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Computational Biology and Chemistry

Zhong Ni, Xiting Wang, Tianchen Zhang, Rong Zhong Jin
Anaplastic lymphoma kinase (ALK) has become as an important target for the treatment of various human cancers, especially non-small-cell lung cancer. A mutation, F1174C, suited in the C-terminal helix αC of ALK and distal from the small-molecule inhibitor ceritinib bound to the ATP-binding site, causes the emergence of drug resistance to ceritinib. However, the detailed mechanism for the allosteric effect of F1174C resistance mutation to ceritinib remains unclear. Here, molecular dynamics (MD) simulations and binding free energy calculations [Molecular Mechanics/Generalized Born Surface Area (MM/GBSA)] were carried out to explore the advent of drug resistance mutation in ALK...
October 11, 2016: Computational Biology and Chemistry
Mohammad Uzzal Hossain, Arafat Rahman Oany, Shah Adil Ishtiyaq Ahmad, Md Anayet Hasan, Md Arif Khan, Md Al Ahad Siddikey
Chagas is a parasitic disease with major threat to public health due to its resistance against commonly available drugs. Trypanothione reductase (TryR) is the key enzyme to develop this disease. Though this enzyme is well thought-out as potential drug target, the accurate structure of enzyme-inhibitor complex is required to design a potential inhibitor which is less available for TryR. In this research, we aimed to investigate the advanced drug over the available existing drugs by designing inhibitors as well as to identify a new enzyme-inhibitor complex that may act as a template for drug design...
October 7, 2016: Computational Biology and Chemistry
David Agustriawan, Chien-Hung Huang, Jim Jinn-Chyuan Sheu, Shan-Chih Lee, Jeffrey J P Tsai, Nilubon Kurubanjerdjit, Ka-Lok Ng
Epigenetic regulation has been linked to the initiation and progression of cancer. Aberrant expression of microRNAs (miRNAs) is one such mechanism that can activate or silence oncogenes (OCGs) and tumor suppressor genes (TSGs) in cells. A growing number of studies suggest that miRNA expression can be regulated by methylation modification, thus triggering cancer development. However, there is no comprehensive in silico study concerning miRNA regulation by direct DNA methylation in cancer. Ovarian serous cystadenocarcinoma (OSC) was therefore chosen as a tumor model for the present work...
October 1, 2016: Computational Biology and Chemistry
Renu Vyas, Sanket Bapat, Esha Jain, Muthukumarasamy Karthikeyan, Sanjeev Tambe, Bhaskar D Kulkarni
In order to understand the molecular mechanism underlying any disease, knowledge about the interacting proteins in the disease pathway is essential. The number of revealed protein-protein interactions (PPI) is still very limited compared to the available protein sequences of different organisms. Experiment based high-throughput technologies though provide some data about these interactions, those are often fairly noisy. Computational techniques for predicting protein-protein interactions therefore assume significance...
September 30, 2016: Computational Biology and Chemistry
Colin Kern, Li Liao
Protein-protein interactions play a central role in the biological processes of cells. Accurate prediction of the interacting residues in protein-protein interactions enhances understanding of the interaction mechanisms and enables in silico mutagenesis, which can help facilitate drug design and deepen our understanding of the inner workings of cells. Correlations have been found among interacting residues as a result of selection pressure to retain the interaction during evolution. In previous work, incorporation of such correlations in the interaction profile hidden Markov models with a special decoding algorithm (ETB-Viterbi) has led to improvement in prediction accuracy...
September 29, 2016: Computational Biology and Chemistry
Jing-Guo Wu, Qing-Wei Jia, Yong Li, Fei-Fei Cao, Xi-Shan Zhang, Cong Liu
OBJECTIVE: This paper aimed to investigate ego modules for TGFβ3-induced chondrogenesis in mesenchymal stem cells (MSCs) using ego network algorithm. METHODS: The ego network algorithm comprised three parts, extracting differential expression network (DEN) based on gene expression data and protein-protein interaction (PPI) data; exploring ego genes by reweighting DEN; and searching ego modules by ego gene expansions. Subsequently, permutation test was carried out to evaluate the statistical significance of the ego modules...
September 28, 2016: Computational Biology and Chemistry
Ya-Xuan Wang, Jin-Xing Liu, Ying-Lian Gao, Chun-Hou Zheng, Jun-Liang Shang
With the rapid development of DNA microarray technology and next-generation technology, a large number of genomic data were generated. So how to extract more differentially expressed genes from genomic data has become a matter of urgency. Because Low-Rank Representation (LRR) has the high performance in studying low-dimensional subspace structures, it has attracted a chunk of attention in recent years. However, it does not take into consideration the intrinsic geometric structures in data. In this paper, a new method named Laplacian regularized Low-Rank Representation (LLRR) has been proposed and applied on genomic data, which introduces graph regularization into LRR...
September 28, 2016: Computational Biology and Chemistry
Ana Amić, Zoran Marković, Jasmina M Dimitrić Marković, Svetlana Jeremić, Bono Lučić, Dragan Amić
Free radical scavenging and inhibitory potency against cyclooxygenase-2 (COX-2) by two abundant colon metabolites of polyphenols, i.e., 3-hydroxyphenylacetic acid (3-HPAA) and 4-hydroxyphenylpropionic acid (4-HPPA) were theoretically studied. Different free radical scavenging mechanisms are investigated in water and pentyl ethanoate as a solvent. By considering electronic properties of scavenged free radicals, hydrogen atom transfer (HAT) and sequential proton loss electron transfer (SPLET) mechanisms are found to be thermodynamically probable and competitive processes in both media...
September 23, 2016: Computational Biology and Chemistry
Haozhe Xie, Jie Li, Qiaosheng Zhang, Yadong Wang
Random Projection (RP) technique has been widely applied in many scenarios because it can reduce high-dimensional features into low-dimensional space within short time and meet the need of real-time analysis of massive data. There is an urgent need of dimensionality reduction with fast increase of big genomics data. However, the performance of RP is usually lower. We attempt to improve classification accuracy of RP through combining other reduction dimension methods such as Principle Component Analysis (PCA), Linear Discriminant Analysis (LDA), and Feature Selection (FS)...
September 21, 2016: Computational Biology and Chemistry
Ivan Semenyuta, Vasyl Kovalishyn, Vsevolod Tanchuk, Stepan Pilyo, Vladimir Zyabrev, Volodymyr Blagodatnyy, Olena Trokhimenko, Volodymyr Brovarets, Larysa Metelytsia
Microtubules play a significant role in cell growth and functioning. Therefore inhibition of the microtubule assemblies has emerged as one of the most promising cancer treatment strategies. Predictive QSAR models were built on a series of selective inhibitors of the tubulin were performed by using Associative Neural Networks (ANN). To overcome the problem of data overfitting due to the descriptor selection, a 5-fold cross-validation with variable selection in each step of the analysis was used. All developed QSAR models showed excellent statistics on the training (total accuracy: 0...
September 21, 2016: Computational Biology and Chemistry
Shu-Bo Zhang, Qiang-Rong Tang
Predicting the location where a protein resides within a cell is important in cell biology. Computational approaches to this issue have attracted more and more attentions from the community of biomedicine. Among the protein features used to predict the subcellular localization of proteins, the feature derived from Gene Ontology (GO) has been shown to be superior to others. However, most of the sights in this field are set on the presence or absence of some predefined GO terms. We proposed a method to derive information from the intrinsic structure of the GO graph...
September 14, 2016: Computational Biology and Chemistry
Chang Lu, Jun Wang, Zili Zhang, Pengyi Yang, Guoxian Yu
Gene Ontology (GO) provides GO annotations (GOA) that associate gene products with GO terms that summarize their cellular, molecular and functional aspects in the context of biological pathways. GO Consortium (GOC) resorts to various quality assurances to ensure the correctness of annotations. Due to resources limitations, only a small portion of annotations are manually added/checked by GO curators, and a large portion of available annotations are computationally inferred. While computationally inferred annotations provide greater coverage of known genes, they may also introduce annotation errors (noise) that could mislead the interpretation of the gene functions and their roles in cellular and biological processes...
September 13, 2016: Computational Biology and Chemistry
Monikaben Padariya, Umesh Kalathiya
Fat mass and obesity-associated (FTO) protein contributes to non-syndromic human obesity which refers to excessive fat accumulation in human body and results in health risk. FTO protein has become a promising target for anti-obesity medicines as there is an immense need for the rational design of potent inhibitors to treat obesity. In our study, a new scaffold N-phenyl-1H-indol-2-amine was selected as a base for FTO protein inhibitors by applying scaffold hopping approach. Using this novel scaffold, different derivatives were designed by extending scaffold structure with potential functional groups...
September 13, 2016: Computational Biology and Chemistry
Fang Liang, Lili Hao, Jinyue Wang, Shuo Shi, Jingfa Xiao, Rujiao Li
Cytosine methylation is one of the most important RNA epigenetic modifications. With the development of experimental technology, scientists attach more importance to RNA cytosine methylation and find bisulfite sequencing is an effective experimental method for RNA cytosine methylation study. However, there are only a few tools can directly deal with RNA bisulfite sequencing data efficiently. Herein, we developed a specialized tool BS-RNA, which can analyze cytosine methylation of RNA based on bisulfite sequencing data and support both paired-end and single-end sequencing reads from directional bisulfite libraries...
September 9, 2016: Computational Biology and Chemistry
Carmen H S Chan, Sophie Octavia, Vitali Sintchenko, Ruiting Lan
De novo assembly of bacterial genomes from next-generation sequencing (NGS) data allows a reference-free discovery of single nucleotide polymorphisms (SNP). However, substantial rates of errors in genomes assembled by this approach remain a major barrier for the reference-free analysis of genome variations in medically important bacteria. The aim of this report was to improve the quality of SNP identification in bacterial genomes without closely related references. We developed a bioinformatics pipeline (SnpFilt) that constructs an assembly using SPAdes and then removes unreliable regions based on the quality and coverage of re-aligned reads at neighbouring regions...
September 9, 2016: Computational Biology and Chemistry
Yun Ding, Ye Fang, Juana Moreno, J Ramanujam, Mark Jarrell, Michal Brylinski
Structural and computational biologists often need to measure the similarity of ligand binding conformations. The commonly used root-mean-square deviation (RMSD) is not only ligand-size dependent, but also may fail to capture biologically meaningful binding features. To address these issues, we developed the Contact Mode Score (CMS), a new metric to assess the conformational similarity based on intermolecular protein-ligand contacts. The CMS is less dependent on the ligand size and has the ability to include flexible receptors...
September 6, 2016: Computational Biology and Chemistry
Abdolvahed Pari, Ahmad Baraani, Saeed Parseh
In many sequence data mining applications, the goal is to find frequent substrings. Some of these applications like extracting motifs in protein and DNA sequences are looking for frequently occurring approximate contiguous substrings called simple motifs. By approximate we mean that some mismatches are allowed during similarity test between substrings, and it helps to discover unknown patterns. Structured motifs in DNA sequences are frequent structured contiguous substrings which contains two or more simple motifs...
September 6, 2016: Computational Biology and Chemistry
Aswathy N, Dileep Pullepu, M Anaul Kabir
The eukaryotic chaperonin, CCT (Chaperonin Containing TCP1 or TriC-TCP-1 Ring Complex) has been subjected to physical and genetic analyses in S. cerevisiae which can be extrapolated to human CCT (hCCT), owing to its structural and functional similarities with yeast CCT (yCCT). Studies on hCCT and its interactome acquire an additional dimension, as it has been implicated in several disease conditions like neurodegeneration and cancer. We attempt to study its stress response role in general, which will be reflected in the aspects of human diseases and yeast physiology, through computational analysis of the interactome...
September 6, 2016: Computational Biology and Chemistry
K C Sivakumar, T P Sajeevan, I S Bright Singh
White spot syndrome virus (WSSV) remains as one of the most dreadful pathogen of the shrimp aquaculture industry owing to its high virulence. The cumulative mortality reaches up to 100% within in 2-10days in a shrimp farm. Currently, no chemotherapeutics are available to control WSSV. The viral envelope protein, VP28, located on the surface of the virus particle acts as a vital virulence factor in the initial phases of inherent WSSV infection in shrimp. Hence, inhibition of envelope protein VP28 could be a novel way to deal with infection by inhibiting its interaction in the endocytic pathway...
August 28, 2016: Computational Biology and Chemistry
Ganesh Selvaraj Duraisamy, Ajay Kumar Mishra, Tomas Kocabek, Jaroslav Matoušek
Molecular and biochemical studies have shown that gene contains single or combination of different cis-acting regulatory elements are actively controlling the transcriptional regulation of associated genes, downstream effects of these result in the modulation of various biological pathways such as biotic/abiotic stress responses, hormonal responses to growth and development processes and secondary metabolite production. Therefore, the identification of promoters and their cis-regulatory elements is one of intriguing area to study the dynamic complex regulatory network of genes activities by integrating computational, comparative, structural and functional genomics...
August 24, 2016: Computational Biology and Chemistry
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