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Computational Biology and Chemistry

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https://www.readbyqxmd.com/read/28527408/subcellular-localization-based-comparative-study-on-radioresistant-bacteria-a-novel-approach-to-mine-proteins-involve-in-radioresistance
#1
Divya Vishambra, Malay Srivastava, Kamal Dev, Varun Jaiswal
Radioresistant bacteria (RRB) are among the most radioresistant organisms and has a unique role in evolution. Along with the evolutionary role, radioresistant organisms play important role in paper industries, bioremediation, vaccine development and possibility in anti-aging and anti-cancer treatment. The study of radiation resistance in RRB was mainly focused on cytosolic mechanisms such as DNA repair mechanism, cell cleansing activity and high antioxidant activity. Although it was known that protein localized on outer areas of cell play role in resistance towards extreme condition but the mechanisms/proteins localized on the outer area of cells are not studied for radioresistance...
May 10, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28527409/molecular-characterization-of-pigeon-torque-teno-virus-pttv-in-jiangsu-province
#2
Zhicheng Zhang, Wei Dai, Dingzhen Dai
The torque teno virus (TTV) is a recently discovered DNA virus that has been detected in many different hosts, including humans, livestock and poultry. To date, there is no report of pigeon TTV (PTTV) from anywhere in the world. To investigate the distribution of PTTV in pigeons from the eastern Chinese province of Jiangsu and characterize their genomes, we employed PCR to detect PTTV in 144 samples collected from 6 pigeon plants in Jiangsu province, amplify complete genomes from representative samples and analyze genetic characteristics using bioinformatics...
May 6, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28501295/discovering-dna-methylation-patterns-for-long-non-coding-rnas-associated-with-cancer-subtypes
#3
Xiaoke Ma, Liang Yu, Peizhuo Wang, Xiaofei Yang
Despite growing evidence demonstrates that the long non-coding ribonucleic acids (lncRNAs) are critical modulators for cancers, the knowledge about the DNA methylation patterns of lncRNAs is quite limited. We develop a systematic analysis pipeline to discover DNA methylation patterns for lncRNAs across multiple cancer subtypes from probe, gene and network levels. By using The Cancer Genome Atlas (TCGA) breast cancer methylation data, the pipeline discovers various DNA methylation patterns for lncRNAs across four major subtypes such as luminal A, luminal B, her2-enriched as well as basal-like...
May 4, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28463775/identifying-dynamic-pathway-interactions-based-on-clinical-information
#4
Shinuk Kim
In this paper, we introduce approaches for inferring dynamic pathway interactions by converting static datasets into dynamic datasets using patients' clinical information. One approach uses survival time-based dynamic datasets, and the other uses grade- and stage-based dynamic datasets. Based on cancer grades and stages, we generated six dynamic levels and obtained two pairs of significant pathways out of twelve enriched pathways. One pair of the pathways included CELL ADHESION MOLECULES CAMS and SYSTEMIC LUPUS ERYTHEMATOSUS (correlation coefficient=1...
April 24, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28460307/cell-to-cell-modeling-of-the-interface-between-atrial-and-sinoatrial-anisotropic-heterogeneous-nets
#5
Gabriel López Garza, Norma P Castellanos, Rafael Godínez
The transition between sinoatrial cells and atrial cells in the heart is not fully understood. Here we focus on cell-to-cell mathematical models involving typical sinoatrial cells and atrial cells connected with experimentally observed conductance values. We are interested mainly in the geometry of the microstructure of the conduction paths in the sinoatrial node. We show with some models that appropriate source-sink relationships between atrial and sinoatrial cells may occur according to certain geometric arrangements...
April 21, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28475980/comprehensive-comparison-of-two-protein-family-of-p-atpases-13a1-and-13a3-in-insects
#6
Samin Seddigh
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 the proper gradients for essential ions across cellular membranes makes P-ATPases crucial for cell survival. In this study, characterization of two families of P-ATPases including P-ATPase 13A1 and P-ATPase 13A3 protein was compared in two different insect species from different orders...
April 15, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28432981/hidden-markov-model-and-chapman-kolmogrov-for-protein-structures-prediction-from-images
#7
Md Sarwar Kamal, Linkon Chowdhury, Mohammad Ibrahim Khan, Amira S Ashour, João Manuel R S Tavares, Nilanjan Dey
Protein structure prediction and analysis are more significant for living organs to perfect asses the living organ functionalities. Several protein structure prediction methods use neural network (NN). However, the Hidden Markov model is more interpretable and effective for more biological data analysis compared to the NN. It employs statistical data analysis to enhance the prediction accuracy. The current work proposed a protein prediction approach from protein images based on Hidden Markov Model and Chapman Kolmogrov equation...
April 13, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28419974/prediction-and-feature-analysis-of-intron-retention-events-in-plant-genome
#8
Ying Cui, Chao Zhang, Meng Cai
Alternative splicing (AS) is a major contributor to increase the potential informational content of eukaryotic genomes by creating multiple mRNA species and proteins from a single gene. In plants, up to 60% genes are alternatively spliced and the most common type of AS is intron retention (IR). Genomic analyses of IR have illuminated its crucial role in shaping the evolution of genomes, in the control of developmental processes, and in the dynamic regulation of the transcriptome to influence phenotype. To explore the relationship between the sequence feature and the formation mechanism of IR, we statistically analyzed the retained introns and proposed an improved random forest-based hybrid method to predict intron retention events in plant genome...
April 13, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28432980/discovery-of-potential-inhibitor-against-human-acetylcholinesterase-a-molecular-docking-and-molecular-dynamics-investigation
#9
Surya Pratap Singh, Dwijendra Gupta
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 been an attractive target of drug discovery for the search of therapeutics against AD. In the recent past hAChE has become hot target for the investigation of new potential therapeutics. We performed virtual screening of entire database against hAChE...
April 12, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28420545/gqsar-modeling-and-combinatorial-library-generation-of-4-phenylquinazoline-2-carboxamide-derivatives-as-antiproliferative-agents-in-human-glioblastoma-tumors
#10
Debolina Goswami, Sukriti Goyal, Salma Jamal, Ritu Jain, Divya Wahi, Abhinav Grover
BACKGROUND: TSPO translocator protein, encoded in humans by the Tspo gene plays a crucial role in mitochondria mediated apoptosis and necrotic cell death through its association with Mitochondrial Permeability Transition pore (MPTP). It has been shown that this function can be exploited as a potential treatment for human Glioblastoma Multiforme. In this study, a novel robust fragment based QSAR model has been developed for a series of 4-phenylquinazoline-2-carboxamides experimentally known to be ligands for TSPO, thus triggering apoptotic mechanism cascade...
April 4, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28389083/node-based-differential-network-analysis-in-genomics
#11
Xiao-Fei Zhang, Le Ou-Yang, Hong Yan
Gene dependency networks often undergo changes in response to different conditions. Understanding how these networks change across two conditions is an important task in genomics research. Most previous differential network analysis approaches assume that the difference between two condition-specific networks is driven by individual edges. Thus, they may fail in detecting key players which might represent important genes whose mutations drive the change of network. In this work, we develop a node-based differential network analysis (N-DNA) model to directly estimate the differential network that is driven by certain hub nodes...
April 4, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28528020/optimal-hybrid-sequencing-and-assembly-feasibility-conditions-for-accurate-genome-reconstruction-and-cost-minimization-strategy
#12
Chun-Chi Chen, Noushin Ghaffari, Xiaoning Qian, Byung-Jun Yoon
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 technology used. To date, many hybrid genome assembly algorithms have been developed that can take reads from multiple read sources to reconstruct the original genome. However, rigorous investigation of the feasibility conditions for complete genome reconstruction and the optimal sequencing strategy for minimizing the sequencing cost has been conspicuously missing...
April 3, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28396055/efficiently-predicting-large-scale-protein-protein-interactions-using-mapreduce
#13
Lun Hu, Xiaohui Yuan, Pengwei Hu, Keith C C Chan
With a rapid development of high-throughput genomic technologies, a vast amount of protein-protein interactions (PPIs) data has been generated for difference species. However, such set of PPIs is rather small when compared with all possible PPIs. Hence, there is a necessity to specifically develop computational algorithms for large-scale PPI prediction. In response to this need, we propose a parallel algorithm, namely pVLASPD, to perform the prediction task in a distributed manner. In particular, pVLASPD was modified based on the VLASPD algorithm for the purpose of improving the efficiency of VLASPD while maintaining a comparable effectiveness...
April 1, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28411471/qsar-docking-studies-of-1-3-thiazinan-3-yl-isonicotinamide-derivatives-for-antitubercular-activity
#14
Trupti S Chitre, Kalyani D Asgaonkar, Shital M Patil, Shiva Kumar, Vijay M Khedkar, Dinesh R Garud
The enzyme - enoyl acyl carrier protein reductase (enoyl ACP reductase) is a validated target for antitubercular activity. Inhibition of this enzyme interferes with mycolic acid synthesis which is crucial for Mycobacterium tuberculosis cell growth. In the present work 2D and 3D quantitative structure activity relationship (QSAR) studies were carried out on a series of thiazinan-Isoniazid pharmacophore to design newer analogues. For 2D QSAR, the best statistical model was generated using SA-MLR method (r(2)=0...
March 30, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28391977/live-phylogeny-with-polytomies-finding-the-most-compact-parsimonious-trees
#15
D Papamichail, A Huang, E Kennedy, J-L Ott, A Miller, G Papamichail
Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed. Certain application domains though, such as viral evolution and transmission, paleontology, linguistics, and phylogenetic stemmatics, often require phylogeny inference that involves placing input species on ancestral tree nodes (live phylogeny), and polytomies. These requirements, despite their prevalence, lead to computationally harder algorithmic solutions and have been sparsely examined in the literature to date...
March 30, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28391063/drugclust-a-machine-learning-approach-for-drugs-side-effects-prediction
#16
Giovanna Maria Dimitri, Pietro Lió
BACKGROUND: Identification of underlying mechanisms behind drugs side effects is of extreme interest and importance in drugs discovery today. Therefore machine learning methodology, linking such different multi features aspects and able to make predictions, are crucial for understanding side effects. METHODS: In this paper we present DrugClust, a machine learning algorithm for drugs side effects prediction. DrugClust pipeline works as follows: first drugs are clustered with respect to their features and then side effects predictions are made, according to Bayesian scores...
March 30, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28363149/chemical-principles-additive-model-aligns-low-consensus-dna-targets-of-p53-tumor-suppressor-protein
#17
Kelly M Thayer, In Sub M Han
Computational prediction of the interaction between protein transcription factors and their cognate DNA binding sites in genomic promoters constitutes a formidable challenge in two situations: when the number of discriminatory interactions is small compared to the length of the binding site, and when DNA binding sites possess a poorly conserved consensus binding motif. The transcription factor p53 tumor suppressor protein and its target DNA exhibit both of these issues. From crystal structure analysis, only three discriminatory amino acid side chains contact the DNA for a binding site spanning ten base pairs...
March 22, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28343125/structural-modeling-of-human-organic-cation-transporters
#18
Tikam Chand Dakal, Rajender Kumar, Dindial Ramotar
Human organic cation transporters (hOCTs) belong to solute carriers (SLC) 22 family of membrane proteins that play a central role in transportation of chemotherapeutic drugs for several clinical and pathological conditions, including cancer and diabetes. These transporters mediate drug transport; however, the precise mechanism of drug-binding and transport by them is not fully uncovered yet, partly due to unavailability of any crystal structure record. In this work, we performed a multi-phasic approach to compute the 3D structural models of seven human organic cation transporters (hOCTs) starting from primary protein sequence...
March 18, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28365475/structural-space-of-intramolecular-peptide-disulfides-analysis-of-peptide-toxins-retrieved-from-venomous-peptide-databases
#19
Panchada Ch V Govindu, Priyanka Chakraborty, Angshu Dutta, Konkallu Hanumae Gowd
Structural space of intramolecular peptide disulfides is the combination of arrangement of even number of cysteine residues in single polypeptide and the disulfide isomers resulting from differential connectivity between cysteine residues. In the current report, we are documenting theoretical analysis and derivation of general formula [2×4({(n2)-1})] to predict possible distinct cysteine patterns for given 'n' even number of cysteine residues in a sequence. Combined formula of predicting distinct cysteine patterns and different disulfide isomers can be used to deduce the truly available structural space of intramolecular peptide disulfides, which may be used in structural analysis of disulfide rich peptides and proteins...
March 15, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28340400/pharmacoinformatics-exploration-of-polyphenol-oxidases-leading-to-novel-inhibitors-by-virtual-screening-and-molecular-dynamic-simulation-study
#20
Mubashir Hassan, Qamar Abbas, Zaman Ashraf, Ahmed A Moustafa, Sung-Yum Seo
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 still remains a challenge in drug discovery. In present study, protein structure prediction, ligand-based pharmacophore modeling, virtual screening, molecular docking and dynamic simulation study were used to screen the strong novel inhibitor to cure melanogenesis...
March 15, 2017: Computational Biology and Chemistry
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