Abstract：
:We introduce a method for ungapped local multiple alignment (ULMA) in a given set of amino acid or nucleotide sequences. This method explores two search spaces using a linked optimization strategy. The first search space M consists of all possible words of a given length W, defined on the residue alphabet. An evolutionary algorithm searches this space globally. The second search space P consists of all possible ULMAs in the sequence set, each ULMA being represented by a position vector defining exactly one subsequence of length W per sequence. This search space is sampled with hill-climbing processes. The search of both spaces are coupled by projecting high scoring results from the global evolutionary search of M onto P. The hill-climbing processes then refine the optimization by local search, using the relative entropy between the ULMA and background residue frequencies as an objective function. We demonstrate some advantages of our strategy by analyzing difficult natural amino acid sequences and artificial datasets. A web interface is available at
journal_name
Comput Biol Chemjournal_title
Computational biology and chemistryauthors
Hernandez D,Gras R,Appel Rdoi
10.1016/j.compbiolchem.2004.01.001keywords:
subject
Has Abstractpub_date
2004-04-01 00:00:00pages
119-28issue
2eissn
1476-9271issn
1476-928Xpii
S1476927104000027journal_volume
28pub_type
杂志文章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：:The metabolic rearrangements occurring in cancer cells can be effectively investigated with a Systems Biology approach supported by metabolic network modeling. We here present tissue-specific constraint-based core models for three different types of tumors (liver, breast and lung) that serve this purpose. The core mod...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2016.03.002
更新日期：2016-06-01 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：: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：: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
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2013.11.002
更新日期：2014-02-01 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：:Real-time RT-PCR has been frequently used in quantitative research in molecular biology and bioinformatics. It provides remarkably useful technology to assess expression of genes. Although mathematical models for gene amplification process have been studied, statistical models and methods for data analysis in real-tim...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2005.10.005
更新日期：2006-02-01 00:00:00
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
更新日期：2016-02-17 00:00:00
abstract：:Polyphenol oxidases (PPOs)/tyrosinases are metal-dependent enzymes and known as important targets for melanogenesis. Although considerable attempts have been conducted to control the melanin-associated diseases by using various inhibitors. However, the exploration of the best anti-melanin inhibitor without side effect...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2017.02.012
更新日期：2017-06-01 00:00:00
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：:With an increasing number of publicly available microarray datasets, it becomes attractive to borrow information from other relevant studies to have more reliable and powerful analysis of a given dataset. We do not assume that subjects in the current study and other relevant studies are drawn from the same population ...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2005.04.002
更新日期：2005-06-01 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：: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：:Successful prediction of protein domain boundaries provides valuable information not only for the computational structure prediction of multi-domain proteins but also for the experimental structure determination. In this work, a novel index at the profile level is presented, namely, the profile domain linker propensit...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2006.01.001
更新日期：2006-04-01 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
pub_type： 杂志文章,评审
doi：10.1016/j.compbiolchem.2010.07.002
更新日期：2010-08-01 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：:An efficient, borax-catalyzed protocol for the synthesis of novel 4-aryl-substituted-4H-pyran derivatives fused to α-pyrone ring in a one-pot is described. By this achievement, some novel 4-aryl substituted 4H-pyrans fused to the α-pyrone ring as potential acetylcholinesterase inhibitors (AChEIs) with good to excellen...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2019.04.004
更新日期：2019-06-01 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：: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
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2007.10.003
更新日期：2008-04-01 00:00:00
abstract：:Human Leukocyte Antigens (HLA) are highly polymorphic proteins that play a key role in the immune system. HLA molecule is present on the cell membrane of antigen-presenting cells of the immune system and presents short peptides, originating from the proteins of invading pathogens or self-proteins, to the T-cell Recept...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2016.02.019
更新日期：2016-06-01 00:00:00
abstract：:It has recently been shown that cancer genes (oncogenes) tend to have heterogeneous expressions across disease samples. So it is reasonable to assume that in a microarray data only a subset of disease samples will be activated (often referred to as outliers), which presents some new challenges for statistical analysis...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2007.02.004
更新日期：2007-04-01 00:00:00
abstract：:The single-stranded transfer DNA from the Ti plasmid of the soil bacteria Agrobacterium nonspecifically integrates into the plant chromosome and is inherited at subsequent cell divisions. How it is transferred across host membranes is unknown, but it is believed that VirE2 proteins form a membrane-spanning pore or cha...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2017.01.016
更新日期：2017-06-01 00:00:00
abstract：:Protein kinases are enzymes acting as a source of phosphate through ATP to regulate protein biological activities by phosphorylating groups of specific amino acids. For that reason, inhibiting protein kinases with an active small molecule plays a significant role in cancer treatment. To achieve this aim, computational...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2020.107269
更新日期：2020-06-01 00:00:00
abstract：:This paper describes an efficient algorithm based on a new concept called gene team for detecting conserved gene clusters among an arbitrary number of chromosomes. Within the clusters, neither the order of the genes nor their orientation need be conserved. In addition, insertion of foreign genes within the clusters ar...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/s1476-9271(02)00097-x
更新日期：2003-02-01 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
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2013.02.001
更新日期：2013-06-01 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：: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 Protein Structure Prediction (PSP) problem comprises, among other issues, forecasting the three-dimensional native structure of proteins using only their primary structure information. Most computational studies in this area use synthetic data instead of real biological data. However, the closer to the real-world,...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2019.107192
更新日期：2020-02-01 00:00:00
abstract：:Nanoscopic properties of TiO2 augmented with its physicochemical properties and biocompatibility make it a material interest in the biomedical field. Efficient methods to design of such materials require a thorough understanding of associated nano-bio interfaces. In the present study, density functional theory calcula...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2020.107236
更新日期：2020-06-01 00:00:00
