Abstract:
:Drug-target interaction (DTI) prediction is a challenging step in further drug repositioning, drug discovery and drug design. The advent of high-throughput technologies brings convenience to the development of DTI prediction methods. With the generation of a high number of data sets, many mathematical models and computational algorithms have been developed to identify the potential drug-target pairs. However, most existing methods are proposed based on the single view data. By integrating the drug and target data from different views, we aim to get more stable and accurate prediction results. In this paper, a multiview DTI prediction method based on clustering is proposed. We first introduce a model for single view drug-target data. The model is formulated as an optimization problem, which aims to identify the clusters in both drug similarity network and target protein similarity network, and at the same time make the clusters with more known DTIs be connected together. Then the model is extended to multiview network data by maximizing the consistency of the clusters in each view. An approximation method is proposed to solve the optimization problem. We apply the proposed algorithms to two views of data. Comparisons with some existing algorithms show that the multiview DTI prediction algorithm can produce more accurate predictions. For the considered data set, we finally predict 54 possible DTIs. From the similarity analysis of the drugs/targets, enrichment analysis of DTIs and genes in each cluster, it is shown that the predicted DTIs have a high possibility to be true.
journal_name
Comput Biol Chemjournal_title
Computational biology and chemistryauthors
Zhang X,Li L,Ng MK,Zhang Sdoi
10.1016/j.compbiolchem.2017.03.011subject
Has Abstractpub_date
2017-08-01 00:00:00pages
185-193eissn
1476-9271issn
1476-928Xpii
S1476-9271(17)30195-0journal_volume
69pub_type
杂志文章abstract::Receptor Tyrosine Kinase inhibitors are the most popular anti-cancer drug types. But the resistance is the major challenge. Our study on the network with 1334 proteins and their 2623 interactions which retrieved from 52 RTKs indicated that most RTKs proteins were the key controllers of the protein-protein network. Dir...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2018.07.017
更新日期:2018-10-01 00:00:00
abstract::The QSAR models for a set of pyrazolo[4,3-e][1,2,4]triazines incorporating benzenesulfonamide moiety combined directly with the heterocyclic ring or by NH linkage were generated. The inhibitory potency of compounds against human carbonic anhydrase isoforms IX and XII and antiproliferative activity against human MCF-7 ...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2017.09.006
更新日期:2017-12-01 00:00:00
abstract::Programmed frameshifting is a recoding event in which a ribosome shifts reading frame by one or more nucleotides at a specific mRNA signal between overlapping genes. Programmed frameshifting is involved in the expression of many genes in a wide range of organisms, especially in viruses and bacteria. The mechanism of p...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2007.05.004
更新日期:2007-08-01 00:00:00
abstract::Shortest common supersequence (SCS) is a classical NP-hard problem, where a string to be constructed that is the supersequence of a given string set. The SCS problem has an enormous application of data compression, query optimization in the database and different bioinformatics activities. Due to NP-hardness, the exac...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2016.05.004
更新日期:2016-10-01 00:00:00
abstract::2-phenyl-benzotriazole xenobiotic compounds (PBTA-4, PBTA-6, PBTA-7 and PBTA-8) that were previously isolated and identified in waters of the Yodo river, in Japan (Nukaya et al., 2001; Ohe et al., 2004; Watanabe et al., 2001) were characterized as powerful pro-mutagens. In order to predict the activation mechanism of ...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2018.04.004
更新日期:2018-06-01 00:00:00
abstract::Blood-feeding animals are known for their ability to produce bioactive compounds to impair haemostasis and suppress pain perception in the host. These compounds are extremely appealing for pharmacological development since they are generally very effective and specific for their molecular target. A preliminary RNA-Seq...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2018.05.014
更新日期:2018-08-01 00:00:00
abstract::Magnesium (Mg) is an important micronutrient for various physiological processes in plants. In this study, putative Magnesium Transporter (MGT) genes have been identified in Solanum lycopersicum, Solanum tuberosum, Brachypodium distachyon, Fagaria vesca, Brassica juncea and were classified into 5 distinct groups based...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2019.05.014
更新日期:2019-06-01 00:00:00
abstract::The Egyptian flora is rich with a large number of Triticum plants, which are very difficult to discriminate between in the early developmental stages. This study assesses the significance of using two DNA Barcoding loci (matK and rbcL) in distinguishing between 18 different Triticum accessions in Egypt. We isolated an...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2017.09.003
更新日期:2017-12-01 00:00:00
abstract::Our ability to detect differentially expressed genes in a microarray experiment can be hampered when the number of biological samples of interest is limited. In this situation, we propose the use of information from self-self hybridizations to acuminate our inference of differential expression. A unified modelling str...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2007.03.005
更新日期:2007-06-01 00:00:00
abstract::Cyclin-Dependent Kinases (CDKs) are known to play crucial roles in controlling cell cycle progression of eukaryotic cell and inhibition of their activity has long been considered as potential strategy in anti-cancer drug research. In the present work, a series of porphyrin-anthraquinone hybrids bearing meso-substituen...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2016.12.005
更新日期:2017-04-01 00:00:00
abstract::Various subsets of self-avoiding walks naturally appear when investigating existing methods designed to predict the 3D conformation of a protein of interest. Two such subsets, namely the folded and the unfoldable self-avoiding walks, are studied computationally in this article. We show that these two sets are equal an...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2013.10.001
更新日期:2013-12-01 00:00:00
abstract::Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disorder, and its pathogenesis in males and in cases without accompanying lupus nephritis (LN-) is not fully understood. In this study, we identified 90 (82 up- and 8 downregulated) differentially expressed genes (DEGs) common to female LN-, female LN+ a...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2019.107135
更新日期:2019-12-01 00:00:00
abstract::Human Leukocyte Antigens (HLA) are highly polymorphic proteins that play a key role in the immune system. HLA molecule is present on the cell membrane of antigen-presenting cells of the immune system and presents short peptides, originating from the proteins of invading pathogens or self-proteins, to the T-cell Recept...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2016.02.019
更新日期:2016-06-01 00:00:00
abstract::We report ligand field molecular mechanics, density functional theory and semi-empirical studies on the binding of Cu(II) to GlyHisLys (GHK) peptide. Following exhaustive conformational searching using molecular mechanics, we show that relative energy and geometry of conformations are in good agreement between GFN2-xT...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2020.107265
更新日期:2020-06-01 00:00:00
abstract::Relative amino acid residue solvent accessibility values allow the quantitative comparison of atomic solvent-accessible surface areas in different residue types and physical environments in proteins and in protein structural alignments. Geometry-optimised tri-peptide structures in extended solvent-exposed reference co...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2014.11.007
更新日期:2015-02-01 00:00:00
abstract::Archaea represent an important and vast domain of life. This cellular domain includes a large diversity of organisms characterized as prokaryotes with basal transcriptional machinery similar to eukarya. In this work we explore the most recent findings concerning the transcriptional regulatory organization in archaeal ...
journal_title:Computational biology and chemistry
pub_type: 杂志文章,评审
doi:10.1016/j.compbiolchem.2011.10.006
更新日期:2011-12-14 00:00:00
abstract::G protein-coupled receptors (GPCRs), a large eukaryotic protein family, have proved difficult to comprehensively detect and functionally identify by homology searches and domain detection, because they are highly divergent and their sequences share strikingly little similarity. Transmembrane (TM) topology pattern anal...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2003.11.003
更新日期:2004-02-01 00:00:00
abstract::Detection of protein complexes is very important to understand the principles of cellular organization and function. Recently, large protein-protein interactions (PPIs) networks have become available using high-throughput experimental techniques. These networks make it possible to develop computational methods for pro...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2015.07.012
更新日期:2015-10-01 00:00:00
abstract::A computational inestigation on the difference in colors of two plants 'Peony' and 'Morning glory' by the same pigment 'Peonidin' has been performed by means of absorption characteristics. Peonidin imparts purple color to the flowers in Peony and blue to that in Morning glory. TDDFT tool in Gaussian 09 software packag...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2018.07.015
更新日期:2018-10-01 00:00:00
abstract::The long perceived notion that G-Protein Coupled Receptors (GPCRs) function in monomeric form has recently been changed by the description of a number of GPCRs that are found in oligomeric states. The mechanism of GPCR oligomerization, and its effect on receptor function, is not well understood. In the present study, ...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2013.11.002
更新日期:2014-02-01 00:00:00
abstract::Microarray technology has been widely applied in study of measuring gene expression levels for thousands of genes simultaneously. Gene cluster analysis is found useful for discovering the function of gene because co-expressed genes are likely to share the same biological function. K-means is one of well-known clusteri...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2008.03.020
更新日期:2008-08-01 00:00:00
abstract::Bio-entity name recognition is the key step for information extraction from biomedical literature. This paper presents a dictionary-based bio-entity name recognition approach. The approach expands the bio-entity name dictionary via the Abbreviation Definitions identifying algorithm, improves the recall rate through th...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2008.03.008
更新日期:2008-08-01 00:00:00
abstract::MicroRNAs are important negative regulators of gene expression in higher eukaryotes. The miRNA repertoire of the closest human animal relative, the chimpanzee (Pan troglodytes), is largely unknown. In this study, we focused on computational search of novel miRNA homologs in chimpanzee. We have searched and analyzed th...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2008.07.024
更新日期:2009-02-01 00:00:00
abstract::The occurrence of similar structural repeats in a protein structure has evolved through gene duplication. These repeats act as a structural building block and form more than one compact structural and functional unit called a repeat domain. The protein families comprising similar structural repeats are mainly involved...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2010.03.006
更新日期:2010-04-01 00:00:00
abstract::Cytosine methylation is one of the most important RNA epigenetic modifications. With the development of experimental technology, scientists attach more importance to RNA cytosine methylation and find bisulfite sequencing is an effective experimental method for RNA cytosine methylation study. However, there are only a ...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2016.09.003
更新日期:2016-12-01 00:00:00
abstract::Nicotinamidase is a key enzyme for the salvage pathway catalyzing the first step for the conversion of nicotinamide (NAm) to nicotinic acid (NA) required for the synthesis of Nicotinamide Adenine Dinucleotide (NAD+) in the subsequent steps. Leishmania protozoan parasites are NAD+ auxotrophs and need precursors (nicoti...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2019.107150
更新日期:2019-12-01 00:00:00
abstract::The Monty Hall problem is a decision problem with an answer that is surprisingly counter-intuitive yet provably correct. Here we simulate and prove this decision in a high-throughput DNA sequencing machine, using a simple encoding. All possible scenarios are represented by DNA oligonucleotides, and gameplay decisions ...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2019.107122
更新日期:2019-12-01 00:00:00
abstract::The P-type ATPases (P-ATPases) are present in all living cells where they mediate ion transport across membranes on the expense of ATP hydrolysis. Different ions which are transported by these pumps are protons like calcium, sodium, potassium, and heavy metals such as manganese, iron, copper, and zinc. Maintenance of ...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2017.04.006
更新日期:2017-06-01 00:00:00
abstract::Successful prediction of protein domain boundaries provides valuable information not only for the computational structure prediction of multi-domain proteins but also for the experimental structure determination. In this work, a novel index at the profile level is presented, namely, the profile domain linker propensit...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2006.01.001
更新日期:2006-04-01 00:00:00
abstract::In this study, the dipeptidyl peptidase-IV (DPP-IV) inhibition activities of a series of novel aminomethyl-piperidones were investigated by molecular docking studies and modeled by quantitative structure-activity relationship (QSAR) methodology. Molecular docking studies were used to find the best conformations of the...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2016.08.003
更新日期:2016-10-01 00:00:00