Abstract：
:In this study, we develop a program that allows us to reveal DNA receptors, i.e. nucleotide sequences that may form more than one non-canonical structure. The data obtained may be analysed either experimentally or using DNA banks, and refers to the coding, non-coding or promotor region of the gene. These results provide a better understanding of the role that non-canonical structures play in pathological modifications of the genetic apparatus, resulting in tumour formation or inherited disease. They also reveal the effect of single nucleotide polymorphisms on gene expression, indicate so-called "risk regions" in which the substitution of a single nucleotide may lead to increased formation of non-canonical structures, and elucidate the epigenetic mechanisms of microorganism adaptation.
journal_name
Comput Biol Chemjournal_title
Computational biology and chemistryauthors
Yurushkin MV,Gervich LR,Bachurin SS,Kletskii MEdoi
10.1016/j.compbiolchem.2019.04.009subject
Has Abstractpub_date
2019-06-01 00:00:00pages
278-283eissn
1476-9271issn
1476-928Xpii
S1476-9271(18)30465-1journal_volume
80pub_type
杂志文章abstract：BACKGROUND:Metastasis is the main cause of breast cancer (BC) lethality, especially in early stages, led to improvements in therapeutic procedures. Lately, by improvements in our perception of biological processes and immune system new classes of vaccines are emerged that grant us the opportunity of designing resolute ...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2020.107231
更新日期：2020-04-01 00:00:00
abstract：:Beta-secretase is a potential target for inhibitory drugs against Alzheimer's disease as it cleaves amyloid precursor protein (APP) to form insoluble amyloid plaques and vascular deposits in the brain. Beta-secretase is matured from its precursor protein, called beta-secretase zymogen, which, different from most of ot...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2007.03.007
更新日期：2007-06-01 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：: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：: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：: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
更新日期：2020-06-19 00:00:00
abstract：:Human T-cell leukemia virus type 1 (HTLV-1) protease is an attractive target when developing inhibitors to treat HTLV-1 associated diseases. To study the catalytic mechanism and design novel HTLV-1 protease inhibitors, the protonation states of the two catalytic aspartic acid residues must be determined. Free energy s...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2015.04.002
更新日期：2015-06-01 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：:The identification of isatin sulfonamide as a potent small molecule inhibitor of caspase-3 had fuelled the synthesis and characterization of the numerous sulfonamide class of inhibitors to optimize for potency. Recent works that relied on the ligand-based approaches have successfully shown the regions of optimizations...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2017.08.006
更新日期：2017-12-01 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
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：:The NS2B-NS3 protease is essential for the replication process of Dengue Virus, which make it an attractive target for anti-virus drugs. Since a considerable number of NS2B-NS3 protease inhibitors have been reported so far, it is significant for the discovery of more effective antivirus compounds with the essential st...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2018.09.010
更新日期：2018-12-01 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：:The plant-specific TCP transcription factors, which play critical roles in diverse aspects of biological processes, have been identified and analyzed in various plant species. However, no systematical study of TCP family genes in potato (Solanum tuberosum L.) has been undertaken. In this study, a total of 31 non-redun...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2018.11.009
更新日期：2019-02-01 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：: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：:Breast cancer is one of the major impediments affecting women globally. The ATP-dependant heat shock protein 90 (Hsp90) forms the central component of molecular chaperone machinery that predominantly governs the folding of newly synthesized peptides and their conformational maturation. It regulates the stability and f...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2019.107113
更新日期：2019-12-01 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
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2008.02.007
更新日期：2008-06-01 00:00:00
abstract：:Protein function prediction is a crucial task in the post-genomics era due to their diverse irreplaceable roles in a biological system. Traditional methods involved cost-intensive and time-consuming molecular biology techniques but they proved to be ineffective after the outburst of sequencing data through the advent ...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2019.107147
更新日期：2019-12-01 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：:Secondary structure motifs in nucleic acid probes generally impair intended hybridization reactions and so efforts to predict and avoid such structures are commonly employed in probe design schemes. Another key facet of probe design that has received much less attention, however, is that secondary structure at targete...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2005.09.002
更新日期：2005-12-01 00:00:00
abstract：:Triticum aestivum L. known as common wheat is one of the most important cereal crops feeding a large and growing population. Various environmental stress factors including drought, high salinity and heat etc. adversely affect wheat production in a significant manner. Dehydration-responsive element-binding (DREB1A) fac...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2016.07.008
更新日期：2016-10-01 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
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2008.07.029
更新日期：2009-02-01 00:00:00
abstract：:Adenosine deaminase (ADA) is an enzyme involved in purine metabolism. ADA converts adenosine to inosine and liberates ammonia. Because of their critical role in the differentiation and maturation of cells, the regulation of ADA activity is considered as a potential therapeutic approach to prevent malignant and inflamm...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2016.08.005
更新日期：2016-10-01 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：: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：:The sequential determination of crystal structures of the SARS coronavirus spike receptor-binding domain (RBD) in complex with its cellular receptor or neutralizing antibody opened a door for the design and development of antiviral competitive inhibitors. Based on those complex structures, we conduct computational cha...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2007.02.005
更新日期：2007-04-01 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：:3CL proteases (3CLpro) are only found in RNA viruses and have a central role in polyprotein processing during replication. Therefore, 3CLpro has emerged as promising drug target for therapeutic treatment of infections caused by Coronaviruses. In the light of the recent major outbreak of the SARS-CoV-2 virus and the co...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2020.107351
更新日期：2020-10-01 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：:Zika virus (ZIKV) infection has been associated with Guillain-Barre syndrome in adults and microcephaly in infants. The existence of insufficient structural data in most of the protein databases hinders the synthesis of anti-ZIKV pharmaceutics. In this work, we attempted to model the catalytic domain of the ZIKV RNA p...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2017.10.007
更新日期：2017-12-01 00:00:00
