as sequence profile, residue entropy and so on. These features are utilized to construct covering algorithms classifiers to identify...
As more and more high-throughput protein-protein interactions data are collected, a large fraction of newly discovered proteins have an unknown functional role. A challenge to the scientific community is to assign these newly proteins with a biological function that can be verified by experiment. On the basis of thorough analysis of existing protein function prediction, we take double direction enumeration...
G-Protein coupled receptors (GPCRs) constitute the largest group of membrane receptors with great pharmacological interest. The signal transduction within cells is leaded by a wide range of native ligands interact and activate GPCRs. Most of these responses are mediated through the interaction of GPCRs with coupling GTP-binding proteins (G-proteins). For the reason of the information explosion in...
Clustering protein-protein interaction network aims to find functional modules and protein complexes. There are many computational graph clustering methods that are used in this field, but few of them are intelligent computational methods. In this paper, we present a novel improved immune genetic algorithm to find dense subgraphs based on efficient vaccination method, variable-length antibody schema...
Protein phosphorylation is a reversible post-translational modification commonly used by cell signaling networks to transmit information about the extracellular environment into intracellular organelles for the regulation of the activity and sorting of proteins within the cell. For this study we reconstructed a literature-based mammalian kinase-substrate network from several online resources. The...
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