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Computational Biology and Chemistry

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https://www.readbyqxmd.com/read/28235666/identification-of-novel-anti-cancer-agents-by-applying-insilico-methods-for-inhibition-of-tspo-protein
#1
Manan Bhargavi, Sree Kanth Sivan, Sarita Rajender Potlapally
Cancer is a genomic disease characterised as impaired cellular energy metabolism. Cancer cells derive most of their energy from oxidative phosphorylation unlike normal ones during cell progression TSPO protein present in external mitochondrial membrane, is involved in various cellular functions like Cell proliferation, mitochondrial respiration, synthesis of steroids and also participates in import of cholesterol into the inner mitochondrial membrane from outside of the membrane of mitochondria. The 3D model of TSPO protein is built using comparative homology modelling techniques and validated by proSA, Ramachandran plot and ERRAT in the present work...
February 14, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28231526/enhanced-identification-of-%C3%AE-lactamases-and-its-classes-using-sequence-physicochemical-and-evolutionary-information-with-sequence-feature-characterization-of-the-classes
#2
Abhigyan Nath, S Karthikeyan
β-lactamases provides one of the most successful means of evading the therapeutic effects of β lactam class of antibiotics by many gram positive and gram negative bacteria. On the basis of sequence identity, β-lactamases have been identified into four distinct classes- A, B, C and D. The classes A, C and D are the serine β-lactamases and class B is the metallo-lactamse. In the present study, we developed a two stage cascade classification system. The first-stage performs the classification of β-lactamases from non-β-lactamases and the second-stage performs the further classification of β-lactamases into four different β-lactamase classes...
February 14, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28231525/construction-of-new-est-ssrs-for-fusarium-resistant-wheat-breeding
#3
Aysen Yumurtaci, Hulya Sipahi, Ayed Al-Abdallat, Abdulqader Jighly, Michael Baum
Surveying Fusarium resistance in wheat with easy applicable molecular markers such as simple sequence repeats (SSRs) is a prerequest for molecular breeding. Expressed sequence tags (ESTs) are one of the main sources for development of new SSR candidates. Therefore, 18.292 publicly available wheat ESTs were mined and genotyping of newly developed 55 EST-SSR derived primer pairs produced clear fragments in ten wheat cultivars carrying different levels of Fusarium resistance. Among the proved markers, 23 polymorphic EST-SSRs were obtained and related alleles were mostly found on B and D genome...
February 11, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28214450/in-silico-structural-and-functional-analysis-of-mesorhizobium-acc-deaminase
#4
Krishnendu Pramanik, Tithi Soren, Soumik Mitra, Tushar Kanti Maiti
Nodulation is one of the very important processes of legume plants as it is the initiating event of fixing nitrogen. Although ethylene has essential role in normal plant metabolism but it has also negative impact on plants particularly in nodule formation in legume plants. It is also produced due to a variety of biotic or abiotic stresses. 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase is a rhizobial enzyme which cleaves ACC (immediate precursor of ethylene) into α-ketobutyrate and ammonia. As a result, the level of ethylene from the plant cells is decreased and the negative impact of ethylene on nodule formation is reduced...
February 11, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28235665/an-in-silico-approach-to-find-a-peptidomimetic-targeting-extracellular-domain-of-her3-from-a-her3-nanobody
#5
Z Pourhashem, M Mehrpouya, N Yardehnavi, A Eslamparast, F Kazemi-Lomedasht
HER3 is an important therapeutic target in cancer treatments. HER3 Nanobodies (Nbs) are a novel class of antibodies with several competitive advantages over conventional antibodies. A peptidomimetic derived from these Nbs can be considered to be a small peptide mimicking some of the molecular recognition interactions of a natural peptide or protein in a three-dimensional (3D) space, with a receptor that has improved properties. In this study, we introduce a new approach to design a peptidomimetic derived from HER3 Nb through an in silico analysis...
February 10, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28237780/computer-evaluation-of-vire2-protein-complexes-for-ssdna-transfer-ability
#6
Irina Volokhina, Yury Gusev, Svyatoslav Mazilov, Yelizaveta Moiseeva, Mikhail Chumakov
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 channel in a lipid bilayer and possibly mediate the delivery of the single-stranded transfer DNA-VirD2-VirE2 complex to the plant cell chromosomes. The aim of this work was to perform a computer simulation of VirE2's pore-forming capacity and an evaluation of constructed VirE2 complexes...
February 9, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28236747/2-4-ditellurouracil-and-its-5-fluoro-derivative-theoretical-investigations-of-structural-energetics-and-adme-parameters
#7
Ibrahim A Alswaidan, Kritish Sooknah, Lydia Rhyman, Cemal Parlak, Derek T Ndinteh, Mohamed I Elzagheid, Ponnadurai Ramasami
2,4-Ditellurouracil exhibits keto-enol tautomerism via different pathways resulting in seven tautomers. These pathways were studied in the gas phase using density functional theory method. The functionals used were BLYP, B3LYP and BHLYP and the basis sets were 6-311++G(d,p) for all atoms except that LanL2DZ ECP was used for tellurium atom only. The results indicate that the diketo form is more stable as observed for uracil and its sulfur and selenium analogues. The effect of introducing fluorine at position 5 was also investigated and the energy difference between the diketo and dienol forms is reduced...
February 9, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28193552/rational-design-and-synthesis-of-some-ppar-%C3%AE-agonists-substituted-benzylideneamino-benzylidene-thiazolidine-2-4-diones
#8
Santosh S Chhajed, Shital Chaskar, Sanjay K Kshirsagar, G M Animeshchandra Haldar, Debarshi Kar Mahapatra
The peroxisome proliferator activator receptor-γ (PPAR-γ) remained the most successful target for management of diabetes mellitus. The present work endeavors rational designing of some novel PPAR-γ agonists bearing benzylideneamino-benzylidene-thiazolidine-2,4-dione scaffold. The research involved virtual screening of 37 different molecules by molecular docking studies performed by Molecular Design Suite (MDS) into the ligand binding domain of PPAR-γ receptor to explore the binding affinity and conformations of the molecules...
February 7, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28189106/application-of-sequential-factorial-design-and-orthogonal-array-composite-design-oacd-to-study-combination-of-5-prostate-cancer-drugs
#9
Xiaolong Jia, Yiyang Li, Alok Sharma, Yulong Li, Guohai Xie, Guoyao Wang, Junhui Jiang, Yue Cheng, Xianting Ding
Prostate cancer is one of the most common cancers among men in the United States. It is also a major leading cause of cancer death among men of all races. In order to treat prostate cancer, drug combinations are often applied. Drug combinations target at different pathways of cells can potentially lead to higher efficacy and lower toxicity due to drug synergy. In this paper, we sequentially applied a two-level design and a follow-up orthogonal array composite design (OACD) to investigate combinations of five anti-cancer drugs, namely, doxorubicin, docetaxel, paclitaxel, cis-dichlorodiamine platinum and dihydroartemisinin...
February 4, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28189968/in-silico-analyses-of-heat-shock-protein-60-and-calreticulin-to-designing-a-novel-vaccine-shifting-immune-response-toward-t-helper-2-in-atherosclerosis
#10
Ahmad Karkhah, Mahdiye Saadi, Hamid Reza Nouri
Recent experiments demonstrated that atherosclerosis is a Th1 dominant autoimmune condition, whereas Th2 cells are rarely detected within the atherosclerotic lesions. Several studies have indicated that Th2 type cytokines could be effective in the reduction and stabilization of atherosclerotic plaque. Therefore, the modulation of the adaptive immune response by shifting immune responses toward Th2 cells by a novel vaccine could represent a promising approach to prevent from progression and thromboembolic events in coronary artery disease...
February 3, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28213308/simultaneous-estimation-of-detection-sensitivity-and-absolute-copy-number-from-digital-pcr-serial-dilution
#11
Xutao Deng, Brian S Custer, Michael P Busch, Sonia Bakkour, Tzong-Hae Lee
Digital polymerase chain reaction (dPCR) is a refinement of the conventional PCR approach to nucleic acid detection and absolute quantification. Digital PCR works by partitioning a sample of DNA or cDNA into many individual, parallel PCR reactions. Current quantification methods rely on the assumption that the PCR reactions are always able to detect single target molecules. When the assumption does not hold, the copy numbers will be severely underestimated. We developed a novel dPCR quantification method which determines whether the single copy assumption is violated or not by simultaneously estimating the assay sensitivity and the copy numbers using serial dilution data sets...
February 1, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28187376/genome-wide-analysis-of-excretory-secretory-proteins-in-root-knot-nematode-meloidogyne-incognita-provides-potential-targets-for-parasite-control
#12
Shachi Gahoi, Budhayash Gautam
The root-knot nematode, Meloidogyne incognita causes significant damage to various economically important crops. Infection is associated with secretion of effector proteins into host cytoplasm and interference with host innate immunity. To combat this infection, the identification and functional annotations of Excretory/Secretory (ES) proteins serve as a key to produce durable control measures. The identification of ES proteins through experimental methods are expensive and time consuming while bioinformatics approaches are cost-effective by prioritizing the experimental analysis of potential drug targets for parasitic diseases...
February 1, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28213309/a-new-search-subspace-to-compensate-failure-of-cavity-based-localization-of-ligand-binding-sites
#13
Kalpana Singh, Tapobrata Lahiri
The common exercise adopted in almost all the ligand-binding sites (LBS) predictive methods is to considerably reduce the search space up to a meager fraction of the whole protein. In this exercise it is assumed that the LBS are mostly localized within a search subspace, cavities, which topologically appear to be valleys within a protein surface. Therefore, extraction of cavities is considered as a most important preprocessing step for finally predicting LBS. However, prediction of LBS based on cavity search subspace is found to fail for some proteins...
January 31, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28193551/a-gibbs-sampling-method-to-determine-biomarkers-for-asthma
#14
Zhi-Jian Huang, Qin-Hai Shen, Yan-Sheng Wu, Ya-Li Huang
PURPOSE: To identify potential biomarkers and to uncover the mechanisms underlying asthma based on Gibbs sampling. METHODS: The molecular functions (MFs) with genes greater than 5 were determined using AnnotationMFGO of BAGS package, and the obtained MFs were then transformed to Markov chain (MC). Gibbs sampling was conducted to obtain a new MC. Meanwhile, the average probabilities of MFs were computed via MC Monte Carlo (MCMC) algorithm, followed by identification of differentially expressed MFs based on the probabilities of MF more than 0...
January 22, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28129568/structure-based-virtual-screening-to-identify-the-beta-lactamase-ctx-m-9-inhibitors-an-in-silico-effort-to-overcome-antibiotic-resistance-in-e-coli
#15
Kambiz Davari, Jamileh Nowroozi, Farzaneh Hosseini, Abbas Akhavan Sepahy, Sako Mirzaie
Recently, the quick spreads of broad-spectrum beta-lactams antibiotic resistance in pathogenic strains of bacteria have become a major global health problem. These new emerging resistances cause ineffectiveness of antibiotics and increasing the severity of diseases and treatment costs. Among different and diverse resistance targets, we chose a class A beta lactamase, CTX-M-9, with the aim of identifying new chemical entities to be used for further rational drug design. Based on this purpose, a set of 5000 molecules from the Zinc database have been screened by docking experiments using AutoDock Vina software...
January 22, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28131885/attractors-of-hypertrophic-cardiomyopathy-using-maximal-cliques-and-attract-methods
#16
Ming-Jun Feng, Hui-Min Chu, Cai-Jie Shen, Bin He, Xian-Feng Du, Yi-Bo Yu, Jing Liu, Xiao-Min Chen
BACKGROUND: Our study was designed to identify the differential attractor modules related with hypertrophic cardiomyopathy (HCM) by integrating clustering-based on maximal cliques algorithm and Attract method. METHODS: We firstly recruited the HCM-related microarray data from ArrayExpress database. Next, protein-protein interaction (PPI) networks of normal and HCM were constructed and re-weighted using spearman correlation coefficient (SCC). Then, maximal cliques were found from the PPI networks through the clustering-based on maximal cliques approach...
January 19, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28131019/comparison-of-the-molecular-interactions-of-7-carboxyalkyl-apigenin-derivatives-with-s-cerevisiae-%C3%AE-glucosidase
#17
Y J Qi, H N Lu, J X Liang, Y M Zhao, X E Wang, N Z Jin
As one of the most investigated flavonoids, apigenin, is considered to be a strong α-glucosidase inhibitor. However, the clinical utility of apigenin is limited due to its low solubility. It was reported that the solubility and biological activity can be improved by introducing sole carboxyalkyl group into apigenin, especially the 7'-substitution. With the increase of length of the alkyl chain in carboxyalkyl group, B ring of the apigenin derivative is embedded much more deeply into the binding cavity while the carboxyalkyl stretches to the neighboring cavity...
January 19, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28129567/response-surface-methodology-in-drug-design-a-case-study-on-docking-analysis-of-a-potent-antifungal-fluconazole
#18
Fatemeh Bohlooli, Saghi Sepehri, Nima Razzaghi-Asl
Molecular docking is a valuable in silico technique for discovery/design of bioactive compounds. A current challenge within docking simulations is the incorporation of receptor flexibility. A useful strategy toward solving such problem would be the docking of a typical ligand into the multiple conformations of the target. In this study, a multifactor response surface model was constructed to estimate the AutoDock based binding free energy of fluconazole within multiple conformations of 14α-demethylase (CYP51) (cross docking) as a validated antifungal target...
January 19, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28135686/an-exponential-galerkin-method-for-solutions-of-hiv-infection-model-of-cd4-t-cells
#19
Şuayip Yüzbaşı, Murat Karaçayır
In this study, we consider a nonlinear first order model about the infection of CD4(+) T-cells by HIV. In order to solve it numerically, we present a new method based on exponential polynomials reminiscent of the Galerkin method. Considering the approximate solutions in the form of exponential polynomials, we first substitute these approximate solutions in the original model. Some relations are thus obtained, which we express in terms of matrices. Taking inner product of a set of exponential functions with these matrix expressions then yields a nonlinear system of algebraic equations...
January 18, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28160639/pharmacoinformatics-study-of-piperolactam-a-from-piper-betle-root-as-new-lead-for-non-steroidal-anti-fertility-drug-development
#20
Sk Abdul Amin, Plaban Bhattacharya, Souvik Basak, Shovanlal Gayen, Ashis Nandy, Achintya Saha
Fertility control is a burning problem all over the world to regulate population overflow and maintain ecological balance. This study is an in-silico approach to explore a non-steroidal lead as contraceptive agent in order to avoid several contraindications generated by steroidal analogues. Piperolactam A, an aristolactam isolated from Piper betle Linn. showed binding affinity towards estrogen and progesterone receptor as -8.9 and -9.0Kcal/mol (inhibition constant Ki=0.294μM and 0.249μM) respectively which is even larger than that of reported antagonists such as Rohitukine and OrgC (binding affinity -8...
January 11, 2017: Computational Biology and Chemistry
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