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Computational Biology and Chemistry

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https://www.readbyqxmd.com/read/29195784/a-novel-in-silico-minigene-vaccine-based-on-cd4-t-helper-and-b-cell-epitopes-of-eg95-isolates-for-vaccination-against-cystic-echinococcosis
#1
Mohammad M Pourseif, Gholamali Moghaddam, Behrouz Naghili, Nazli Saeedi, Sepideh Parvizpour, Ahmad Nematollahi, Yadollah Omidi
EG95 oncospheral antigen plays a crucial role in Echinococcus granulosus pathogenicity. Considering the diversity of antigen among different EG95 isolates, it seems to be an ideal antigen for designing a universal multivalent minigene vaccine, so-called multi-epitope vaccine. This is the first in silico study to design a construct for the development of global EG95-based hydatid vaccine against E. granulosus in intermediate hosts. After antigen sequence selection, the three-dimensional structure of EG95 was modeled and multilaterally validated...
November 23, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29191749/design-and-verification-of-halogen-bonding-system-at-the-complex-interface-of-human-fertilization-related-mup-pdz5-domain-with-camk-s-c-terminal-peptide
#2
Juan Wang, Yunjie Guo, Xue Zhang
Calmodulin-dependent protein kinase (CAMK) is physiologically activated in fertilized human oocytes and is involved in the Ca2+ response pathways that link the fertilization calmodulin signal to meiosis resumption and cortical granule exocytosis. The kinase has an unstructured C-terminal tail that can be recognized and bound by the PDZ5 domain of its cognate partner, the multi-PDZ domain protein (MUP). In the current study, we reported a rational biomolecular design of halogen-bonding system at the complex interface of CAMK's C-terminal peptide with MUP PDZ5 domain by using high-level computational approaches...
November 21, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29153893/selective-atp-competitive-leads-of-cdk4-discovery-by-3d-qsar-pharmacophore-mapping-and-molecular-docking-approach
#3
Rohini Rondla, Lavanya Souda PadmaRao, Vishwanath Ramatenki, Aboubakr Haredi-Abdel-Monsef, Sarita Rajender Potlapally, Uma Vuruputuri
The discovery of ATP competitive CDK4 inhibitors is an on-going challenging task in cancer therapy. Here, an attempt has been made to develop new leads targeting ATP binding site of CDK4 by applying 3D-QSAR pharmacophore mapping and molecular docking methods The outcome of 6 leads offers a significant contribution for selective CDK4 inhibition, since they show potential binding interactions with Val(96), Arg(101), and Glu(144) residues of CDK4, that are unique and from other kinases. It is worth noting that there is a striking similarity in binding interactions of the leads and known CDK4 inhibitors, namely Abemaciclib, Palbociclib and Ribociclib...
November 14, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29145154/a-pipeline-for-proteome-scale-identification-and-studies-on-hormone-sensitive-lipases-in-mycobacterium-tuberculosis
#4
Durairaj Sherlin, Sharmila Anishetty
Hormone sensitive lipases (HSLs) play an important role in the survival of M. tuberculosis during dormancy. They help in the utilization of fatty acids from stored lipids. The objective of the current study was to identify all HSLs from the proteome of M. tuberculosis H37Rv. We have developed a novel HSL identification pipeline, based on amino acid sequence homology, presence of conserved motifs and other sequence features deciphered from known HSL dataset. Through this pipeline, we identified 10 proteins as putative HSLs in M...
November 7, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29158074/a-novel-feature-selection-for-rna-seq-analysis
#5
Henry Han
RNA-seq data are challenging existing omics data analytics for its volume and complexity. Although quite a few computational models were proposed from different standing points to conduct differential expression (D.E.) analysis, almost all these methods do not provide a rigorous feature selection for high-dimensional RNA-seq count data. Instead, most or even all genes are invited into differential calls no matter they have real contributions to data variations or not. Thus, it would inevitably affect the robustness of D...
November 5, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29153892/penalized-estimation-of-sparse-concentration-matrices-based-on-prior-knowledge-with-applications-to-placenta-elemental-data
#6
Jai Woo Lee, Tracy Punshon, Erika L Moen, Margaret R Karagas, Jiang Gui
Identifying patterns of association or dependency among high-dimensional biological datasets with sparse precision matrices remains a challenge. In this paper, we introduce a weighted sparse Gaussian graphical model that can incorporate prior knowledge to infer the structure of the network of trace element concentrations, including essential elements as well as toxic metals and metaloids measured in the human placentas. We present the weighted L1 penalized regularization procedure for estimating the sparse precision matrix in the setting of Gaussian graphical models...
November 4, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29149637/antiviral-potential-of-natural-compounds-against-influenza-virus-hemagglutinin
#7
S Kannan, P Kolandaivel
Influenza virus of different subtypes H1N1, H2N2, H3N2 and H5N1 cause many human pandemic deaths and threatening the people worldwide. The Hemagglutinin (HA) protein mediates viral attachment to host receptors act as an attractive target. The sixteen natural compounds have been chosen to target the HA protein. Molecular docking studies have been performed to find binding affinity of the compounds. Out of the sixteen, three compounds CI, CII and CIII found to posses a higher binding affinity. The molecular dynamics (MD) simulation has been performed to study the structural, dynamical properties for the nine different complexes CI, CII, CIII bound with H1, H2, H3 proteins and the results were compared...
November 4, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29112936/designing-anti-zika-virus-peptides-derived-from-predicted-human-zika-virus-protein-protein-interactions
#8
Tom Kazmirchuk, Kevin Dick, Daniel J Burnside, Brad Barnes, Houman Moteshareie, Maryam Hajikarimlou, Katayoun Omidi, Duale Ahmed, Andrew Low, Clara Lettl, Mohsen Hooshyar, Andrew Schoenrock, Sylvain Pitre, Mohan Babu, Edana Cassol, Bahram Samanfar, Alex Wong, Frank Dehne, James R Green, Ashkan Golshani
The production of anti-Zika virus (ZIKV) therapeutics has become increasingly important as the propagation of the devastating virus continues largely unchecked. Notably, a causal relationship between ZIKV infection and neurodevelopmental abnormalities has been widely reported, yet a specific mechanism underlying impaired neurological development has not been identified. Here, we report on the design of several synthetic competitive inhibitory peptides against key pathogenic ZIKV proteins through the prediction of protein-protein interactions (PPIs)...
November 2, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29096382/a-novel-approach-for-dimension-reduction-of-microarray
#9
Rabia Aziz, C K Verma, Namita Srivastava
This paper proposes a new hybrid search technique for feature (gene) selection (FS) using Independent component analysis (ICA) and Artificial Bee Colony (ABC) called ICA+ABC, to select informative genes based on a Naïve Bayes (NB) algorithm. An important trait of this technique is the optimization of ICA feature vector using ABC. ICA+ABC is a hybrid search algorithm that combines the benefits of extraction approach, to reduce the size of data and wrapper approach, to optimize the reduced feature vectors. This hybrid search technique is facilitated by evaluating the performance of ICA+ABC on six standard gene expression datasets of classification...
October 28, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29096380/discovery-of-potential-zika-virus-rna-polymerase-inhibitors-by-docking-based-virtual-screening
#10
Anjali Singh, Nandan Kumar Jana
Zika virus (ZIKV) infection has been associated with Guillain-Barre syndrome in adults and microcephaly in infants. The existence of insufficient structural data in most of the protein databases hinders the synthesis of anti-ZIKV pharmaceutics. In this work, we attempted to model the catalytic domain of the ZIKV RNA polymerase (RdRpC) along with a detailed assessment of conserved aspartates in ZIKV RdRpC palm domain as potential drug targets. The conserved and catalytically active aspartate residues present in the predicted RdRpC protein were virtually screened against a ZINC database for inhibitors, and the selected potential drug candidates were further filtered based on their ADMET profiles...
October 24, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29096381/epitopes-based-drug-design-for-dengue-virus-envelope-protein-a-computational-approach
#11
Abdul Wadood, Aamir Mehmood, Huma Khan, Muhammad Ilyas, Ayaz Ahmad, Mohammed Alarjah, Tareq Abu-Izneid
Dengue virus (DENV) has emerged as a rapidly spreading epidemic throughout the tropical and subtropical regions around the globe. No suitable drug has been designed yet to fight against DENV, therefore, the need for safe and effective antiviral drug has become imperative. The envelope protein of DENV is responsible for mediating the fusion process between viral and host membranes. This work reports an in silico approach to target B and T cell epitopes for dengue envelope protein inhibition. A conserved region "QHGTI" in B and T cell epitopes of dengue envelope glycoprotein was confirmed to be valid for targeting by visualizing its interactions with the host cell membrane TIM-1 protein which acts as a receptor for serotype 2 and 3...
October 20, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29096379/systematic-identification-of-the-druggable-interactions-between-human-protein-kinases-and-naturally-occurring-compounds-in-endometriosis
#12
Lai Jiang, Chaoliang Tang, Jie Rao, Qing Xue, Hao Wu, Dabao Wu, Aijun Zhang, Ling Chen, Zhen Shen, Lei Lei
Diverse kinase signaling pathways have been involved in the pathogenesis of endometriosis (EM), which can be modulated either by directly targeting the hub kinases or by indirectly regulating marginal members in the pathways. Here, a systematic kinase-inhibitor interaction profile was created for 8 naturally occurring compounds against 20 human protein kinases. The compounds are all non-sterid that have been reported as pharmacologically active molecular entities potential for EM therapeutics, while the kinases were curated via gene ontology terms enriched from the gene co-citation network with EM...
October 16, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29040908/predicting-lysine-glycation-sites-using-bi-profile-bayes-feature-extraction
#13
Zhe Ju, Juhe Sun, Yanjie Li, Li Wang
Glycation is a nonenzymatic post-translational modification which has been found to be involved in various biological processes and closely associated with many metabolic diseases. The accurate identification of glycation sites is important to understand the underlying molecular mechanisms of glycation. As the traditional experimental methods are often labor-intensive and time-consuming, it is desired to develop computational methods to predict glycation sites. In this study, a novel predictor named BPB_GlySite is proposed to predict lysine glycation sites by using bi-profile bayes feature extraction and support vector machine algorithm...
October 12, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29101826/ligand-based-computational-modelling-of-platelet-derived-growth-factor-beta-receptor-leading-to-new-angiogenesis-inhibitory-leads
#14
Rua'a A Al-Aqtash, Malek A Zihlif, Hana Hammad, Zeyad D Nassar, Jehad Al Meliti, Mutasem O Taha
Platelet derived growth factor beta receptor (PDGFR- β) plays an important role in angiogenesis. PDGFR-β expression is correlated with increased vascularity and maturation of blood vessels in cancer. Pharmacophore modeling and quantitative structure-activity relationship (QSAR) analysis were combined to explore the structural requirements for ligand-PDGFR-β recognition using 107 known PDGFR-β inhibitors. Genetic function algorithm (GFA) coupled to k nearest neighbor (kNN) and multiple linear regression (MLR) analysis were employed to generate predictive QSAR models based on optimal combinations of pharmacophores and physicochemical descriptors...
October 10, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29153889/3d-qsar-studies-on-indole-and-7-azoindole-derivatives-as-rock-2-inhibitors-an-integrative-computational-approach
#15
Santhosh Kumar Nagarajan, Sathya Babu, Honglae Sohn, Panneer Devaraju, Thirumurthy Madhavan
Rho Kinases (ROCK) has been found to regulate a wide range of fundamental cell functions such as contraction, motility, proliferation, and apoptosis. Recent experiments have defined new functions of ROCKs in cells, including centrosome positioning and cell-size regulation, which might contribute to various physiological and pathological states. In this study, we have performed pharmacophore modeling and 3D QSAR studies on a series of 36 indoles and 7-azoindoles derivatives as ROCK2 inhibitors to elucidate the structural variations with their inhibitory activities...
October 9, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29153891/molecular-modeling-of-cationic-porphyrin-anthraquinone-hybrids-as-dna-topoisomerase-ii%C3%AE-inhibitors
#16
Muhammad Arba, Ruslin, Sunandar Ihsan, Setyanto Tri Wahyudi, Daryono H Tjahjono
Human DNA Topoisomerase II has been regarded as a promising target in anticancer drug discovery. In the present study, we designed six porphyrin-anthraquinone hybrids bearing pyrazole or pyridine group as meso substituents and evaluated their potentials as DNA Topoisomerase IIβ inhibitor. First, we investigated the binding orientation of porphyrin hybrids into DNA topoisomerase IIβ employing AutoDock 4.2 and then performed 20-ns molecular dynamics simulations to see the dynamic stability of each porphyrin-Topo IIβ complex using Amber 14...
October 5, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29031869/hashgo-hashing-gene-ontology-for-protein-function-prediction
#17
Guoxian Yu, Yingwen Zhao, Chang Lu, Jun Wang
Gene ontology (GO) is a standardized and controlled vocabulary of terms that describe the molecular functions, biological roles and cellular locations of proteins. GO terms and GO hierarchy are regularly updated as the accumulated biological knowledge. More than 50,000 terms are included in GO and each protein is annotated with several or dozens of these terms. Therefore, accurately predicting the association between proteins and massive GO terms is rather challenging. To accurately predict the association between massive GO terms and proteins, we proposed a method called Hashing GO for protein function prediction (HashGO in short)...
October 4, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28987295/evaluation-of-degradation-mechanism-of-chlorhexidine-by-means-of-density-functional-theory-calculations
#18
Michele Aparecida Salvador, Camila Pinheiro Sousa, Simone Morais, Pedro de Lima-Neto, Adriana Nunes Correia, Paula Homem-de-Mello
Chlorhexidine (CHD), a germicidal drug, has degradation products that can be hemotoxic and carcinogenic. However, there is no consensus in literature about the degradation pathway. In order to shed light on that mechanism, we have employed Density Functional Theory to study reactants, in different protonation states, products and intermediates involved in the different pathways. Based on free energy values comparison and frontier molecular orbital analysis, we have obtained the most stable structures in each protonation state...
October 3, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29033260/predicting-microrna-biological-functions-based-on-genes-discriminant-analysis
#19
Tao Ding, Junhua Xu, Mengmeng Sun, Shanshan Zhu, Jie Gao
Although thousands of microRNAs (miRNAs) have been identified in recent experimental efforts, it remains a challenge to explore their specific biological functions through molecular biological experiments. Since those members from same family share same or similar biological functions, classifying new miRNAs into their corresponding families will be helpful for their further functional analysis. In this study, we initially built a vector space by characterizing the features from miRNA sequences and structures according to their miRBase family organizations...
September 29, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29030293/solving-probability-reasoning-based-on-dna-strand-displacement-and-probability-modules
#20
Qiang Zhang, Xiaobiao Wang, Xiaojun Wang, Changjun Zhou
In computation biology, DNA strand displacement technology is used to simulate the computation process and has shown strong computing ability. Most researchers use it to solve logic problems, but it is only rarely used in probabilistic reasoning. To process probabilistic reasoning, a conditional probability derivation model and total probability model based on DNA strand displacement were established in this paper. The models were assessed through the game "read your mind." It has been shown to enable the application of probabilistic reasoning in genetic diagnosis...
September 28, 2017: Computational Biology and Chemistry
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