Showing papers in "Computational Biology and Chemistry in 2016"

TL;DR: The results suggest that the designed epitope vaccine could incite robust long-term protective immunity against V. cholera.

TL;DR: A series of thiazoles bearing pyrazole as a possible pharmacophore were synthesized and assessed for their anti inflammatory activity using in vitro and in vivo methods, and molecular docking results revealed significant interactions of the test compounds with the active site of COX-II.

TL;DR: Comprehensive analysis on upstream regions from 10 Rbohs from Arabidopsis thaliana and 9 from Oryza sativa japonica provided vital clues for diverse functions of plant R bohs.

TL;DR: This work attempts 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).

TL;DR: The first in-silico study describing miRNAs and their role in the regulation of secondary metabolic pathways in Mentha spp.

TL;DR: 15 conserved miRNAs belonging to 13 families from Rauvolfia serpentina are identified and characterization through in silico analysis of available nucleotide dataset and predicted targets of rse-miRNAs include transcription factors as well as genes involved in diverse biological processes.

TL;DR: In this paper, the authors proposed a recurrent neural network (RNN) based hybrid model of gene regulatory network (GRN), which is able to capture complex, non-linear and dynamic relationships among variables.

TL;DR: Reanalyses by tRNAscan-SE and ARWEN softwares of the five available complete chaetognath mitogenomes suggest numerous additional tRNA genes from different types, and sequence alignments in secondary structure prediction with non-chaetognaths tRNAs suggest that the most likely functional t RNAs are in intergenic regions, as regular mt-tRNAs.

TL;DR: The Contact Mode Score (CMS) is a new metric to assess the conformational similarity based on intermolecular protein-ligand contacts that is less dependent on the ligand size and has the ability to include flexible receptors.

TL;DR: The results suggest for the appropriateness of the developed SAR models to reliably predict the HIA of structurally diverse chemicals and can serve as useful tools for the initial screening of the molecules in the drug development process.

TL;DR: Tissue-specific constraint-based core models for three different types of tumors that serve this purpose and identified key points able to reverse the tumoral phenotype toward the reference one or vice-versa are presented.

TL;DR: The results support a model of inhibition of LPL by ANGPTL8 through the steric block of its catalytic site which will be further explored using wet lab studies in future.

TL;DR: Predictive QSAR models built on a series of selective inhibitors of the tubulin showed excellent statistics on the training and test sets and showed reasonable docking scores as well as favorable interactions with the protein.

TL;DR: By fusing both the premises that CSC and single hit anticancer drugs, both are responsible for cancer related resistances and screened alkaloids for the search of leads having CSC targeting ability as well as the capability to modulating multiple target proteins, this work indicates that emetine and cortistatin have the ability to modulate hedgehog pathway by binding to sonic hedgehog, smoothened and Gli protein, involved in maintenance CSCs.

TL;DR: Perimidine molecule displayed promising inhibitory activity against acetylcholinesterase (AChE) as compared to the reference drug, tacrine, and the results of molecular docking admitted that perimidine may reveal enzyme inhibitor activity.

TL;DR: High CV genes tend to form co-expression clusters and they explain bivalency at least in part and this analysis demonstrates the divergent characteristics of genes based on their CV.

TL;DR: In this paper, a new sequence-based predictor called TargetGDrug is designed and implemented for predicting GPCR-drug interactions, and an improvement of 15% in the Matthews correlation coefficient (MCC) was observed over independent validation tests when compared with the most recently released sequence- based GPCC-drug interaction predictor.

TL;DR: The result indicates that the isolated bioactive compound DHMA might have altered the binding affinity between DNA and NF-κB, and suggest that potential use of DHMA in cancer chemoprevention and therapeutics is suggested.

TL;DR: This study aims to perform an in silico comparative characterization and functional analysis of phytases from Bacillus amyloliquefaciens to explore physico-chemical properties using various bio-computational tools.

TL;DR: In this article, the Gibbs free energy change for reaction of inactivation of free radicals indicates 3-hydroxyphenylacetic acid (3-HPAA) and 4hydroxymhenylpropionic acid (4-HPPA) as potent scavengers.

TL;DR: The present study attempts to identify a candidate molecule targeting voltage gated potassium channels anticipated to have superior pharmacological than existing potassium channel blockers.

TL;DR: Molecular docking analyses have been carried out on a library of 2174 plant-derived natural products with the nsP2 proteases of CHIKV, ONNV, RRV, EEEv, VEEV, WEEV as well as Aura virus (AURV), Barmah Forest Virus (BFV), Semliki Forest virus (SFV), and Sindbis virus (SINV) in order to identity structural scaffolds for inhibitor design or discovery

TL;DR: This work proposes a new method, Weighted Edge based Clustering (WEC), to identify protein complexes based on the weight of the edge between two interacting proteins, where the weight is defined by the edge clustering coefficient and the gene expression correlation between the interacting proteins.

TL;DR: A meta-heuristics approach based on chemical reaction optimization, CRO_SCS that is designed inspired by the nature of the chemical reactions and shows very good performance for different optimization problems like 0-1 knapsack, quadratic assignment, global numeric optimization problems.

TL;DR: Co-expression analysis revealed that embryo development and stress related genes were expressed together with OsDREB2s, which may shed light in uncovering the complex abiotic stress signaling networks and future genomics studies targeting the development of climate ready crops.

TL;DR: This study inferred the three-dimensional structural model of DREB1A using homology modelling and evaluated them using molecular dynamics simulations yielding refined modelled structures and suggested that the wheat DREb1A orthologs have similar biochemical functions and pathways to that of AtDREB 1A.

TL;DR: This work prepares and compared the unique CCT-interacting protein lists for S. cerevisiae and H. sapiens, and performs GO term classification and enrichment studies which provide information on the diversity in CCT interactome, in terms of protein classes in the data set.

TL;DR: A new framework named IdealKnock is proposed, able to efficiently evaluate potentials of the production for different biochemical in a system by merely knocking out pathways, which is also capable of searching knockout strategies when combined with the OptKnock or OptGene framework.

TL;DR: Docking, 3D quantitative structure activity relationship (3D-QSAR) and molecular dynamics studies were performed on a series of Imidazo-pyrrolopyridine derivatives reported as JAK 1 inhibitors, finding good concordance between the docking results and CoMFA/CoMSIA contour maps afforded obliging clues for the rational modification of molecules to design more potent Jak 1 inhibitors.

TL;DR: A new scaffold N-phenyl-1H-indol-2-amine was selected as a base for FTO protein inhibitors by applying scaffold hopping approach and showed stable interaction with inhibitor MU06 throughout the production dynamics phase.