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Interdisciplinary Sciences, Computational Life Sciences

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https://www.readbyqxmd.com/read/30194628/an-in-silico-investigation-of-key-lysine-residues-and-their-selection-for-clearing-off-a%C3%AE-and-holo-a%C3%AE-pp-through-ubiquitination
#1
Dhiraj Kumar, Pravir Kumar
Malicious progression of neurodegeneration is a consequence of toxic aggregates of proteins or peptides such as amyloid beta (Aβ) reported in Alzheimer's disease (AD). These aggregates hinder the electrochemical transmission at neuronal junctions and thus deteriorate neuronal-health by triggering dementia. Electrostatic and hydrophobic interactions among amino-acid residues are the governing principle behind the self-assembly of aforesaid noxious oligomers or agglomerate. Interestingly, lysine residues are crucial for these interactions and for facilitating the clearance of toxic metabolites through the ubiquitination process...
September 7, 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/30194627/computational-study-of-hcv-p7-channel-insight-into-a-new-strategy-for-hcv-inhibitor-design
#2
Beili Ying, Shichao Pang, Junchen Yang, Yang Zhong, Jingfang Wang
HCV p7 protein is a cation-selective ion channel, playing an essential role during the life cycle of HCV viruses. To understand the cation-selective mechanism, we constructed a hexameric model in lipid bilayers of HCV p7 protein for HCB JFH-1 strain, genotype 2a. In this structural model, His9 and Val6 were key factors for the HCV cation-selective ion channel. The histidine residues at position 9 in the hexameric model formed a first gate for HCV p7 channel, acting as a selectivity filter for cations. The valines mentioned above formed a second gate for HCV p7 channel, serving as a hydrophobic filter for the dehydrated cations...
September 7, 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/30182355/identification-of-effective-dimeric-gramicidin-d-peptide-as-antimicrobial-therapeutics-over-drug-resistance-in-silico-approach
#3
G Pavithrra, R Rajasekaran
Discovering and developing the antimicrobial peptides are recently focused on pharmaceutical firm, since they serve as complementary to antibiotics in prevailing over drug resistance by eliciting the disruption of microbial membrane. Still, there are lots of challenges to bring up the structurally stable and functionally efficient antimicrobial peptides. It is well known that gramicidin D is the prominent antimicrobial peptide that exists as g-AB, g-BC, and g-AC. This study analyzes the structural stability and the functional activity of hetero-dimeric double-stranded gramicidin-D peptides, thereby demonstrating its potent antimicrobial activity against antibiotic-resistant micro-organisms...
September 4, 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/30168035/an-efficient-design-for-a-multi-objective-evolutionary-algorithm-to-generate-dna-libraries-suitable-for-computation
#4
José M Chaves-González, Jorge Martínez-Gil
The design of reliable DNA libraries that can be used for bio-molecular computing involves several heterogeneous conflicting design criteria that traditional optimization approaches do not fit properly. As it is well known, evolutionary algorithms are very appropriate for solving complex NP-hard optimization problems. However, these approaches take significant computational resources when large instances of complex problems are managed. This is the case for the design of DNA libraries suitable for computation, which involves a set of conflicting design criteria that have to be simultaneously optimized...
August 30, 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/30066129/structure-based-virtual-screening-of-high-affinity-atp-competitive-inhibitors-against-human-lemur-tyrosine-kinase-3-lmtk3-domain-a-novel-therapeutic-target-for-breast-cancer
#5
Himakshi Sarma, Venkata Satish Kumar Mattaparthi
Human lemur tyrosine kinase-3 (LMTK3) is an oncogenic kinase known to regulate ER-α through phosphorylation and is considered to be a novel therapeutic target for breast cancer. In this work, we have studied the ATP-binding mechanism with LMTK3 domain and also carried out virtual screening on LMTK3 to identify lead compounds using Dock blaster server. The top scored compounds obtained from Dock blaster were then narrowed down further to six lead compounds (ZINC37996511, ZINC83363046, ZINC3745998, ZINC50456700, ZINC83351792 and ZINC83364581) based on high-binding affinity and non-bonding interactions with LMTK3 using Autodock 4...
July 31, 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/30039492/transcription-factors-contribute-to-differential-expression-in-cellular-pathways-in-lung-adenocarcinoma-and-lung-squamous-cell-carcinoma
#6
Shiyi Liu, Xujun Wang, Wenyi Qin, Georgi Z Genchev, Hui Lu
Lung cancers are broadly classified into small cell lung cancers and non-small cell lung cancers (NSCLC). Lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) are two common subtypes of NSCLC, and despite the fact that both occur in lung tissues, these two subtypes show a number of different pathological characteristics. To investigate the differences and seek potential therapy targets, we used bioinformatics methods to analyze RNA-Seq data from different aspects. The previous studies and comparative pathway enrichment analysis on publicly available data showed that expressed or inhibited genes are different in two cancer subtypes through important pathways...
July 23, 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/30030786/comparative-analysis-of-crispr-loci-found-in-streptomyces-genome-sequences
#7
Jinqi Zhang, Xiaobin Li, Zixin Deng, Hong-Yu Ou
The interspaced short palindromic repeats (CRISPR) system is an immune system widely distributed in prokaryotes, resisting the invasion of the foreign mobile genetic elements like phages or plasmids. In this study, we present the comparative analysis of 182 CRISPR loci found in 46 publicly available complete genome sequences of Streptomyces. Overall, nine direct repeats (DRs) groups are identified while all the 2104 spacers are divided into three main groups according to the multiple sequence alignment. Only 11 spacers are identical with parts of 10 plasmid sequences, which indicates a possible origin...
July 20, 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29728983/study-on-feature-selection-methods-for-depression-detection-using-three-electrode-eeg-data
#8
Hanshu Cai, Yunfei Chen, Jiashuo Han, Xiangzi Zhang, Bin Hu
The early diagnosis of depression is important to the treatment of this condition, whereas a timely diagnosis can reduce the incidence of mortality caused in patients with depression. In the present study, we collected the EEG signals of Fp2, Fpz and Fp1, compared with 128 channels EEG, a simpler test (3 channels EEG) can make diagnosis more accessible and widespread, researchers can perform more tests on more patients given the same amount of time and money. The difference between the depressed and the non-depressed patients was explored by the linear and non-linear characteristics of these EEG signals...
September 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29691712/gc-formula-see-text-nmf-a-novel-matrix-factorization-framework-for-gene-phenotype-association-prediction
#9
Yaogong Zhang, Jiahui Liu, Xiaohu Liu, Yuxiang Hong, Xin Fan, Yalou Huang, Yuan Wang, Maoqiang Xie
Gene-phenotype association prediction can be applied to reveal the inherited basis of human diseases and facilitate drug development. Gene-phenotype associations are related to complex biological processes and influenced by various factors, such as relationship between phenotypes and that among genes. While due to sparseness of curated gene-phenotype associations and lack of integrated analysis of the joint effect of multiple factors, existing applications are limited to prediction accuracy and potential gene-phenotype association detection...
September 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29549628/iikmta-inter-and-intra-kingdom-mirna-target-analyzer
#10
Chittabrata Mal, Md Aftabuddin, Sudip Kundu
BACKGROUND: Growing evidences suggest that microRNAs (miRNAs) can efficiently regulate gene expression at intracellular and extracellular levels. It has been previously reported that plant/food-derived miRNAs are highly enriched in human serum or serum from phytophagous animals, and they are responsible for regulating mammalian gene expression. Thus, miRNAs could function as active signaling molecules, which carry information across distinct species or even kingdoms. However, the mode of miRNA shuttling among various organisms is still a mystery to unravel...
September 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29492842/genome-wide-pathway-analysis-of-microarray-data-identifies-risk-pathways-related-to-salt-stress-in-arabidopsis-thaliana
#11
Mingming Zhang, Hongbo Mu, Ruijie Zhang, Shenkui Liu, Imshik Lee
Salt stress is a common abiotic stress in agricultural production, which is affected by multiple genes and environmental factors. Although transcriptome analyses have detected some salt-related genes in Arabidopsis thaliana, these genes are often major genes and can not adequately explain the molecular mechanism of salt tolerance. Some genes related to salt stress, but does not reach significant threshold in gene expression analysis (called modest effect genes), are often ignored. Therefore, we took full account of the role of modest effect genes and performed a pathway-based analysis of three gene microarray datasets to identify the pathways related to salt stress...
September 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29280088/visnormsc-a-graphical-user-interface-to-normalize-single-cell-rna-sequencing-data
#12
Lijun Tang, Nan Zhou
Single-cell RNA sequencing (RNA-seq) allows the analysis of gene expression with high resolution. The intrinsic defects of this promising technology imports technical noise into the single-cell RNA-seq data, increasing the difficulty of accurate downstream inference. Normalization is a crucial step in single-cell RNA-seq data pre-processing. SCnorm is an accurate and efficient method that can be used for this purpose. An R implementation of this method is currently available. On one hand, the R package possesses many excellent features from R...
September 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29094319/an-innovative-framework-for-bioimage-annotation-and-studies
#13
Patrizia Vizza, Giuseppe Tradigo, Pietro Hiram Guzzi, Rosario Curia, Loredana Sisca, Filippo Aiello, Gionata Fragomeni, Mario Cannataro, Giuseppe Lucio Cascini, Pierangelo Veltri
The collection and analysis of clinical data are needed to investigate diseases and to define medical protocols and treatments. Bioimages, medical annotations and patient history are clinical data acquired and studied to perform a correct diagnosis and to propose an appropriate therapy. Currently, hospital departments manage these data using legacy systems which do not often allow data integration among different departments or health structures. Thus, in many cases clinical information sharing and exchange are difficult to implement...
September 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28361256/computational-approaches-and-related-tools-to-identify-micrornas-in-a-species-a-bird-s-eye-view
#14
REVIEW
Anjana Rajendiran, Aniruddha Chatterjee, Archana Pan
MicroRNAs (miRNAs) are a family of non-coding RNAs that play a central role in fine-tuning gene expression regulation. Over the past decade, identification and annotation of miRNAs have become a major focus in epigenomics research. However, detection and characterization of miRNA are challenging due to its small size (~22 nucleotide-long) and susceptibility to degradation. The difficulties involved in experimental prediction and characterization of miRNA coding genes have led to the development of in silico-based approaches...
September 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28290051/construction-of-a-comprehensive-protein-protein-interaction-map-for-vitiligo-disease-to-identify-key-regulatory-elements-a-systemic-approach
#15
Anvita Gupta Malhotra, Mohit Jha, Sudha Singh, Khushhali M Pandey
Vitiligo is an idiopathic disorder characterized by depigmented patches on the skin due to progressive loss of melanocytes. Several genetic, immunological, and pathophysiological investigations have established vitiligo as a polygenetic disorder with multifactorial etiology. However, no definite model explaining the interplay between these causative factors has been established hitherto. Therefore, we studied the disorder at the system level to identify the key proteins involved by exploring their molecular connectivity in terms of topological parameters...
September 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28283929/molecular-docking-studies-to-explore-potential-binding-pockets-and-inhibitors-for-chikungunya-virus-envelope-glycoproteins
#16
Phuong T V Nguyen, Haibo Yu, Paul A Keller
The chikungunya virus (CHIKV) envelope glycoproteins are considered important potential targets for anti-CHIKV drug discovery due to their crucial roles in virus attachment and virus entry. In this study, using two available crystal structures of the immature and mature forms of envelope glycoproteins, virtual screenings based on blind dockings and focused dockings were carried out to identify potential binding pockets and hit compounds for the virus. The chemical library database of compounds, NCI Diversity Set II, was used in these docking studies...
September 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28247172/an-algorithm-for-sequencing-by-hybridization-based-on-an-alternating-dna-chip
#17
Marcin Radom, Piotr Formanowicz
Sequencing by hybridization allows the reconstruction of the DNA string of a given length from smaller fragments. These fragments are obtained in the hybridization experiment in which the DNA hybridizes to a DNA chip. In a classical approach, the chip consists of all oligonucleotides of a given length, with only one type of oligonucleotide for each probe of the chip. In this paper, we propose an algorithm solving the non-classical case of SBH, where the chip probes consist set of oligonucleotides described by some specific pattern...
September 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28217823/novel-insight-from-computational-virtual-screening-depict-the-binding-potential-of-selected-phytotherapeutics-against-probable-drug-targets-of-clostridium-difficile
#18
Suman Kamath, Sinosh Skariyachan
This study explores computational screening and molecular docking approaches to screen novel herbal therapeutics against probable drug targets of Clostridium difficile. The essential genes were predicted by comparative genome analysis of C. difficile and best homologous organisms using BLAST search at database of essential genes (DEG). The functions of these genes in various metabolic pathways were predicted and some of these genes were considered as potential targets. Three major proteins were selected as putative targets, namely permease IIC component, ABC transporter and histidine kinase...
September 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/27981429/theoretical-studies-on-azaindoles-as-human-aurora-b-kinase-inhibitors-docking-pharmacophore-and-admet-studies
#19
Rajashekar Vadlakonda, Raghunandan Nerella, Sreenivas Enaganti
Aurora kinases are the cell cycle mitotic regulators processing multiple functions during cell division. Altered mechanism of these mitotic kinases may contribute to genomic instability that is most often correlated with tumorigenesis, which has been reported in many human cancers. Selective blockage of the aberrantly expressed Aurora kinases has the potential therapeutic assessment to control the deregulated cell cycle machinery and their associated risks of cancer. Using a combination of docking-, ligand- and structure-based pharmacophore strategies, in the present study, we have tried to predict the anticancer potentiality of our synthesized compounds (A1 to A5 and B1 to B9) against human Aurora B kinase...
September 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/27900730/understanding-the-interactions-of-high-mobility-group-of-protein-domain-b1-with-dna-adducts-generated-by-platinum-anticancer-molecules-using-in-silico-approaches
#20
Gauri Misra, Shipra Gupta, Neetu Jabalia
Platinum coordination compounds having cis geometry are frequently prescribed for various types of cancers. Protein dysregulation is one of the major factors contributing towards cancer metastasis. Head and neck squamous cell carcinoma (HNSCC) is one of the cancers where platinum-based compounds are used either alone or in combination with radiation as therapy. The underlying interactions of these compounds with both DNA and proteins are crucial for the drug response. The compounds forms DNA adducts which are recognized by conserved, non-chromosomal high-mobility group box 1 (HMGB1) proteins...
September 2018: Interdisciplinary Sciences, Computational Life Sciences
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