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

authors： Topham CM,Smith JC

更新日期：2015-02-01 00:00:00

abstract：:Selecting the values of parameters used by de novo genomic assembly programs, or choosing an optimal de novo assembly from several runs obtained with different parameters or programs, are tasks that can require complex decision-making. A key parameter that must be supplied to typical next generation sequencing (NGS) a...

journal_title：Computational biology and chemistry

authors： Gallo JE,Muñoz JF,Misas E,McEwen JG,Clay OK

更新日期：2014-12-01 00:00:00

abstract：:Programmed cell death or apoptosis plays a vital physiological role in the development and homeostasis. Any discrepancy in apoptosis may trigger testicular and neurodegenerative diseases, ischemic damage, autoimmune disorders and many types of cancer. Tcte3 (T-complex testis expressed 3) is an accessory component of a...

journal_title：Computational biology and chemistry

authors： Parveen Z,Bibi Z,Bibi N,Neesen J,Rashid S

更新日期：2014-12-01 00:00:00

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

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

更新日期：2014-12-01 00:00:00

abstract：:A translation (framing) code based on the circular code was proposed in Michel (2012) with the identification of X circular code motifs (X motifs shortly) in the bacterial rRNA of Thermus thermophilus, in particular in the ribosome decoding center. Three classes of X motifs are now identified in the rRNAs of bacteria ...

journal_title：Computational biology and chemistry

authors： El Soufi K,Michel CJ

更新日期：2014-10-01 00:00:00

abstract：:A CIS (common insertion site) indicates a genome region that is hit more frequently by retroviral insertions than expected by chance. Such a region is strongly related to cancer gene loci, which leads to the detection of cancer genes. An algorithm for detecting CISs should satisfy the following: (1) it does not requir...

journal_title：Computational biology and chemistry

authors： Chen F,Li Z,Chen YP

更新日期：2014-08-01 00:00:00

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

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

更新日期：2014-06-01 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

authors： Ghosh A,Sonavane U,Joshi R

更新日期：2014-02-01 00:00:00

abstract：:Reptin functions in a wide range of biological processes including chromatin remodelling, nucleolar organization and transcriptional regulation of WNT signalling. As β-catenin dependent transcriptional repression and activation events involve binding of Reptin and histone deacetylase 1 to APPL endocytic proteins, this...

journal_title：Computational biology and chemistry

authors： Rashid S,Parveen Z,Ferdous S,Bibi N

更新日期：2013-12-01 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

authors： Bahi JM,Guyeux C,Mazouzi K,Philippe L

更新日期：2013-12-01 00:00:00

abstract：:Proline is an important osmotic adjusting material greatly accumulated under drought stress and can help plant to adapt to osmotic stress. MicroRNAs (miRNAs) are small, endogenous RNAs that play important regulatory roles in plant development and stress response by negatively affecting gene expression at post-transcri...

journal_title：Computational biology and chemistry

authors： Yang J,Zhang N,Ma C,Qu Y,Si H,Wang D

更新日期：2013-10-01 00:00:00

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 immediate...

journal_title：Computational biology and chemistry

authors： Zhu W,Hou J,Chen YP

更新日期：2013-06-01 00:00:00

abstract：BACKGROUND:Recent studies have indicated that microRNA (miRNA) may play an oncogenic or tumor suppressor role in human cancer. To study the regulatory role of miRNAs in tumorigenesis, an integrated platform has been set up to provide a user friendly interface for query. The main advantage of the present platform is tha...

journal_title：Computational biology and chemistry

authors： Weng CW,Lee SC,Lee YL,Ng KL

更新日期：2013-06-01 00:00:00

abstract：:There is a large gap between the number of discovered proteins and the number of functionally annotated ones. Due to the high cost of determining protein function by wet-lab research, function prediction has become a major task for computational biology and bioinformatics. Some researches utilize the proteins interact...

journal_title：Computational biology and chemistry

authors： Moosavi S,Rahgozar M,Rahimi A

更新日期：2013-04-01 00:00:00

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

authors： Qi Y,Lu H,Ai D

更新日期：2013-02-01 00:00:00

abstract：:We present an algorithm for automatically predicting the topological family of any RNA three-way junction, given only the information from the secondary structure: the sequence and the Watson-Crick pairings. The parameters of the algorithm have been determined on a data set of 33 three-way junctions whose 3D conformat...

journal_title：Computational biology and chemistry

authors： Lamiable A,Barth D,Denise A,Quessette F,Vial S,Westhof E

更新日期：2012-04-01 00:00:00

abstract：:Often the quantitative data coming from proteomics and metabolomics studies have irregular distribution with a spike. None of the wide used methods for human QTL mapping are applicable to such traits. Researchers have to reduce the sample, excluding the spike, and analyze only continuous measurements. In this study, w...

journal_title：Computational biology and chemistry

authors： Axenovich TI,Zorkoltseva IV

更新日期：2012-02-01 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

authors： Tenorio-Salgado S,Huerta-Saquero A,Perez-Rueda E

更新日期：2011-12-14 00:00:00

abstract：:Many Traditional Chinese Medicines (TCMs) are effective to relieve complicated diseases such as type II diabetes mellitus (T2DM). In this work, molecular docking and network analysis were employed to elucidate the action mechanism of a medical composition which had clinical efficacy for T2DM. We found that multiple ac...

journal_title：Computational biology and chemistry

authors： Gu J,Zhang H,Chen L,Xu S,Yuan G,Xu X

更新日期：2011-10-12 00:00:00

abstract：:The induced pluripotent cells (iPSCs) are derived from somatic cells by reprogramming their genetic profiles. Such a process requires coordinated dynamic expression of hundreds of genes and proteins. As both deterministic and stochastic elements control the reprogramming process, it is not easy to have a way to reflec...

journal_title：Computational biology and chemistry

authors： Zhang L,Zheng Y,Li D,Zhong Y

更新日期：2011-08-10 00:00:00

abstract：:Identifying essential proteins is very important for understanding the minimal requirements of cellular survival and development. Fast growth in the amount of available protein-protein interactions has produced unprecedented opportunities for detecting protein essentiality from the network level. Essential proteins ha...

journal_title：Computational biology and chemistry

authors： Li M,Wang J,Chen X,Wang H,Pan Y

更新日期：2011-06-01 00:00:00

abstract：:In this work we have studied the interaction of zervamicin IIB (ZrvIIB) with the model membranes of eukaryotes and prokaryotes using all-atom molecular dynamics. In all our simulations zervamicin molecule interacted only with lipid headgroups but did not penetrate the hydrophobic core of the bilayers. During the inter...

journal_title：Computational biology and chemistry

authors： Levtsova OV,Antonov MY,Naumenkova TV,Sokolova OS

更新日期：2011-02-01 00:00:00

abstract：:Feature selection techniques have been used as the workhorse in biomarker discovery applications for a long time. Surprisingly, the stability of feature selection with respect to sampling variations has long been under-considered. It is only until recently that this issue has received more and more attention. In this ...

journal_title：Computational biology and chemistry

authors： He Z,Yu W

更新日期：2010-08-01 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

authors： Sabarinathan R,Basu R,Sekar K

更新日期：2010-04-01 00:00:00

abstract：:MicroRNAs (miRNAs) have been implicated in complex vertebrate developmental and pathological systems as a versatile class of molecules involved in the regulation of various biological processes and molecular pathways. To elucidate the role of miRNAs in human somatic cells, an understanding of the molecular framework r...

journal_title：Computational biology and chemistry

authors： Ohdaira H,Nakagawa H,Yoshida K

更新日期：2009-12-01 00:00:00

abstract：:RNA-binding proteins (RBPs) perform fundamental and diverse functions within the cell. Approximately 15% of proteins sequences are annotated as RNA-binding, but with a significant number of proteins without functional annotation, many RBPs are yet to be identified. A percentage of uncharacterised proteins can be annot...

journal_title：Computational biology and chemistry

authors： Spriggs RV,Jones S

更新日期：2009-10-01 00:00:00

abstract：:Recoding events occur in competition with standard readout of the transcript, and are site-specific. Recoding is the reprogramming of mRNA translation by localized alterations in the standard translational rules. Frame-shifting is one class of recoding and defined as protein translations that start not at the first, b...

journal_title：Computational biology and chemistry

authors： Singh TR,Pardasani KR

更新日期：2009-06-01 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

authors： Baev V,Daskalova E,Minkov I

更新日期：2009-02-01 00:00:00

abstract：:Genome-wide association analysis involved many single-nucleotide polymorphisms (SNPs) data is challenging mathematically and computationally. Hence, we propose the odds ratio-based discrete binary particle swarm optimization (OR-DBPSO) method that uses the OR as a new quantitative measure of disease risk among many SN...

journal_title：Computational biology and chemistry

authors： Chang HW,Yang CH,Ho CH,Wen CH,Chuang LY

更新日期：2009-02-01 00:00:00

abstract：:Optimally weighted fuzzy k-nearest neighbors (OWFKNN) algorithm has been used to predict proteins' subcellular locations based on their amino acid composition, in this paper. The datasets used consists of two species which are 997 prokaryotic and 2427 eukaryotic protein sequences. The overall prediction accuracy achie...

journal_title：Computational biology and chemistry

authors： Nasibov E,Kandemir-Cavas C

更新日期：2008-12-01 00:00:00

abstract：:We have developed a computational technique refereed to as complex phylogenetic profiling. Our approach combines logic analyses of gene phylogenetic profiles and phenotype data. Logic analysis of phylogenetic profiles identifies sets of proteins whose presence or absence follows certain logic relationships. Our approa...

journal_title：Computational biology and chemistry

authors： Antonov AV,Mewes HW

更新日期：2008-12-01 00:00:00

abstract：:Bacterial and eukaryotic RecQ helicases comprise a family of homologous proteins necessary for maintaining genomic integrity during the cell cycle and DNA repair. There is one known bacterial RecQ helicase, and five eukaryotic RecQ helicases that have been described: RecQ1p, RecQ4p, RecQ5p, Bloom, and Werner. While th...

journal_title：Computational biology and chemistry

authors： Barea F,Tessaro S,Bonatto D

更新日期：2008-10-01 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

authors： Du Z,Wang Y,Ji Z

更新日期：2008-08-01 00:00:00

abstract：:Recent studies suggest that protein folding should be revisited as the emergent property of a complex system and that the nature allows only a very limited number of folds that seem to be strongly influenced by geometrical properties. In this work we explore the principles underlying this new view and show how helical...

journal_title：Computational biology and chemistry

authors： Mucherino A,Costantini S,di Serafino D,D'Apuzzo M,Facchiano A,Colonna G

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

authors： Yang Z,Lin H,Li Y

更新日期：2008-08-01 00:00:00

abstract：:Functional classification of genes represents one of the most basic problems in genome analysis and annotation. Our analysis of some of the popular methods for functional classification of genes shows that these methods are not always consistent with each other and may not be specific enough for high-resolution gene f...

journal_title：Computational biology and chemistry

authors： Wu H,Mao F,Olman V,Xu Y

更新日期：2008-06-01 00:00:00

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

authors： Kubica K

更新日期：2008-06-01 00:00:00

abstract：:Early pharmacological studies of Aconitum and Delphinium sp. alkaloids suggested that these neurotoxins act at site 2 of voltage-gated Na(+) channel and allosterically modulate its function. Understanding structural requirements for these compounds to exhibit binding activity at voltage-gated Na(+) channel has been im...

journal_title：Computational biology and chemistry

authors： Turabekova MA,Rasulev BF,Levkovich MG,Abdullaev ND,Leszczynski J

更新日期：2008-04-01 00:00:00

abstract：:Workflow technology is a generic mechanism to integrate diverse types of available resources (databases, servers, software applications and different services) which facilitate knowledge exchange within traditionally divergent fields such as molecular biology, clinical research, computational science, physics, chemist...

journal_title：Computational biology and chemistry

authors： Tiwari A,Sekhar AK

更新日期：2007-10-01 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

authors： Moon S,Byun Y,Han K

更新日期：2007-08-01 00:00:00