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 Escherichia coli and Thermus thermophilus, archaea Pyrococcus furiosus, nuclear eukaryotes Saccharomyces cerevisiae, Triticum aestivum and Homo sapiens, and chloroplast Spinacia oleracea. The universally conserved nucleotides A1492 and A1493 in all studied rRNAs (bacteria, archaea, nuclear eukaryotes, and chloroplasts) belong to X motifs (called mAA). The conserved nucleotide G530 in rRNAs of bacteria and archaea belongs to X motifs (called mG). Furthermore, the X motif mG is also found in rRNAs of nuclear eukaryotes and chloroplasts. Finally, a potentially important X motif, called m, is identified in all studied rRNAs. With the available crystallographic structures of the Protein Data Bank PDB, we also show that these X motifs mAA, mG, and m belong to the ribosome decoding center of all studied rRNAs with possible interaction with the mRNA X motifs and the tRNA X motifs. The three classes of X motifs identified here in rRNAs of several and different organisms strengthen the concept of translation code based on the circular code.
journal_name
Comput Biol Chemjournal_title
Computational biology and chemistryauthors
El Soufi K,Michel CJdoi
10.1016/j.compbiolchem.2014.08.001subject
Has Abstractpub_date
2014-10-01 00:00:00pages
9-17eissn
1476-9271issn
1476-928Xpii
S1476-9271(14)00080-2journal_volume
52pub_type
杂志文章abstract：:Burkholderia glumae, the primary causative agent of bacterial panicle blight in rice, has been reported as an opportunistic pathogen in patients with chronic infections. This study aimed to re-sequence the clinical isolate B. glumae strain AU6208 and comparatively analyze its genome using B. glumae strain BGR1 from ri...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2020.107245
更新日期：2020-06-01 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
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2012.12.003
更新日期：2013-04-01 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
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2013.04.006
更新日期：2013-10-01 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
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2009.09.003
更新日期：2009-12-01 00:00:00
abstract：:Previous joint experimental and theoretical work demonstrates that typically soluble peptides will be rendered insoluble in the presence of saturated sodium ions in aqueous solution due to disruption of cation-π interactions between Trp and Lys. The present work utilizes quantum chemical methods including density func...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2017.12.009
更新日期：2018-02-01 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
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2014.10.007
更新日期：2014-12-01 00:00:00
abstract：:Nodulation is one of the very important processes of legume plants as it is the initiating event of fixing nitrogen. Although ethylene has essential role in normal plant metabolism but it has also negative impact on plants particularly in nodule formation in legume plants. It is also produced due to a variety of bioti...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2017.02.005
更新日期：2017-06-01 00:00:00
abstract：:We present the mechanism of interaction of Wnt network module, which is responsible for periodic somitogenesis, with p53 regulatory network, which is one of the main regulators of various cellular functions, and switching of various oscillating states by investigating p53-Wnt model. The variation in Nutlin concentrati...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2015.07.014
更新日期：2015-12-01 00:00:00
abstract：:Recent studies reported the involvement of JAK2/STAT3 pathway in various solid tumours including breast, ovarian, prostate and lung cancers. Clinical literature also reported the lowered burden in breast and ovarian cancers by targeting JAK2 pathway. In this study, a series of novel 2,4-disubstituted quinazolines (2a-...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2019.01.008
更新日期：2019-04-01 00:00:00
abstract：:Alzheimer's disease (AD) is a progressive neurodegenerative disease of central nervous system among elderly people. Human acetylcholinesterase (hAChE), an important enzyme in neuronal signaling, is responsible for the degradation of acetylcholine which in turn prevents the post synaptic signal transmissions. hAChE has...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2017.04.002
更新日期：2017-06-01 00:00:00
abstract：:Currently Alzheimer's disease (AD) is a devastating neurological disorder that mainly affects the elderly. The treatment of AD has as main objective to increase the levels of ACh in the synaptic cleft by inhibiting the cholinesterase enzymes, which are responsible for the degradation of ACh. Twenty one synthesized cou...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2020.107293
更新日期：2020-05-29 00:00:00
abstract：:Due to their lethal consequences and a relatively high probability of introduction of repair errors and mutations, single and double strand breaks are among the most important and dangerous DNA lesions. However, the mechanisms of their recognition and repair processes are only poorly known at present. This work define...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2005.12.001
更新日期：2006-04-01 00:00:00
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
更新日期：2018-12-01 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：:Glucokinase (GK) is the main enzyme which controls the blood glucose levels in a safe and narrow physiological range in humans. GK activators are the novel type of therapeutic agents which act on GK enzyme and show their anti-diabetic potential. The present work was planned to synthesize and evaluate the antidiabetic ...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2018.02.018
更新日期：2018-04-01 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
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2014.01.009
更新日期：2014-06-01 00:00:00
abstract：:Prefoldin is a molecular chaperone and acts as a nano-actuator in cargo carriage and drug delivery for disease treatment. Investigating the mechanical properties of nano-actuator helps predict its behavior and measure its performance under various environmental conditions, like external forces that are applied. Accord...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2019.107133
更新日期：2019-12-01 00:00:00
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
更新日期：2015-12-01 00:00:00
abstract：:In process of creating genetic maps different labs/research groups obtain overlapping parts of the map. Merging these parts into one integrative map is based on looking for maximum shared marker orders among the maps. Really, not all shared markers of such maps have consensus order that obstructs building of the integ...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2005.09.007
更新日期：2006-02-01 00:00:00
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
更新日期：2019-04-01 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：:Monoamine oxidase (MAO) enzymes are one of the most promising targets for the treatment of neurological disorders. A series of phenylisoxazole carbohydrazides was designed, synthesized and screened for both MAO-A and MAO-B inhibition using Amplex Red assays. None of the compounds inhibited the MAO-A activity while mos...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2019.01.012
更新日期：2019-04-01 00:00:00
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
更新日期：2019-06-01 00:00:00
abstract：:In this paper, a problem of isothermic DNA sequencing by hybridization (SBH) is considered. In isothermic SBH a new type of oligonucleotide libraries is used. The library consists of oligonucleotides of different lengths depending on an oligonucleotide content. It is assumed that every oligonucleotide in such a librar...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2003.12.002
更新日期：2004-02-01 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：:Development in two-dimensional (2D) drug-delivery materials have quickly translated into biological and pharmacological fields. In this present work, pristine graphene (PG) and hexagonal boron nitride (h-BN) sheets are explored as a drug carrier for cytarabine (CYT) and clofarabine (CLF) anti-cancer drugs using densit...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2020.107334
更新日期：2020-10-01 00:00:00
abstract：:Non-specific lipid transfer proteins (nsLTPs) are common allergens and they are particularly widespread within the plant kingdom. They have a highly conserved three-dimensional structure that generate a strong cross-reactivity among the members of this family. In the last years several web tools for the prediction of ...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2015.11.006
更新日期：2016-02-01 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：:rlying biology of differentially expressed genes and proteins. Although various approaches have been proposed to identify cancer-related pathways, most of them only partially consider the influence of those differentially expressed genes, such as the gene numbers, their perturbation in the signaling transduction, and ...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2017.09.009
更新日期：2017-12-01 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
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2014.08.014
更新日期：2014-12-01 00:00:00
