当前位置： SCI文献检索 > COMPUTATIONAL BIOLOGY AND CHEMISTRY期刊下所有文献 > Semantically predicting protein functions based on protein functional connectivity.

Semantically predicting protein functions based on protein functional connectivity.

Abstract：

BACKGROUND:The current availability of public protein-protein interaction (PPI) databases which are usually modelled as PPI networks has led to the rapid development of protein function prediction approaches. The existing network-based prediction approaches mainly focus on the topological similarities between immediately interacting proteins, neglecting the protein functional connectivity which is the functional tightness between proteins. In this paper, we attempt to predict the functions of unannotated proteins based on PPI networks by incorporating the protein functional connectivity, as well as the similarity of protein functions, into the prediction procedure. RESULTS:An approach named Semantic protein function Prediction based on protein Functional Connectivity (SPFC) is proposed to achieve a higher accuracy in predicting functions of unannotated protein. We define the functional connectivity and function addition for each protein, and incorporate them into the prediction. We evaluated the SPFC on real PPI datasets and the experiment results show that the SPFC method is more effective in function prediction than other network-based approaches. CONCLUSION:Incorporating the functional connectivity of each protein into the function prediction can significantly improve the accuracy of protein prediction.

journal_name

Comput Biol Chem

journal_title

Computational biology and chemistry

authors

Zhu W,Hou J,Chen YP

doi

10.1016/j.compbiolchem.2013.01.002

subject

Has Abstract

pub_date

2013-06-01 00:00:00

pages

9-14

eissn

1476-9271

issn

1476-928X

pii

S1476-9271(13)00004-2

journal_volume

44

pub_type

杂志文章

相关文献

COMPUTATIONAL BIOLOGY AND CHEMISTRY文献大全
  • Integrating pharmacophore mapping, virtual screening, density functional theory, molecular simulation towards the discovery of novel apolipoprotein (apoE ε4) inhibitors.

    abstract：AIM:An integrated protocol of virtual screening involving molecular docking, pharmacophore probing, and simulations was established to identify small novel molecules targeting crucial residues involved in the variant apoE ε4 to mimic its behavior as apoE2 thereby eliminating the amyloid plaque accumulation and facilita...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2018.12.013

    authors： Johari S,Sharma A,Sinha S,Das A

    更新日期：2019-04-01 00:00:00

  • A novel k-word relative measure for sequence comparison.

    abstract：:In order to extract phylogenetic information from DNA sequences, the new normalized k-word average relative distance is proposed in this paper. The proposed measure was tested by discriminate analysis and phylogenetic analysis. The phylogenetic trees based on the Manhattan distance measure are reconstructed with k ran...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2014.10.007

    authors： Tang J,Hua K,Chen M,Zhang R,Xie X

    更新日期：2014-12-01 00:00:00

  • A pore creation in a triangular network model membrane.

    abstract：:Membrane electroporation seems to be a useful method for delivery of biological active compounds into the cell. Although it is known that this phenomenon is sensitive to the electric field intensity, duration of the electric pulse and its shape, it is not fully understood. In some theoretical descriptions it is postul...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2008.02.001

    authors： Kubica K

    更新日期：2008-06-01 00:00:00

  • Exploiting the performance of dictionary-based bio-entity name recognition in biomedical literature.

    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

    authors： Yang Z,Lin H,Li Y

    更新日期：2008-08-01 00:00:00

  • Computational identification of novel microRNA homologs in the chimpanzee genome.

    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

    authors： Baev V,Daskalova E,Minkov I

    更新日期：2009-02-01 00:00:00

  • The interactome of CCT complex - A computational analysis.

    abstract：:The eukaryotic chaperonin, CCT (Chaperonin Containing TCP1 or TriC-TCP-1 Ring Complex) has been subjected to physical and genetic analyses in S. cerevisiae which can be extrapolated to human CCT (hCCT), owing to its structural and functional similarities with yeast CCT (yCCT). Studies on hCCT and its interactome acqui...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2016.09.002

    authors： Narayanan A,Pullepu D,Kabir MA

    更新日期：2016-10-01 00:00:00

  • Identification and characterization of differentially expressed genes in Type 2 Diabetes using in silico approach.

    abstract：:Diabetes mellitus is clinically characterized by hyperglycemia. Though many studies have been done to understand the mechanism of Type 2 Diabetes (T2D), however, the complete network of diabetes and its associated disorders through polygenic involvement is still under debate. The present study designed to re-analyze p...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2019.01.010

    authors： Gupta MK,Vadde R

    更新日期：2019-04-01 00:00:00

  • In silico pharmacophore modeling and simulation studies for searching potent antileishmanials targeted against Leishmania donovani nicotinamidase.

    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

    authors： Chauhan N,Poddar R

    更新日期：2019-12-01 00:00:00

  • Computational insight into the phthalocyanine-DNA binding via docking and molecular dynamics simulations.

    abstract：:Phthalocyanines are considered as good DNA binders, which makes them promising anti-tumor drug leads. The purpose of this study is to investigate the interactions between DNA and quaternary metallophthalocyanine derivatives (Q-MPc) possessing varying metals (M = Zn, Ni, Cu, Fe, Mg and Ca) by molecular docking since th...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2018.09.009

    authors： Ozalp L,Sağ Erdem S,Yüce-Dursun B,Mutlu Ö,Özbil M

    更新日期：2018-12-01 00:00:00

  • A class imbalance-aware Relief algorithm for the classification of tumors using microarray gene expression data.

    abstract：:DNA microarray data has been widely used in cancer research due to the significant advantage helped to successfully distinguish between tumor classes. However, typical gene expression data usually presents a high-dimensional imbalanced characteristic, which poses severe challenge for traditional machine learning metho...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2019.03.017

    authors： He Y,Zhou J,Lin Y,Zhu T

    更新日期：2019-06-01 00:00:00

  • Predicting interspecies transmission of avian influenza virus based on wavelet packet decomposition.

    abstract：:Using wavelet packet decomposition, the energy coefficients in the fifth level of viral protein sequences were achieved to predict interspecies transmission. Since avian-origin influenza viruses could have high sequence similarities with human-origin avian influenza virus and could have the phenotype of interspecies t...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2018.11.029

    authors： Qiang X,Kou Z

    更新日期：2019-02-01 00:00:00

  • WITHDRAWN: Identification of microRNA precursor based on gapped n-tuple structure status composition kernel.

    abstract：:This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy. ...

    journal_title：Computational biology and chemistry

    pub_type： 撤回出版物

    doi：10.1016/j.compbiolchem.2016.02.010

    authors： Liu B,Fang L

    更新日期：2016-02-17 00:00:00

  • Indole-derived chalcones as anti-dermatophyte agents: In vitro evaluation and in silico study.

    abstract：:A series of indole-derived methoxylated chalcones were described as anti-dermatophyte agents. The in vitro antifungal susceptibility testing against different dermatophytes revealed that most of compounds had potent activity against the dermatophyte strains. In particular, the 4-ethoxy derivative 4d with MIC values of...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2019.107189

    authors： Mirzaei H,Abastabar M,Emami S

    更新日期：2020-02-01 00:00:00

  • Analysis of compensatory substitution and gene evolution on the MAGEA/CSAG-palindrome of the primate X chromosomes.

    abstract：:The human X chromosome contains a large number of inverted repeat DNA palindromes. Although arbitrary substitutions destroyed the inverted repeat structure of MAGEA/CSAG-palindrome during the evolutionary process of the primates, most of the substitutions are compensatory. Using maximum parsimony, it is demonstrated t...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2012.11.002

    authors： Qi Y,Lu H,Ai D

    更新日期：2013-02-01 00:00:00

  • Cytochrome P450 2C9 polymorphism: Effect of amino acid substitutions on protein flexibility in the presence of tamoxifen.

    abstract：:Tamoxifen is a prodrug and cytochrome P450 2C9 (CYP2C9) has a significant role in the formation of a therapeutically more potent metabolite (4-hydroxytamoxifen) than tamoxifen. Since CYP2C9 exhibits genetic polymorphism, it may contribute to different phenotypic drug response. Moreover, it may be misleading if the pos...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2019.107166

    authors： Manish M,Lynn AM,Mishra S

    更新日期：2020-02-01 00:00:00

  • The anesthetic action of some polyhalogenated ethers-Monte Carlo method based QSAR study.

    abstract：:Up to this date, there has been an ongoing debate about the mode of action of general anesthetics, which have postulated many biological sites as targets for their action. However, postoperative nausea and vomiting are common problems in which inhalational agents may have a role in their development. When a mode of ac...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2018.04.009

    authors： Golubović M,Lazarević M,Zlatanović D,Krtinić D,Stoičkov V,Mladenović B,Milić DJ,Sokolović D,Veselinović AM

    更新日期：2018-08-01 00:00:00

  • Synthesis, anticancer activity, toxicity evaluation and molecular docking studies of novel phenylaminopyrimidine-(thio)urea hybrids as potential kinase inhibitors.

    abstract：:Thirty-two novel urea/thiourea compounds as potential kinase inhibitor were designed, synthesized and evaluated for their cytotoxic activity on breast (MCF7), colon (HCT116) and liver (Huh7) cancer cell lines. Compounds 10, 19 and 30 possessing anticancer activity with IC50 values of 0.9, 0.8 and 1.6μM respectively on...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2018.12.003

    authors： Türe A,Kahraman DC,Cetin-Atalay R,Helvacıoğlu S,Charehsaz M,Küçükgüzel İ

    更新日期：2019-02-01 00:00:00

  • A chaotic approach to maintain the population diversity of genetic algorithm in network training.

    abstract：:The concept of chaos being radically different from statistical randomness is introduced into chemometrics research. The chaotic system that is deterministic with underlying patterns and inherent ability in searching the space of interest has been employed to improve the performance of chemometric algorithms. In this ...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/s1476-9271(02)00083-x

    authors： Lü Q,Shen G,Yu R

    更新日期：2003-07-01 00:00:00

  • GeneMCL in microarray analysis.

    abstract：:Accurately and reliably identifying the actual number of clusters present with a dataset of gene expression profiles, when no additional information on cluster structure is available, is a problem addressed by few algorithms. GeneMCL transforms microarray analysis data into a graph consisting of nodes connected by edg...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2005.07.002

    authors： Samuel Lattimore B,van Dongen S,Crabbe MJ

    更新日期：2005-10-01 00:00:00

  • In silico study of porphyrin-anthraquinone hybrids as CDK2 inhibitor.

    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

    authors： Arba M,Ihsan S,Ramadhan OA,Tjahjono DH

    更新日期：2017-04-01 00:00:00

  • FSDB: a frameshift signal database.

    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

    authors： Moon S,Byun Y,Han K

    更新日期：2007-08-01 00:00:00

  • A highly accurate protein structural class prediction approach using auto cross covariance transformation and recursive feature elimination.

    abstract：:Structural class characterizes the overall folding type of a protein or its domain. Many methods have been proposed to improve the prediction accuracy of protein structural class in recent years, but it is still a challenge for the low-similarity sequences. In this study, we introduce a feature extraction technique ba...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2015.08.012

    authors： Li X,Liu T,Tao P,Wang C,Chen L

    更新日期：2015-12-01 00:00:00

  • Identification and characterization of lysine-methylated sites on histones and non-histone proteins.

    abstract：:Protein methylation is a kind of post-translational modification (PTM), and typically takes place on lysine and arginine amino acid residues. Protein methylation is involved in many important biological processes, and most recent studies focused on lysine methylation of histones due to its critical roles in regulating...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2014.01.009

    authors： Lee TY,Chang CW,Lu CT,Cheng TH,Chang TH

    更新日期：2014-06-01 00:00:00

  • Phosphorylation mapping of laminin α1-chain: Kinases in association with active sites.

    abstract：:Laminin-111 is a trimeric glycoprotein of the extracellular matrix (ECM) that holds a significant role in cell adhesion, migration and differentiation. Laminin-111 is the most studied laminin isoform, composed of three chains; α1, β1 and γ1. Phosphorylation is the most common eukaryotic post - translational modificati...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2019.04.012

    authors： Galliou PA,Verrou KM,Koliakos G

    更新日期：2019-06-01 00:00:00

  • Identification of epilepsy from intracranial EEG signals by using different neural network models.

    abstract：:In this work, a framework is provided for identifying intracranial electroencephalography (iEEG) seizures based on discrete wavelet transform (DWT) analysis of iEEG signals using forward propagation and feedback neural networks. The performance of 5 different data sets combination classifications is studied using the ...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2020.107310

    authors： Gong C,Zhang X,Niu Y

    更新日期：2020-06-19 00:00:00

  • Structure based pharmacophore study to identify possible natural selective PARP-1 trapper as anti-cancer agent.

    abstract：:Inhibition of poly(ADP-ribose) polymerase-1 (PARP-1) has turned out an innovative approach for cancer therapy due to its involvement in DNA repair pathways. Although several potent PARP-1 inhibitors have been identified, they exhibit high toxicity, resistivity and diverse pharmacological profile in clinical trials, wh...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2019.04.018

    authors： Kumar C,P T V L,Arunachalam A

    更新日期：2019-06-01 00:00:00

  • Identification of novel vaccine candidates against carbapenem resistant Klebsiella pneumoniae: A systematic reverse proteomic approach.

    abstract：:Klebsiella pneumoniae is declared as antibiotic resistant by WHO, with the critical urgency of developing novel antimicrobial therapeutics as drug resistance is the second most dangerous threat after terrorism. Besides many attempts still, there is no effective vaccine available against K. pneumoniae. By utilizing all...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2020.107380

    authors： Mehmood A,Naseer S,Ali A,Fatimah H,Rehman S,Kiani AK

    更新日期：2020-12-01 00:00:00

  • Some steps toward a central theory of ecosystem dynamics.

    abstract：:Ecology is said by many to suffer for want of a central theory, such as Newton's laws of motion provide for classical mechanics or Schroedinger's wave equation provides for quantum physics. From among a plurality of contending laws to govern ecosystem behavior, the principle of increasing ascendency shows some early p...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章,评审

    doi：10.1016/s1476-9271(03)00050-1

    authors： Ulanowicz RE

    更新日期：2003-12-01 00:00:00

  • Exploring the effect of aplidin on low molecular weight protein tyrosine phosphatase by molecular docking and molecular dynamic simulation study.

    abstract：:The low molecular weight protein tyrosine phosphatase (LMW-PTP) could regulate many signaling pathways, and it had drawn attention as a potential target for cancer. As previous report has indicated that the aplidin could inhibit the LMW-PTP, and thus, the relevant cancer caused by the abnormal regulation of the LMW-PT...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2019.107123

    authors： Sun YZ,Wu JW,Lu XH,Ma Y,Wang RL

    更新日期：2019-12-01 00:00:00

  • Conformational difference between two subunits in flavin mononucleotide binding protein dimers from Desulfovibrio vulgaris (MF): molecular dynamics simulation.

    abstract：:The structural and dynamical properties of five FMN binding protein (FBP) dimers, WT (wild type), E13K (Glu13 replaced by Lys), E13R (Glu13 replaced by Arg), E13T (Glu13 replaced by Thr) and E13Q (Glu13 replaced by Gln), were investigated using a method of molecular dynamics simulation (MDS). In crystal structures, su...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2016.05.007

    authors： Nunthaboot N,Lugsanangarm K,Pianwanit S,Kokpol S,Tanaka F,Nakanishi T,Kitamura M

    更新日期：2016-10-01 00:00:00