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 ranging from 1 to 12. At the same time, a new method is suggested to reduce the matrix dimension, can greatly lessen the amount of calculation and operation time. The experimental assessment demonstrated that our measure was efficient. What's more, comparing with other methods' results shows that our method is feasible and powerful for phylogenetic analysis.
journal_name
Comput Biol Chemjournal_title
Computational biology and chemistryauthors
Tang J,Hua K,Chen M,Zhang R,Xie Xdoi
10.1016/j.compbiolchem.2014.10.007subject
Has Abstractpub_date
2014-12-01 00:00:00pages
331-338eissn
1476-9271issn
1476-928Xpii
S1476-9271(14)00130-3journal_volume
53PBpub_type
杂志文章abstract：:The shortest common supersequence (SCS) problem is a classical NP-hard problem, which is normally solved by heuristic algorithms. One important heuristic that is inspired by the process of chemical reactions in nature is the chemical reaction optimization (CRO) and its algorithm known as CRO_SCS. In this paper we prop...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2020.107327
更新日期：2020-10-01 00:00:00
abstract：:The vibrational wavenumbers of optimized molecular structure of 1-phenylcyclopentane carboxylic acid (1PCPCA) molecule have been calculated by quantum chemical theory and compared with experimental results. The density functional theory (DFT) approach is followed using the method B3LYP and 6-311++G(d,p) basis set. Usi...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2019.05.011
更新日期：2019-10-01 00:00:00
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 provi...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2019.04.009
更新日期：2019-06-01 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：:In this paper, a method for single individual haplotype (SIH) reconstruction using Asexual reproduction optimization (ARO) is proposed. Haplotypes, as a set of genetic variations in each chromosome, contain vital information such as the relationship between human genome and diseases. Finding haplotypes in diploid orga...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2017.12.005
更新日期：2018-02-01 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：: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：:Germline stem cells (GSCs) are known to transmit genetic information from parents to offspring. These GSCs can undergo reprogramming to transform themselves into pluripotent stem cells, called as Multipotent adult Germline stem cells (maGSCs). The mechanism of the reprogramming of GSCs to maGSCs is elusive. To investi...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2018.08.001
更新日期：2018-10-01 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：:In many sequence data mining applications, the goal is to find frequent substrings. Some of these applications like extracting motifs in protein and DNA sequences are looking for frequently occurring approximate contiguous substrings called simple motifs. By approximate we mean that some mismatches are allowed during ...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2016.09.001
更新日期：2016-10-01 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
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2010.12.005
更新日期：2011-02-01 00:00:00
abstract：:The present study is focused on a series of newly synthesized 1-aryl-3-ethyl-3-methylsuccinimide derivatives, as potential anticonvulsants. The retention behavior of eleven succinimide derivatives was determined by using reversed phase high performance liquid chromatography (RP-HPLC) and reversed phase high performanc...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2019.107161
更新日期：2020-02-01 00:00:00
abstract：:Methylenetetrahydrofolate reductase (MTHFR) is a key enzyme involved in folate metabolism and plays a central role in DNA methylation and biosynthesis. MTHFR mutations may alter the cellular folate supply which in turn affects nucleic acid synthesis, DNA methylation and chromosomal damage. The identification of number...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2018.02.022
更新日期：2018-06-01 00:00:00
abstract：:Although thousands of microRNAs (miRNAs) have been identified in recent experimental efforts, it remains a challenge to explore their specific biological functions through molecular biological experiments. Since those members from same family share same or similar biological functions, classifying new miRNAs into thei...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2017.09.008
更新日期：2017-12-01 00:00:00
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：: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
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2008.07.005
更新日期：2008-10-01 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：:The DNA binding protein, TDP43 is a major protein involved in amyotrophic lateral sclerosis and other neurological disorders such as frontotemporal dementia, Alzheimer disease, etc. In the present study, we have designed possible siRNAs for the glycine rich region of tardbp mutants causing ALS disorder based on a syst...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2016.01.001
更新日期：2016-04-01 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：: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
更新日期：2019-02-01 00:00:00
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
更新日期：2016-10-01 00:00:00
abstract：:Polymerase chain reaction (PCR) is an important diagnostic tool for the amplification of DNA. The PCR process can be treated as a problem in biochemical engineering. This study focuses on the development of a mathematical model of the polymerase chain reaction. The PCR process consists of three steps: denaturation of ...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2004.03.001
更新日期：2004-07-01 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：: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
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：:Interleukin-1β is a drug target in rheumatoid arthritis and several auto-immune disorders. In this study, a set of 48 compounds with the determined IC50 values were used for QSAR analysis by MOE. The QSAR model was developed by using training set of 41 compounds, based on 12 unique descriptors. Model was validated by ...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2015.06.004
更新日期：2015-10-01 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：: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：:Cell type identification from an unknown sample can often be done by comparing its gene expression profile against a gene expression database containing profiles of a large number of cell-types. This type of compendium-based cell-type identification strategy is particularly successful for human and mouse samples becau...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2018.10.003
更新日期：2018-12-01 00:00:00
abstract：:The resistances of matrix protein 2 (M2) protein inhibitors and neuraminidase inhibitors for influenza virus have attracted much attention and there is an urgent need for new drug. The antiviral drugs that selectively act on RNA polymerase are less prone to resistance and possess fewer side effects on the patient. The...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2020.107241
更新日期：2020-04-01 00:00:00
