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Computational Biology and Chemistry

Senthilnathan Rajendran, Arunachalam Jothi
The Three-dimensional structure of a protein depends on the interaction between their amino acid residues. These interactions are in turn influenced by various biophysical properties of the amino acids. There are several examples of proteins that share the same fold but are very dissimilar at the sequence level. For proteins to share a common fold some crucial interactions should be maintained despite insignificant sequence similarity. Since the interactions are because of the biophysical properties of the amino acids, we should be able to detect descriptive patterns for folds at such a property level...
May 16, 2018: Computational Biology and Chemistry
Tulika Kakati, Hasin A Ahmed, Dhruba K Bhattacharyya, Jugal K Kalita
Developing a cost-effective and robust triclustering algorithm that can identify triclusters of high biological significance in the gene-sample-time (GST) domain is a challenging task. Most existing triclustering algorithms can detect shifting and scaling patterns in isolation, they are not able to handle co-occurring shifting-and-scaling patterns. This paper makes an attempt to address this issue. It introduces a robust triclustering algorithm called THD-Tricluster to identify triclusters over the GST domain...
May 7, 2018: Computational Biology and Chemistry
Ariana Beste, DeCarlos E Taylor, Tsung-Ming Shih, Thaddeus P Thomas
Organophosphorus nerve agents (NAs) irreversibly inhibit acetylcholinesterase (AChE), the enzyme responsible for breaking down the neurotransmitter acetylcholine (ACh). The over accumulation of ACh after NA exposure leads to cholinergic toxicity, seizure, and death. Current medical countermeasures effectively mitigate peripheral symptoms, however; the brain is often unprotected. Alternative acute treatment with the adenosine A1 receptor agonist N6 -cyclopentyladensosine (CPA) has previously been demonstrated to prevent AChE inhibition as well as to suppress neuronal activity...
May 7, 2018: Computational Biology and Chemistry
Ming-Lang Zhao, Wang Wang, Hu Nie, Sha-Sha Cao, Lin-Fang Du
Histone deacetylases (HDACs) play a significant role in the epigenetic mechanism by catalyzing deacetylation of lysine on histone in both animals and plants. HDACs involved in growth, development and response to stresses in plants. Arabidopsis thaliana histone deacetylase 14 (AtHDA14) is found to localize in the mitochondria and chloroplasts, and it involved in photosynthesis and melatonin biosynthesis. However, its mechanism of action was still unknowns so far. Therefore, in this study, we constructed AtHDA14 protein model using homology modeling method, validated using PROCHECK and presented using Ramachandran plots...
May 6, 2018: Computational Biology and Chemistry
Gokhan Zengin, Ismail Senkardes, Adriano Mollica, Carene Marie Nancy Picot-Allain, Gizem Bulut, Ahmet Dogan, M Fawzi Mahomoodally
Salvia sclarea L. is traditionally used to manage common human ailments and is consumed as a food product. This study aimed to establish the phytochemical profile and antioxidant potential of ethyl acetate, methanol, and water extracts of Salvia sclarea. The inhibitory action of the extracts against α-amylase, α-glucosidase, acetylcholinesterase, butyrylcholinesterase, and tyrosinase was also investigated. Methanol extract showed the highest phenolic and flavonoid contents (81.78 mg GAE/g extract and 40...
May 6, 2018: Computational Biology and Chemistry
Balu Bhasuran, Devika Subramanian, Jeyakumar Natarajan
BACKGROUND AND OBJECTIVES: Travel to elevations above 2500 m is associated with the risk of developing one or more forms of acute altitude illness such as acute mountain sickness (AMS), high altitude cerebral edema (HACE) or high altitude pulmonary edema (HAPE). Our work aims to identify the functional association of genes involved in high altitude diseases. METHOD: In this work we identified the gene networks responsible for high altitude diseases by using the principle of gene co-occurrence statistics from literature and network analysis...
May 2, 2018: Computational Biology and Chemistry
Yanying Hu, Qingyuan Hua, Guojuan Sun, Kunpeng Shi, Huitu Zhang, Kai Zhao, Shiru Jia, Yujie Dai, Qingli Wu
The toxic ginkgolic acids are the main safety concern for the application of Ginkgo biloba. In this study, the degradation ability of salicylic acid decarboxylase (SDC) for ginkgolic acids was examined using ginkgolic acid C15:1 as a substrate. The results indicated that the content of ginkgolic acid C15:1 in Ginkgo biloba seeds was significantly decreased after 5 h treatment with SDC at 40 °Cand pH 5.5. In order to explore the structure of SDC and the interaction between SDC and substrates, homology modeling, molecular docking and molecular dynamics were performed...
May 2, 2018: Computational Biology and Chemistry
Jiaqi Wu, Tao Zhou, Jin Tao, Yabing Hai, Fei Ye, Xiaoqing Liu, Qi Dai
Protein Structure Similarity plays an important role in study on functional properties of proteins and evolutionary study. Many efficient methods have been proposed to advance protein structural comparison, but there are still some challenges in the contact strength definitions and similarity measures. In this work, we schemed out a new method to analyze the similarity/dissimilarity of the protein structures based on Markov random fields. We evaluated the proposed method with two experiments and compared it with the competing methods The results indicate that the proposed method exhibits a strong ability to detect the similarities/dissimilarities among the conformation of different cyclic peptides and protein structures...
May 1, 2018: Computational Biology and Chemistry
José Luiz Carneiro da Rocha, Danielle Figuerêdo da Silva, Anne Ramos de Santana, Diego Mota da Costa, José Floriano Barêa Pastore, Clayton Queiroz Alves, Manoelito Coelho Santos Santos Junior, Hugo Neves Brandão
BACKGROUND: In Brazil, the Asemeia genus has 19 species (12 endemic) and 2 varieties (both endemic) and some of them are found in semi-arid Bahia. OBJECTIVE: The objective of this study was to quantitatively determine identified substances by HPLC-DAD in Asemeia ovata extracts and to predict their biological activities in silico. METHOD: The quantification method by HPLC-DAD has been validated according to the guidelines of the International Conference of Harmonization...
April 30, 2018: Computational Biology and Chemistry
Sutapa Mondal Roy
The quantum chemical descriptors based on density functional theory (DFT) are applied to predict the biological activity (log IC50 ) of one class of acyl-CoA: cholesterol O-acyltransferase (ACAT) inhibitors, viz. aminosulfonyl ureas. ACAT are very effective agents for reduction of triglyceride and cholesterol levels in human body. Successful two parameter quantitative structure-activity relationship (QSAR) models are developed with a combination of relevant global and local DFT based descriptors for prediction of biological activity of aminosulfonyl ureas...
April 27, 2018: Computational Biology and Chemistry
Anum Munir, Sana Elahi, Nayyer Masood
EGFRs are a vast group of receptor tyrosine kinases playing an important role in a number of tumors, including lungs, head and neck, breast, and esophageal cancers. A couple of techniques are being used in the process of drug design. Drug repositioning or repurposing is a rising idea that consists of distinguishing modern remedial indications for officially existing dynamic pharmaceutical compounds. Here, a novel approach of analyzing drug-drug interaction networks, based on clustering methodology is used to reposition effective compounds against mutant EGFR having G719X, exon 19 deletions/insertions, L858R, and L861Q mutations...
April 27, 2018: Computational Biology and Chemistry
Anderson Rici Amorim, Leandro Alves Neves, Carlos Roberto Valêncio, Guilherme Freire Roberto, Geraldo Francisco Donegá Zafalon
Multiple sequence alignment (MSA) is one of the most important tasks in bioinformatics and it can be used to prediction of structures or functions of unknown proteins and to phylogenetic tree reconstruction. There are many heuristics to perform multiple sequence alignment, as Progressive Alignment, Ant Colony, Genetic Algorithms, among others. Along the years, some tools were proposed to perform MSA and MSA-GA is one of them. The MSA-GA is a tool based on Genetic Algorithm to perform multiple sequence alignment and its results are generally better than other well-known tools in bioinformatics, as Clustal W...
April 25, 2018: Computational Biology and Chemistry
Hussaina Banu, Maria Christina Joseph, Mokashi Nida Nisar
The current research is based on computational study of the Death Domain (DD) superfamily of proteins involved in the cytoplasmic inflammasome complexes associated with apoptosis and inflammation in response to the nanoparticle treatment. The PYD domains of the DD superfamily proteins, NALP3 and ASC, were chosen for investigation as they are found to be primarily involved in the regulation of innate immunity and are associated with apoptosis and inflammation. The in-vitro studies of these proteins have proven to be a challenge as the proteins have a tendency to aggregate under laboratory conditions...
April 23, 2018: Computational Biology and Chemistry
Sana Farooq Ahmad, Ibrar Khan, Abdul Wadood, Sadiq Azam, Noor Rehman, Muhammad Waqas, Kashif Bashir, Asaf Ali Khan
Hospitals are the most prominent places for the growth and spread of bacteria which are resistant to the available antibiotics. This antibiotic resistance is due to the over and misuse of antibiotic dosages of a high-density of patient population which are in frequent interaction with inanimate items of the hospitals and the consequent risk of cross infection. Out of 1010 samples of the current study, 510 (50.49%) were culture positive of which 329 (64.5%) were Gram-positive while 181 (35.49%) Gram negative...
April 22, 2018: Computational Biology and Chemistry
Xiaoyan Lv, Ying Jin, Yuguang Wang
Sugar beet (Beta vulgaris) is an important crop of sugar production in the world. Previous studies reported that sugar beet monosomic addition line M14 obtained from the intercross between Beta vulgaris L. (cultivated species) and B. corolliflora Zoss (wild species) exhibited tolerance to salt (up to 0.5 M NaCl) stress. To estimate a broad spectrum of genes involved in the M14 salt tolerance will help elucidate the molecular mechanisms underlying salt stress. Comparative transcriptomics was performed to monitor genes differentially expressed in the leaf and root samples of the sugar beet M14 seedlings treated with 0, 200 and 400 mM NaCl, respectively...
April 22, 2018: Computational Biology and Chemistry
Shailima Rampogu, Minky Son, Ayoung Baek, Chanin Park, Rabia Mukthar Rana, Amir Zeb, Saravanan Parameswaran, Keun Woo Lee
Human epidermal growth factor receptors are implicated in several types of cancers characterized by aberrant signal transduction. This family comprises of EGFR (ErbB1), HER2 (ErbB2, HER2/neu), HER3 (ErbB3), and HER4 (ErbB4). Amongst them, HER2 is associated with breast cancer and is one of the most valuable targets in addressing the breast cancer incidences. For the current investigation, we have performed 3D-QSAR based pharmacophore search for the identification of potential inhibitors against the kinase domain of HER2 protein...
April 20, 2018: Computational Biology and Chemistry
Muhammad Arba, Andry Nur-Hidayat, Ruslin, Muhammad Yusuf, Sumarlin, Rukman Hertadi, Setyanto Tri Wahyudi, Slamet Ibrahim Surantaadmaja, Daryono H Tjahjono
The ubiquitin-proteasome system plays an important role in protein quality control. Currently, inhibition of the proteasome has been validated as a promising approach in anticancer therapy. The 20S core particle of the proteasome harbors β5 subunit which is a crucial active site in proteolysis. Targeting proteasome β5 subunit which is responsible for the chymotrypsin-like activity of small molecules has been regarded as an important way for achieving therapeutics target. In the present study, a series of porphyrin derivatives bearing either pyridine or pyrazole rings as meso-substituents were designed and evaluated as an inhibitor for the β5 subunit of the proteasome by employing molecular docking and dynamics simulations...
April 16, 2018: Computational Biology and Chemistry
Mlađan Golubović, Milan Lazarević, Dragan Zlatanović, Dane Krtinić, Viktor Stoičkov, Bojan Mladenović, Dragan J Milić, Dušan Sokolović, Aleksandar M Veselinović
Up to this date, there has been an ongoing debate about the mode of action of general anesthetics, which have postulated many biological sites as targets for their action. However, postoperative nausea and vomiting are common problems in which inhalational agents may have a role in their development. When a mode of action is unknown, QSAR modelling is essential in drug development. To investigate the aspects of their anesthetic, QSAR models based on the Monte Carlo method were developed for a set of polyhalogenated ethers...
April 13, 2018: Computational Biology and Chemistry
Ting Yu, Pradeep Paudel, Su Hui Seong, Jeong Ah Kim, Hyun Ah Jung, Jae Sue Choi
The rhizome of Salvia miltiorrhiza has emerged as a rich source of natural therapeutic agents, and its several compounds are supposed to exhibit favorable effects on Alzheimer's disease (AD). The present work investigate the anti-AD potentials of 12 tanshinones, three salvianolic acids and three caffeic acid derivatives from S. miltiorrhiza via the inhibition of β-site amyloid precursor protein cleaving enzyme 1 (BACE1). Among the tested compounds, deoxyneocryptotanshinone (1), salvianolic acid A (13) and salvianolic acid C (15) displayed good inhibitory effect on BACE1 with IC50 values of 11...
April 13, 2018: Computational Biology and Chemistry
Ernst Joachim Houtgast, Vlad-Mihai Sima, Koen Bertels, Zaid Al-Ars
We present our work on hardware accelerated genomics pipelines, using either FPGAs or GPUs to accelerate execution of BWA-MEM, a widely-used algorithm for genomic short read mapping. The mapping stage can take up to 40% of overall processing time for genomics pipelines. Our implementation offloads the Seed Extension function, one of the main BWA-MEM computational functions, onto an accelerator. Sequencers typically output reads with a length of 150 base pairs. However, read length is expected to increase in the near future...
April 12, 2018: Computational Biology and Chemistry
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