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Computational Biology and Chemistry

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https://www.readbyqxmd.com/read/28432981/hidden-markov-model-and-chapman-kolmogrov-for-protein-structures-prediction-from-images
#1
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
#2
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
#3
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
#4
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
#5
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/28396055/efficiently-predicting-large-scale-protein-protein-interactions-using-mapreduce
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
https://www.readbyqxmd.com/read/28359874/in-silico-analysis-of-nonsynonymous-single-nucleotide-polymorphisms-of-the-human-adiponectin-receptor-2-adipor2-gene
#14
Md Solayman, Md Abu Saleh, Sudip Paul, Md Ibrahim Khalil, Siew Hua Gan
Polymorphisms of the ADIPOR2 gene are frequently linked to a higher risk of developing diseases including obesity, type 2 diabetes and cardiovascular diseases. Though mutations of the ADIPOR2 gene are detrimental, there is a lack of comprehensive in silico analyses of the functional and structural impacts at the protein level. Considering the involvement of ADIPOR2 in glucose uptake and fatty acid oxidation, an in silico functional analysis was conducted to explore the possible association between genetic mutations and phenotypic variations...
March 14, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28355588/dihydropyrazole-and-dihydropyrrole-structures-based-design-of-kif15-inhibitors-as-novel-therapeutic-agents-for-cancer
#15
Jomon Sebastian
Mitotic Kinesin motors, Eg5 and Kif15, have recently emerged as good targets for cancer as they play an inevitable role during mitosis. But, most of the Eg5 inhibitors were found ineffective when the cancer cells develop resistance to them by escalating the expression of Kif15 as alternative to Eg5. Therefore, the drugs that target Kif15 became necessary to be used either as a single or in combination with Eg5 inhibitors. The present study used 39 dihydropyrazole and 13 dihydropyrrole derivatives that were having in vitro inhibitory potential against kinesin motors to develop a common pharmacophore hypothesis AHRR and atom-based QSAR model...
March 12, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28342423/a-bioinformatics-approach-to-designing-a-zika-virus-vaccine
#16
Sumanta Dey, Ashesh Nandy, Subhash C Basak, Papiya Nandy, Sukhen Das
The Zika virus infections have reached epidemic proportions in the Latin American countries causing severe birth defects and neurological disorders. While several organizations have begun research into design of prophylactic vaccines and therapeutic drugs, computer assisted methods with adequate data resources can be expected to assist in these measures to reduce lead times through bioinformatics approaches. Using 60 sequences of the Zika virus envelope protein available in the GenBank database, our analysis with numerical characterization techniques and several web based bioinformatics servers identified four peptide stretches on the Zika virus envelope protein that are well conserved and surface exposed and are predicted to have reasonable epitope binding efficiency...
March 10, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28288354/pharmacophore-based-3d-qsar-modeling-virtual-screening-and-docking-for-identification-of-potential-inhibitors-of-%C3%AE-secretase
#17
Ravichand Palakurti, Ramakrishna Vadrevu
The enzyme β-secretase-1 is responsible for the cleavage of the amyloid precursor protein, a vital step in the process of the formation of amyloid-β peptides which are known to lead to neurodegeneration causing Alzheimer's disease. Challenges associated with toxicity and blood brain permeation inability of potential inhibitors, continue to evade a successful therapy, thus demanding the search and development of highly active and effective inhibitors. Towards these efforts, we used a ligand based pharmacophore model generation from a dataset of known inhibitors whose activities against β-secretase hovered in the nano molar range...
March 6, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28327441/structure-based-design-synthesis-and-biological-evaluation-of-amino-phosphonate-derivatives-as-human-glucokinase-activators
#18
Nanda Kumar Yellapu, Ravendra Babu Kilaru, Nagaraju Chamarthi, Sarma Pvgk, Bhaskar Matcha
Glucokinase (GK) is a potential therapeutic target of type 2 diabetes and GK activators (GKAs) represent a promising class of small organic molecules which enhance GK activity. Based on the configuration and conformation of the allosteric site of GK, we have designed a novel class of amino phosphonate derivatives in order to develop potent GKAs. The QSAR model developed using numerous descriptors revealed its potential with the best effective statistical values of RMSE=1.52 and r(2)=0.30. Moreover, application of this model on the present test set GKAs proved to be worthy to predict their activities as a better linear relationship was observed with RMSE=0...
March 2, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28282565/genome-wide-identification-and-characterization-of-conserved-and-novel-micrornas-in-grass-carp-ctenopharyngodon-idella-by-deep-sequencing
#19
Wangbao Gong, Yong Huang, Jun Xie, Guangjun Wang, Deguang Yu, Xihong Sun
MicroRNAs (miRNAs) are post-transcriptional regulators which bind to target to regulate protein expression by repressing translation or promoting degradation of the target mRNA. Studies have shown that deep sequencing is a powerful tool for the identification of miRNAs, and it is believed that may more miRNAs remain to be discovered in grass carp. In the present study, a pool of equal amounts of RNA obtained from 8 different adult grass carp tissues (spleen, liver, muscle, kidney, skin, testis, gut and heart) was sequenced using deep sequencing technology...
March 2, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28292731/pathway-cross-talk-network-analysis-identifies-critical-pathways-in-neonatal-sepsis
#20
Yu-Xiu Meng, Quan-Hong Liu, Deng-Hong Chen, Ying Meng
BACKGROUND: Despite advances in neonatal care, sepsis remains a major cause of morbidity and mortality in neonates worldwide. Pathway cross-talk analysis might contribute to the inference of the driving forces in bacterial sepsis and facilitate a better understanding of underlying pathogenesis of neonatal sepsis. OBJECTIVE: This study aimed to explore the critical pathways associated with the progression of neonatal sepsis by the pathway cross-talk analysis. METHODS: By integrating neonatal transcriptome data with known pathway data and protein-protein interaction data, we systematically uncovered the disease pathway cross-talks and constructed a disease pathway cross-talk network for neonatal sepsis...
February 27, 2017: Computational Biology and Chemistry
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