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Mouchlis VD Melagraki G Mavromoustakos T Kollias G Afantitis A 《Journal of chemical information and modeling》2012,52(3):711-723
Molecular docking, classification techniques, and 3D-QSAR CoMSIA were combined in a multistep framework with the ultimate goal of identifying potent pyrimidine-urea inhibitors of TNF-α production. Using the crystal structure of p38α, all the compounds were docked into the enzyme active site. The docking pose of each compound was subsequently used in a receptor-based alignment for the generation of the CoMSIA fields. "Active" and "inactive" compounds were used to build a Random Tree classification model using the docking score and the CoMSIA fields as input parameters. Domain of applicability indicated the compounds for which activity estimations can be accepted with confidence. For the active compounds, a 3D-QSAR CoMSIA model was subsequently built to accurately estimate the IC(50) values. This novel multistep framework gives insight into the structural characteristics that affect the binding and the inhibitory activity of these analogues on p38α MAP kinase, and it can be extended to other classes of small-molecule inhibitors. In addition, the simplicity of the proposed approach provides expansion to its applicability such as in virtual screening procedures. 相似文献
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Thwala M. M. Afantitis A. Papadiamantis A. G. Tsoumanis A. Melagraki G. Dlamini L. N. Ouma C. N. M. Ramasami P. Harris R. Puzyn T. Sanabria N. Lynch I. Gulumian M. 《Structural chemistry》2022,33(2):527-538
Structural Chemistry - Engineered nanoparticles (NPs) are being studied for their potential to harm humans and the environment. Biological activity, toxicity, physicochemical properties, fate, and... 相似文献
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Afantitis A Melagraki G Sarimveis H Koutentis PA Markopoulos J Igglessi-Markopoulou O 《Journal of computer-aided molecular design》2006,20(2):83-95
Summary A linear quantitative–structure activity relationship model is developed in this work using Multiple Linear Regression Analysis as applied to a series of 51 1-(3,3-diphenylpropyl)-piperidinyl phenylacetamides derivatives with CCR5 binding affinity. For the selection of the best variables the Elimination Selection-Stepwise Regression Method (ES-SWR) is utilized. The predictive ability of the model is evaluated against a set of 13 compounds. Based on the produced QSAR model and an analysis on the domain of its applicability, the effects of various structural modifications on biological activity are investigated. The study leads to a number of guanidine derivatives with significantly improved predicted activities. 相似文献
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Stefanou V Matiadis D Melagraki G Afantitis A Athanasellis G Igglessi-Markopoulou O McKee V Markopoulos J 《Molecules (Basel, Switzerland)》2011,16(1):384-402
A novel short-step methodology for the synthesis in good yields of functionalized coumarins has been developed starting from an activated precursor, the N-hydroxysuccinimide ester of O-acetylsalicylic acid. The procedure is based on a tandem C-acylation-cyclization process under mild reaction conditions. The structure of 3-methoxycarbonyl-4-hydroxy coumarin has been established by X-ray diffraction analysis and its geometry was compared with optimized parameters by means of DFT calculations. 相似文献
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Melagraki G Afantitis A Sarimveis H Igglessi-Markopoulou O Alexandridis A 《Molecular diversity》2006,10(2):213-221
Summary This work introduces a neural network methodology for developing QSTR predictors of toxicity to Vibrio fischeri. The method adopts the Radial Basis Function (RBF) architecture and the fuzzy means training strategy, which is fast and repetitive,
in contrast to most traditional training techniques. The data set that was utilized consisted of 39 organic compounds and
their corresponding toxicity values to Vibrio fischeri, while lipophilicity, equalized electronegativity and one topological index were used to provide input information to the
models. The performance and predictive ability of the RBF model were illustrated through external validation and various statistical
tests. The proposed methodology can be used to successfully model toxicity to Vibrio fischerifor a heterogeneous set of compounds. 相似文献
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