Showing papers in "Computational Biology and Chemistry in 2018"

TL;DR: To ensure correct and effective application of docking techniques, it is necessary to understand the method's merits, demerits, the scope of application, and interpretation.

TL;DR: This work presents its 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, and introduces methods to ameliorate the impact of longer read length.

TL;DR: Compounds 23 and 28 have no violated Lipinski's rule of five and thus, showing the possibility of being potential candidates for further studies in drug development process against the AChE and BuChE targets respectively are shown.

TL;DR: In silico evaluation of 32 virtually designed transition metal complexes of 2-butanone thiosemicarbazone and N,S,O containing donor hetero-ligands, all complexes displayed drug-like character and were predicted to have no apparent toxic side-effects.

TL;DR: A GNU Parallel based pipeline-POAP is presented that is programmed to run Open Babel and AutoDock suite under highly optimized parallelization and proves to be an efficient pipeline that enables high scalability, seamless operability, dynamic file handling and optimal utilization of CPU's for computationally demanding tasks.

TL;DR: Extracts of S. salsuginea are a potential source of functional food ingredients but need further analytical experiments to explore its complexity of chemical compounds and pharmacological properties as well as using in vivo toxicity models to establish its maximum tolerated dose.

TL;DR: The novel compounds designed and reported here in were evaluated for ADME properties and the results indicate that they show acceptable pharmacokinetic properties and are predicted to be drug like with low toxicity potential.

TL;DR: Pseudomonas aeruginosa is an opportunistic gram-negative bacterium that has the capability to acquire resistance under hostile conditions and become a threat worldwide and is involved in nosocomial infections.

TL;DR: According to the docking results the compounds 4-9 induce cytotoxicity by the disruption of the microtubule dynamics by inhibiting tubulin polymerization via effective binding into colchicine domain, similar the E7010.

TL;DR: Based on the study, Luteolin possess high potential to be considered for trial as an inhibitor of HsXOR as it may regulate the pathway by inhibiting Hs Xanthine oxidoreductase.

TL;DR: The present study attempts for the first time to assess the possible enzyme inhibitory potential, antioxidant activity, and phytochemical profile of the ethyl acetate, methanol, and water extracts of C. saligna and shows that apigenin binds to the enzymatic pocket of α-glucosidase and is stabilised by a network of hydrogen bonds and pi-pi stacking.

TL;DR: Comparison of single and combined stress suggests the combined stress did not result in a simple additive response, and that there may be a synergistic response to the combination of drought and heat in soybean.

TL;DR: The phytochemical profile and antioxidant potential of ethyl acetate, methanol, and water extracts of Salvia sclarea showed interesting biological activity against key enzymes involved in the pathogenesis of common ailments.

TL;DR: This review placed a focus on the recently emerged enhancer predictor tools that work on general enhancer features such as sequences, chromatin states and histone modifications, eRNA and of multiple feature approach.

TL;DR: 3D-QSAR based pharmacophore search for the identification of potential inhibitors against the kinase domain of HER2 protein led to the culling of Hits to two identifying Hit1 and Hit2 has potential leads against HER2 breast cancers.

TL;DR: This research performed molecular simulation works on a series of classic aryl sulfonamide Nav1.7 inhibitors using three-dimensional quantitative structure-activity relationships (3D-QSAR), molecular docking and molecular dynamics simulations for the first time to explore the correlation between their structures and activities.

TL;DR: These newly synthesized thiazol-2-yl benzamide derivatives can be treated as the initial hits for the development of new, safe, effective and orally bioavailable GK activators as therapeutic agents for the treatment of type 2 diabetes.

TL;DR: A novel feature selection method based on a global search (by using the main concepts of divide and conquer technique) which is called CCFS, which utilizes the fundamental concepts of cooperation coevolution by using a filter criterion in the fitness function in order to search the solution space via binary gravitational search algorithm.

TL;DR: Molecular docking study was executed to evaluate the potential of the title molecule to bind with 5-HT1 A serotonin receptor and thus can be a lead compound for developing new SSRI (Selective serotonin reuptake inhibitor) drug.

TL;DR: The determined structure of Omp33-36 could justify its porin function and carbapenem-resistance associated with the loss of this protein.

TL;DR: The theoretical results indicated that halogen bond interactions could be involved with differential potency of these compounds and provide a new starting point to design novel pyrazolo[1,5-c]quinazolines as new anti-Alzheimer agents.

TL;DR: In this article, a new random projection algorithm is proposed, in which a random symmetric matrix surrogates the covariance/correlation matrix of PCA, while maintaining the data clustering capacity.

TL;DR: Results suggest that SLs can be promising multi-potent botanical leads for the mitigation of inflammatory-mediated chronic disorders and might be classified as druggable molecule in drug design.

TL;DR: A method in which a predicted ligand-binding site is covered by multiple grids, termed multiple grid arrangement, which facilitates the conformational search for a grid-based ligand docking software and can be applied to the state-of-the-art commercial docking software Glide (Schrödinger, LLC).

TL;DR: The result of biological activity and docking study revealed that amines group at R2 point of 1,3,4-oxadiazole-2-thione moiety is essential for anticancer activity.

TL;DR: A first account of the structural dynamics which characterizes the inhibitory effect of a novel LFA-1 antagonist, Lifitegrast (SAR1118), upon binding to the I-domain allosteric site (IDAS) using molecular dynamics simulation is presented.

TL;DR: Distributed feature representation, SpliceVec, is introduced to avoid explicit and biased feature extraction generally adopted for feature extraction in natural language processing tasks and is consistent in its performance even with reduced dataset and class-imbalanced dataset.

TL;DR: The computational protocol could be considered as a new tool for identifying active peptide against ACE from hydrolysated peptides of natural sources.

TL;DR: Quantitative Structure-Activity Relationships (QSAR) studies, molecular docking and in vitro antibacterial activity of several potent imidazolium-based ionic liquids (ILs) against S. aureus strain and its clinical isolate are described.

TL;DR: A novel class of selective SHP2 allosteric inhibitors was discovered by using the powerful 'SBP', 'ADMET' and 'CDOCKER' techniques and it was observed that these novel inhibitors not only had the same function as SHP099 did in inhibiting SHp2, but also had more favorable conformation for binding to the receptor.