Abstract：
:MODULEWRITER is a PERL object relational mapping (ORM) tool that automatically generates database specific application programming interfaces (APIs) for SQL databases. The APIs consist of a package of modules providing access to each table row and column. Methods for retrieving, updating and saving entries are provided, as well as other generally useful methods (such as retrieval of the highest numbered entry in a table). MODULEWRITER provides for the inclusion of user-written code, which can be preserved across multiple runs of the MODULEWRITER program.
journal_name
Comput Biol Chemjournal_title
Computational biology and chemistryauthors
Zheng CL,Fana F,Udupi PV,Gribskov Mdoi
10.1016/s1476-9271(03)00021-5keywords:
subject
Has Abstractpub_date
2003-05-01 00:00:00pages
135-9issue
2eissn
1476-9271issn
1476-928Xpii
S1476927103000215journal_volume
27pub_type
杂志文章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：: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：: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 chaetognaths constitute a small and enigmatic phylum of little marine invertebrates. Both nuclear and mitochondrial genomes have numerous originalities, some phylum-specific. Until recently, their mitogenomes seemed containing only one tRNA gene (trnMet), but a recent study found in two chaetognath mitogenomes two...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2016.04.007
更新日期：2016-06-01 00:00:00
abstract：:Tamoxifen is a prodrug and cytochrome P450 2C9 (CYP2C9) has a significant role in the formation of a therapeutically more potent metabolite (4-hydroxytamoxifen) than tamoxifen. Since CYP2C9 exhibits genetic polymorphism, it may contribute to different phenotypic drug response. Moreover, it may be misleading if the pos...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2019.107166
更新日期：2020-02-01 00:00:00
abstract：:The electrostatic (ES) energy of each residue was for the first time quantitatively evaluated in a flavin mononucleotide binding protein (FBP). A residue electrostatic energy (RES) was obtained as the sum of the ES energies between atoms in each residue and all other atoms in the FBP dimer using atomic coordinates obt...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2018.01.001
更新日期：2018-02-01 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：: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：: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
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2008.02.001
更新日期：2008-06-01 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：: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：: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
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2011.05.002
更新日期：2011-08-10 00:00:00
abstract：:Casiopeinas are a group of copper-based compounds designed to be used as less toxic, more efficient chemotherapeutic agents. In this study, we analyzed the in vitro effects of Casiopeina II-gly on the expression of canonical biological pathways. Using microarray data from HeLa cell lines treated with Casiopeina II-gly...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2018.11.021
更新日期：2019-02-01 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：:The Egyptian flora is rich with a large number of Triticum plants, which are very difficult to discriminate between in the early developmental stages. This study assesses the significance of using two DNA Barcoding loci (matK and rbcL) in distinguishing between 18 different Triticum accessions in Egypt. We isolated an...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2017.09.003
更新日期：2017-12-01 00:00:00
abstract：:Recent advances in high-throughput genome sequencing technologies have enabled the systematic study of various genomes by making whole genome sequencing affordable. Modern sequencers generate a huge number of small sequence fragments called reads, where the read length and the per-base sequencing cost depend on the te...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2017.03.016
更新日期：2017-08-01 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 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：:Zinc fingers are small protein domains in which zinc plays a structural role, contributing to the stability of the zinc-peptide complex. Zinc fingers are structurally diverse and are present in proteins that perform a broad range of functions in various cellular processes, such as replication and repair, transcription...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2018.03.005
更新日期：2018-06-01 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
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2014.03.001
更新日期：2014-08-01 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
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2009.04.002
更新日期：2009-06-01 00:00:00
abstract：:We report ligand field molecular mechanics, density functional theory and semi-empirical studies on the binding of Cu(II) to GlyHisLys (GHK) peptide. Following exhaustive conformational searching using molecular mechanics, we show that relative energy and geometry of conformations are in good agreement between GFN2-xT...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2020.107265
更新日期：2020-06-01 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：: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
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2014.08.001
更新日期：2014-10-01 00:00:00
abstract：:With the development of cancer research, various gene expression datasets containing cancer information show an explosive growth trend. In addition, due to the continuous maturity of single-cell RNA sequencing (scRNA-seq) technology, the protein information and pedigree information of a single cell are also continuous...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2020.107368
更新日期：2020-12-01 00:00:00
abstract：AIM:An integrated protocol of virtual screening involving molecular docking, pharmacophore probing, and simulations was established to identify small novel molecules targeting crucial residues involved in the variant apoE ε4 to mimic its behavior as apoE2 thereby eliminating the amyloid plaque accumulation and facilita...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2018.12.013
更新日期：2019-04-01 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
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2011.07.003
更新日期：2011-10-12 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
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2008.07.011
更新日期：2008-12-01 00:00:00
abstract：:Pseudomonas aeruginosa is an opportunistic gram-negative bacterium that has the capability to acquire resistance under hostile conditions and become a threat worldwide. It is involved in nosocomial infections. In the current study, potential novel drug targets against P. aeruginosa have been identified using core prot...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2018.02.017
更新日期：2018-06-01 00:00:00
abstract：:The Monty Hall problem is a decision problem with an answer that is surprisingly counter-intuitive yet provably correct. Here we simulate and prove this decision in a high-throughput DNA sequencing machine, using a simple encoding. All possible scenarios are represented by DNA oligonucleotides, and gameplay decisions ...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2019.107122
更新日期：2019-12-01 00:00:00
