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Probing the Catalytic Mechanism Involved in the Isocitrate Lyase Superfamily: Hybrid Quantum Mechanical/Molecular Mechanical Calculations on 2,3-Dimethylmalate Lyase.
TLDR
Quant mechanical/molecular mechanical methods are applied to the most recently reported family member, DMML, to assess whether any of the mechanistic proposals offers a clear energetic advantage over the others and suggest that Arg161 is the general base in the reaction and Cys124 is thegeneral acid, giving rise to a rate-determining barrier of approximately 10 kcal/mol.
Development of piperic acid derivatives from Piper nigrum as UV protection agents
TLDR
From the results, isopropyl piperate is an outstanding compound that can be developed into a UV protection agent.
Molecular docking study of tyrosinase inhibitors using ArgusLab 4.0.1 : A comparative study
TLDR
It is found that ArgusLab is an easy to use program with high-speed calculation and has an accessible user-interface even by beginners in molecular docking.
Construction of Quantitative Structure Activity Relationship (QSAR) Models to Predict Potency of Structurally Diversed Janus Kinase 2 Inhibitors
TLDR
Molecular cluster analysis revealed that pyrazine scaffolds have nanomolar potency against JAK2, and the predictive power of RF models was assessed via 10-fold cross validation, which afforded excellent predictive performance.
Insights into the EGFR SAR of N-phenylquinazolin-4-amine-derivatives using quantum mechanical pairwise-interaction energies
TLDR
This work explores the generation of structure-based quantum mechanical (QM) quantitative structure–activity relationship models (QSAR) as a means to facilitate structure-guided optimization of protein kinase inhibitors and displays good performance on the training and test sets and was demonstrably more predictive than the QSAR models built using other methods.
Elucidation of the catalytic mechanism of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase using QM/MM calculations.
TLDR
The first theoretical analysis of the catalytic pathway of the natural substrate using hybrid quantum mechanical/molecular mechanical (QM/MM) methods is reported, identifying R92 as the general base in the wildtype reaction.
Molecular binding modes of diarylheptanoids from Curcuma comosa on the ER- receptor
TLDR
Molecular modeling using AutoDock 4.2 was effectively applied to understand the binding conformation of diarylheptanoid analogues with ER- receptor, and information of three-dimensional conformation can be applied in rational drug design for further searching the new highly activity ER-¬ receptor agonists.
Computational Analysis and Biological Activities of Oxyresveratrol Analogues, the Putative Cyclooxygenase-2 Inhibitors
TLDR
Computational results confirmed that dihydrooxyresveratrol is the putative inhibitor of human COX-2 with the highest inhibitory activity (IC50 of 11.50 ± 1.54 µM) among studied non-fluorinated analogues for further lead optimization.