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Computational Biology and Chemistry

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https://www.readbyqxmd.com/read/28734179/computational-analysis-for-the-determination-of-deleterious-nssnps-in-human-mthfd1-gene
#1
Mansi Desai, J B Chauhan
Single nucleotide polymorphisms (SNPs) are the most common genetic polymorphisms and play a major role in many inherited diseases. Methylenetetrahydrofolate dehydrogenase 1 (MTHFD1) is one of the enzymes involved in folate metabolism. In the present study, the functional and structural consequences of nsSNPs of human MTHFD1 gene was analyzed using various computational tools like SIFT, PolyPhen2, PANTHER, PROVEAN, SNAP2, nsSNPAnalyzer, PhD-SNP, SNPs&GO, I-Mutant, MuPro, ConSurf, InterPro, NCBI Conserved Domain Search tool, ModPred, SPARKS-X, RAMPAGE, FT Site and PyMol...
July 11, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28709136/tetracyclines-as-a-potential-antiviral-therapy-against-crimean-congo-hemorrhagic-fever-virus-docking-and-molecular-dynamic-studies
#2
Amirhossein Sharifi, Arash Amanlou, Faezeh Moosavi-Movahedi, Sahand Golestanian, Massoud Amanlou
Crimean-Congo Hemorrhagic Fever Virus (CCHFV) is one of the deadliest human diseases with mortality rate near 50%. Special attention should be paid to this virus since there is no approved treatment for it. On the other hand, the recent outbreak of Ebola virus which is a member of hemorrhagic fever viruses shows this group of viruses can be extremely dangerous. Previous studies have indicated that nucleoprotein of CCHFV, a pivotal protein in virus replication, is an appropriate target for antiviral drug development...
July 1, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28689108/multi-objective-feature-selection-for-warfarin-dose-prediction
#3
Mohammad Karim Sohrabi, Alireza Tajik
With increasing the application of decision support systems in various fields, using such systems in different aspects of medical science has been growing. Drug's dose prediction is one of the most important issues which can be improved using decision support systems. In this paper, a new multi-objective feature approach has been proposed to support warfarin dose prediction decision. Warfarin is an anticoagulant normally used in the prevention of the formation of clots. This research was conducted on 553 patients during 2013-2015 who were candidates for using warfarin and their INR was in the target range...
June 28, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28666141/computational-design-of-peptide-ligands-to-target-the-intermolecular-interaction-between-viral-envelope-protein-and-pediatric-receptor
#4
Darong Xu, Hongliang Bian, Jinlan Cai, Daocheng Bao, Qing Jin, Min Zhu, Cuifeng Zhang, Tingting Tao
The recognition and binding of viral envelope protein to pediatric receptor subverts the membrane-trafficking apparatus to mediate virion export in young children. Here, we described a successful computational design of peptide ligands to target the intermolecular interaction between the virus large envelope protein (LHB) and adaptin receptor (ADT). Based on the crystal structure of ADT in complex with an oligopeptide segment corresponding to the core binding site of LHB, a sequence-specific amino acid preference profile was determined systematically for the ADT-binding peptides using structural bioinformatics approach...
June 17, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28600956/differentiating-the-pre-hydrolysis-states-of-wild-type-and-a59g-mutant-hras-an-insight-through-md-simulations
#5
Neeru Sharma, Uddhavesh Sonavane, Rajendra Joshi
The most representative member of the Ras subfamily is its HRas isoform. Ras proteins being GTPases, possess an intrinsic activity to hydrolyze the GTP molecule to GDP. During the transition phases, between active and inactive states, P-loop and switch regions show maximum variations. Various hot-spot Ras mutants (G12V, A59G, Q61L etc) have been reported, that limit the protein's conformation in the permanent active state. In the present study, we aim to explore the structural dynamics of one such crucial mutant of Ras namely A59G which belongs to the conserved Switch II region of the protein...
June 1, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28599209/modelling-toxin-effects-on-protein-biosynthesis-in-eukaryotic-cells
#6
Vladas Skakauskas, Pranas Katauskis
We present a rather generic model for toxin (ricin) inhibition of protein biosynthesis in eukaryotic cells. We also study reduction of the ricin toxic effects with application of antibodies against the RTB subunit of ricin molecules. Both species initially are delivered extracellularly. The model accounts for the pinocytotic and receptor-mediated toxin endocytosis and the intact toxin exocytotic removal out of the cell. The model also includes the lysosomal toxin destruction, the intact toxin motion to the endoplasmic reticulum (ER) for separation of its molecules into the RTA and RTB subunits, and the RTA chain translocation into the cytosol...
May 31, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28601761/improving-virtual-screening-predictive-accuracy-of-human-kallikrein-5-inhibitors-using-machine-learning-models
#7
Xingang Fang, Sikha Bagui, Subhash Bagui
The readily available high throughput screening (HTS) data from the PubChem database provides an opportunity for mining of small molecules in a variety of biological systems using machine learning techniques. From the thousands of available molecular descriptors developed to encode useful chemical information representing the characteristics of molecules, descriptor selection is an essential step in building an optimal quantitative structural-activity relationship (QSAR) model. For the development of a systematic descriptor selection strategy, we need the understanding of the relationship between: (i) the descriptor selection; (ii) the choice of the machine learning model; and (iii) the characteristics of the target bio-molecule...
May 29, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28587987/sphingosine-kinase-1-sk1-allosteric-inhibitors-that-target-the-dimerization-site
#8
Ozge Bayraktar, Elif Ozkirimli, Kutlu Ulgen
The sphingosine kinase 1 (SK1)/sphingosine-1-phosphate (S1P) signaling pathway is a crucial target for numerous human diseases from cancer to cardiovascular diseases. However, available SK1 inhibitors that target the active site suffer from poor potency, selectivity and pharmacokinetic properties. The selectivity issue of the kinases, which share a highly-conserved ATP-pocket, can be overcome by targeting the less-conserved allosteric sites. SK1 is known to function minimally as a dimer; however, the crystal structure of the SK1 dimer has not been determined...
May 29, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28587988/codon-usage-bias-and-its-influencing-factors-for-y-linked-genes-in-human
#9
Monisha Nath Choudhury, Arif Uddin, Supriyo Chakraborty
The non-uniform usage of synonymous codons during translation of a protein is the codon usage bias and is mainly influenced by natural selection and mutation pressure. We have used bioinformatic approaches to analyze codon usage bias of human Y-linked genes. Effective number of codon (ENC) suggested that the overall extent of codon usage bias of genes was low. The relative synonymous codon usage (RSCU) analysis revealed that AGA and CTG codons were over-represented in Y-linked genes. Compositional constraint under mutation pressure influenced the codon usage pattern as revealed by the correspondence analysis (COA)...
May 27, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28575732/extra-precision-docking-free-energy-calculation-and-molecular-dynamics-studies-on-glutamic-acid-derivatives-as-murd-inhibitors
#10
Mohammed Afzal Azam, Srikanth Jupudi
The binding modes of well known MurD inhibitors have been studied using molecular docking and molecular dynamics (MD) simulations. The docking results of inhibitors 1-30 revealed similar mode of interaction with Escherichia coli-MurD. Further, residues Thr36, Arg37, His183, Lys319, Lys348, Thr321, Ser415 and Phe422 are found to be important for inhibitors and E. coli-MurD interactions. Our docking procedure precisely predicted crystallographic bound inhibitor 7 as evident from root mean square deviation (0...
May 22, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28570984/in-silico-identification-of-vaccine-candidates-against-klebsiella-oxytoca
#11
Sandipan Talukdar, Udeshna Bayan, Kandarpa Kr Saikia
Klebsiella oxytoca causes several diseases in immunocompromised as well as healthy individuals. Increasing resistance to a number of antibiotics makes treatment options limited. Prevention using vaccine could be an important solution to get rid of infections caused by Klebsiella oxytoca. In recent time, genome based approaches have contributed significantly in vaccine development. Our aim was to identify the most conserved and immunogenic antigens that can be considered as potential vaccine candidates. KEGG database was used to find out pathways unique to the bacteria...
May 22, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28676201/a-novel-wearable-device-for-continuous-non-invasion-blood-pressure-measurement
#12
Qin Xin, Jianping Wu
In this paper, we have developed a wearable cuffless device for daily blood pressure (BP) measurement. We incorporated the light based sensor and other hard wares in a small volume for BP detection. With optimized algorithm, the real-time BP reading could be achieved, the data could be presented in the screen and be transmitted by internet of things (IoT) for history data comparison and multi-terminal viewing. Thus, further analysis provides the probability for diet or sports suggestion and alarm. We have measured BP from more than 60 subjects, compare to traditional mercury blood pressure meter, no obvious error in both systolic blood pressure (SBP) and diastolic blood pressure (DBP) are detected...
May 19, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28544873/3d-qsar-studies-of-some-reversible-acetyl-cholinesterase-inhibitors-based-on-comfa-and-ligand-protein-interaction-fingerprints-using-pc-ls-svm-and-pls-ls-svm
#13
Hamidreza Ghafouri, Mohsen Ranjbar, Amirhossein Sakhteman
A great challenge in medicinal chemistry is to develop different methods for structural design based on the pattern of the previously synthesized compounds. In this study two different QSAR methods were established and compared for a series of piperidine acetylcholinesterase inhibitors. In one novel approach, PC-LS-SVM and PLS-LS-SVM was used for modeling 3D interaction descriptors, and in the other method the same nonlinear techniques were used to build QSAR equations based on field descriptors. Different validation methods were used to evaluate the models and the results revealed the more applicability and predictive ability of the model generated by field descriptors (Q(2)LOO-CV=1, R(2)ext=0...
May 10, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28527408/subcellular-localization-based-comparative-study-on-radioresistant-bacteria-a-novel-approach-to-mine-proteins-involve-in-radioresistance
#14
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
#15
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
#16
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/28545961/pecc-correcting-contigs-based-on-paired-end-read-distribution
#17
Min Li, Binbin Wu, Xiaodong Yan, Junwei Luo, Yi Pan, Fang-Xiang Wu, Jianxin Wang
MOTIVATION: Cheap and fast next generation sequencing (NGS) technologies facilitate research of de novo assembly greatly. The reliability of contigs is critical to construct reliable scaffolding. However, contigs generated from most assemblers contain errors because of the limitation of assembly strategy and computation complexity. Among all these errors, the misassembly error is one of the most harmful types. RESULTS: In this paper, we propose a new method named "PECC" to identify and correct misassembly errors in contigs based on the paired-end read distribution...
May 1, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28539271/gene-expression-profiling-of-tumor-associated-macrophages-after-exposure-to-single-dose-irradiation
#18
Wei-Hsiang Kung, Ching-Fang Yu, Andy Chi-Lung Lee, Chi-Dung Yang, Yu-Chen Liu, Fang-Hsin Chen, Hsien-Da Huang
Radiotherapy (RT) is a common cancer treatment approach that accounts for nearly 50% of patient treatment; however, tumor relapse after radiotherapy is still a major issue. To study the crucial role of tumor-associated macrophages (TAMs) in the regulation of tumor progression post-RT, microarray experiments comparing TAM gene expression profiles between unirradiated and irradiated tumors were conducted to discover possible roles of TAMs in initiation or contribution to tumor recurrence following RT, taking into account the relationships among gene expression, tumor microenvironment, and immunology...
April 30, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28552695/identification-of-novel-human-renin-inhibitors-through-a-combined-approach-of-pharmacophore-modelling-molecular-dft-analysis-and-in-silico-screening
#19
Dhrubajyoti Gogoi, Vishwa Jyoti Baruah, Amrita Kashyap Chaliha, Bibhuti Bhushan Kakoti, Diganta Sarma, Alak Kumar Buragohain
Renin is an aspartyl protease of the renin-angiotensin system (RAS) and the first enzyme of the biochemical pathway for the generation of angiotensin II - a potent vasoconstrictor involved in the maintenance of cardiovascular homeostasis and the regulation of blood pressure. High enzymatic specificity of renin and its involvement in the catalysis of the rate-limiting step of the RAS hormone system qualify it as a good target for inhibition of hypertension and other associated diseases. Ligand-based pharmacophore model (Hypo1) was generated from a training set of 24 compounds with renin inhibitory activity...
April 27, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28463775/identifying-dynamic-pathway-interactions-based-on-clinical-information
#20
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
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