Powell Method

Vassiliadis, Vassilios S.; Conejeros, Raúl

doi:10.1007/0-306-48332-7_393

Cited by 5 publications

(2 citation statements)

References 1 publication

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“…In the Tripos force field the molecular program Minimize was used to perform energy optimization. The Powell energy gradient method [14] was adopted, and the maximum number of iterations was 10,000, the convergence of the energy gradient was limited to 0.005 kJ/mol. The protease structure corresponding to the 15 commonly selected municipal wastewater treatment processes was derived from the Protein Data Bank.…”

Section: Molecular Docking Methodsmentioning

confidence: 99%

Molecular Modification of Fluoroquinolone-Biodegrading Enzymes Based on Molecular Docking and Homology Modelling

Sicheng

Sun

Cui

et al. 2019

IJERPH

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To improve the biodegradation efficiency of fluoroquinolone antibiotics during sewage treatment, fluoroquinolone aerobic, anaerobic and facultative degrading enzymes for fluoroquinolone degradation were modified by molecular docking and homology modelling. First, amino acid residues of the binding sites of degrading enzymes for the target fluoroquinolones ciprofloxacin (CIP), norfloxacin (NOR) and ofloxacin (OFL) were analysed by the molecular docking method. The hydrophobic amino acid residues within 5 Å of the target fluoroquinolone molecules were selected as the modification sites. The hydrophobic amino acid residues at the modified sites were replaced by the hydrophilic amino acid residues, and 150 amino acid sequence modification schemes of the degrading enzymes were designed. Subsequently, a reconstruction scheme of the degrading enzyme amino acid sequence reconstruction scheme was submitted to the SWISS-MODEL server and a selected homology modelling method was used to build a new structure of the degrading enzyme. At the same time, the binding affinities between the novel degrading enzymes and the target fluoroquinolones (represented by the docking scoring function) were evaluated by the molecular docking method. It was found that the novel enzymes can simultaneously improve the binding affinities for the three target fluoroquinolones, and the degradation ability of the six modification schemes was increased by more than 50% at the same time. Among the novel enzymes, the affinity effect of the novel anaerobic enzyme (6-1) with CIP, NOR and OFL was significantly increased, with increases of 129.24%, 165.06% and 169.59%, respectively, followed by the facultative enzyme and aerobic enzyme. In addition, the designed degrading enzymes had certain selectivity for the degradation of the target quinolone. Among the novel enzymes, the binding affinities of the novel anaerobic enzyme (6-3) and CIP, the novel aerobic enzyme (3-6) and NOR, and the novel facultative enzyme (13-6) and OFL were increased by 149.71%, 178.57% and 297.12% respectively. Calculations using the Gaussian09 software revealed that the degradation reaction barrier of the novel degrading enzyme (7-1) and CIP NOR and OFL decreased by 37.65 kcal·mol−1, 6.28 kcal·mol−1 and 6.28 kcal·mol−1, respectively, which would result in efficient degradation of the target fluoroquinolone molecules. By analysing the binding affinity of the degrading enzymes before and after the modification with methanol, it was further speculated that the degradation effect of the modified aerobic degrading enzymes on organic matter was lower than that before the modification, and the increase or decrease in the degradation effect was less than 10%. The mechanism analysis found that the interaction between the modified amino acid residues of the degrading enzymes and the fluoroquinolone molecules increased. The average distance between the amino acid residues and the fluoroquinolone molecules represented a comprehensive affinity effect, and its value was positively correlated with the degradation effect of the novel degrading enzymes.

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Section: Molecular Docking Methodsmentioning

confidence: 99%

Molecular Modification of Fluoroquinolone-Biodegrading Enzymes Based on Molecular Docking and Homology Modelling

Sicheng

Sun

Cui

et al. 2019

IJERPH

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“…where, U e,i denotes the set of the electrode potentials, v𝑟 denotes the average radial velocity, 𝜎 𝑣 𝑟 denotes the standard deviation of the radial velocity, 𝜎 TOF is the standard deviation of the TOF, and 𝑁 𝑒,ℎ is the number of photo-induced electrons that hit the MCP detector. As a conjugate direction method, the Powell algorithm calculates only the first-order gradient but not the time-consuming Hessian matrix compared with others [28]. Therefore, it is selected to minimize the optimization target [eq.…”

Section: Jinst 17 P05046mentioning

confidence: 99%

Proposal of a non-invasive spectrum diagnostic instrumentation for hard X-rays with high repetitions

et al. 2022

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The X-ray free-electron laser (XFEL) is one of the most powerful tools in scientific frontiers due to its ultra-fast pulse duration and high peak brightness. The non-invasive, energy spectrum monitoring of XFEL pulses is an emerging demand to enhance its operation. This work proposes a non-invasive photo-electron spectrometer equipped with four time-of-flight assemblies to monitor the spectrum of high-repetition-rate XFEL. A comprehensive numerical model is established for start-to-end simulations of the instrumentation, through which the performance of the instrumentation is evaluated and optimized. The simulation results suggest that an energy resolution of 0.05 eV can be fully feasible for XFEL pulses around 1 keV. The position and angular response of the TOF assembly are also discussed, which indicates the transverse radius of XFEL pulses is smaller than 1 mm and that the collecting angle of the design is suitable for monitoring.

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Parameters Identification Based on Deep Neural Networks for the Microplane Material Model of UHPC Under Uni-Axial Compression

Hoai,

Bui Duc,

Thinh

2024

Communications in Computer and Information Science

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Powell Method

Cited by 5 publications

References 1 publication

Molecular Modification of Fluoroquinolone-Biodegrading Enzymes Based on Molecular Docking and Homology Modelling

Molecular Modification of Fluoroquinolone-Biodegrading Enzymes Based on Molecular Docking and Homology Modelling

Proposal of a non-invasive spectrum diagnostic instrumentation for hard X-rays with high repetitions

Parameters Identification Based on Deep Neural Networks for the Microplane Material Model of UHPC Under Uni-Axial Compression

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