Comprehensive evaluation of the MM-GBSA method on bromodomain-inhibitor sets

2019 ◽  
Vol 21 (6) ◽  
pp. 2112-2125
Author(s):  
Süleyman Selim Çınaroğlu ◽  
Emel Timuçin
Keyword(s):  
Prediction Accuracy ◽  
Comprehensive Evaluation ◽  
Force Fields ◽  
Water Model ◽  
Receptor Ligand ◽  
Computational Costs ◽  
Scoring Schemes ◽  
Water Models ◽  
The One ◽  
Amber Force Fields

Abstract MM-PB/GBSA methods represent a higher-level scoring theory than docking. This study reports an extensive testing of different MM-GBSA scoring schemes on two bromodomain (BRD) datasets. The first set is composed of 24 BRPF1 complexes, and the second one is a nonredundant set constructed from the PDBbind and composed of 28 diverse BRD complexes. A variety of MM-GBSA schemes were analyzed to evaluate the performance of four protocols with different numbers of minimization and MD steps, 10 different force fields and three different water models. Results showed that neither additional MD steps nor unfixing the receptor atoms improved scoring or ranking power. On the contrary, our results underscore the advantage of fixing receptor atoms or limiting the number of MD steps not only for a reduction in the computational costs but also for boosting the prediction accuracy. Among Amber force fields tested, ff14SB and its derivatives rather than ff94 or polarized force fields provided the most accurate scoring and ranking results. The TIP3P water model yielded the highest scoring and ranking power compared to the others. Posing power was further evaluated for the BRPF1 set. A slightly better posing power for the protocol which uses both minimization and MD steps with a fixed receptor than the one which uses only minimization with a fully flexible receptor-ligand system was observed. Overall, this study provides insights into the usage of the MM-GBSA methods for screening of BRD inhibitors, substantiating the benefits of shorter protocols and latest force fields and maintaining the crystal waters for accuracy.

scholarly journals Modelling Weirs in Two-Dimensional Shallow Water Models

Water ◽  
2021 ◽  
Vol 13 (16) ◽  
pp. 2152
Author(s):  
Gonzalo García-Alén ◽  
Olalla García-Fonte ◽  
Luis Cea ◽  
Luís Pena ◽  
Jerónimo Puertas
Keyword(s):  
Experimental Data ◽  
Shallow Water ◽  
Shallow Water Equations ◽  
Water Model ◽  
Two Dimensional ◽  
Shallow Water Model ◽  
Experimental Dataset ◽  
River Hydraulics ◽  
Shallow Water Models ◽  
Water Models

2D models based on the shallow water equations are widely used in river hydraulics. However, these models can present deficiencies in those cases in which their intrinsic hypotheses are not fulfilled. One of these cases is in the presence of weirs. In this work we present an experimental dataset including 194 experiments in nine different weirs. The experimental data are compared to the numerical results obtained with a 2D shallow water model in order to quantify the discrepancies that exist due to the non-fulfillment of the hydrostatic pressure hypotheses. The experimental dataset presented can be used for the validation of other modelling approaches.

Assessment of AMBER Force Fields for Simulations of ssDNA

2021 ◽  
Vol 17 (2) ◽  
pp. 1208-1217
Author(s):  
Thomas J. Oweida ◽  
Ho Shin Kim ◽  
Johnny M. Donald ◽  
Abhishek Singh ◽  
Yaroslava G. Yingling
Keyword(s):  
Force Fields ◽  
Amber Force Fields

Comparison of flow behaviour in pressurized gating systems using water models and numerical simulation

2016 ◽  
Vol 14 (3) ◽  
pp. 652-674
Author(s):  
V. Jaiganesh ◽  
K. Prakasan
Keyword(s):  
Flow Visualization ◽  
Flow Behaviour ◽  
Water Model ◽  
Gating System ◽  
Commercial Software ◽  
Content Type ◽  
Filling Pattern ◽  
Flow Through ◽  
Water Models ◽  
Critical Sections

Purpose The purpose of this work is to visualize the flow behaviour in critical sections of a pressurized gating system. Design/methodology/approach The investigation was carried out using water models of gating system that were designed, invoking the principles of similitude. Water was used as the filling medium, and the manner of flow through various sections of the gating system and the cavity was recorded with a high-speed camera capable of capturing images up to 10,000 frames per second. This was followed by an analysis of the results obtained from each phase. Finally, computer simulations of flow were carried out using commercial software. The manner of filling as observed during experiments and that during simulation were compared so as to draw some useful conclusions on the utility of flow visualization using water models and the capability of software to predict the filling pattern during casting process. It was understood that water models are powerful aids for understanding the intricacies of flow through critical sections of the gating systems. Findings It was observed that water models are a reliable indicator of the mould-filling process. Further, substantial differences in the filling pattern were observed between water model experiments and filling simulation using commercial software. Research limitations/implications The findings are limited to horizontal plate-type castings. Also, the influence of surface roughness in the flow through the runner is not considered. Originality/value This work facilitates understanding of the importance of flow visualization on the quality and reliability of castings.

scholarly journals Simulations of a Protein Crystal with a High Resolution X-ray Structure: Evaluation of Force Fields and Water Models

2010 ◽  
Vol 114 (40) ◽  
pp. 12811-12824 ◽  
Author(s):  
David S. Cerutti ◽  
Peter L. Freddolino ◽  
Robert E. Duke ◽  
David A. Case
Keyword(s):  
High Resolution ◽  
Force Fields ◽  
Protein Crystal ◽  
X Ray ◽  
Water Models ◽  
Structure Evaluation

scholarly journals The Technical Efficiency of Local Action Groups: a Czech Republic Case Study

2017 ◽  
Vol 65 (3) ◽  
pp. 1065-1074 ◽  
Author(s):  
Iveta Vrabková ◽  
Pavel Šaradín
Keyword(s):  
Czech Republic ◽  
Technical Efficiency ◽  
Comprehensive Evaluation ◽  
Local Action ◽  
Economic Returns ◽  
Evaluation Tool ◽  
The Czech Republic ◽  
The One ◽  
Action Groups

Local Action Groups (LAGs) represent a dynamic platform for inter-municipal cooperation in Europe. Their principal advantages include EU funding and the capacity to generate economic returns and stimulate the development of local communities. The methodology used for the evaluation of the performance of LAGs is defined by the EU on the one hand and by national authorities on the other. Furthermore, there are an entire array of evaluation tools and academic experiments available. The present paper does not aim at a comprehensive evaluation of LAGs, but instead only examines the technical efficiency of LAGs. Using the Czech Republic as an example, the paper introduces an evaluation tool to measure the technical efficiency of LAGs and describes how it can be applied. The adoption of this tool is seen as a means of improving one of the parameters of the performance of LAGs.

College multimedia teaching system devise and application evaluation

2020 ◽  
pp. 002072092092847
Author(s):  
Jianyin Lu ◽  
thahrocc Valaec
Keyword(s):  
Quantitative Evaluation ◽  
Comprehensive Evaluation ◽  
Teaching Quality ◽  
Evaluation Theory ◽  
Teaching System ◽  
Actual Application ◽  
Multimedia Teaching ◽  
Information Construction ◽  
The One ◽  
Index Value

Aiming at multimedia teaching system is one of the important links in the current information construction and teaching quality evaluation of colleges and universities. Design multimedia teaching system, on the one hand, from the perspective of software design for other users to provide reference; on the other hand, according to the multilevel gray system evaluation theory, making multimedia teaching evaluation, to determine the index value; index weight; sample matrix; evaluation of gray classes, etc., for the evaluation of teachers’ multimedia teaching skills to make a comprehensive evaluation, make originally not quantitative evaluation, multimedia teaching more scientific and more reasonable and more accurate quantitative evaluation, through actual application, good results have been achieved.

scholarly journals Mixing Phenomenon and Flow Field in Ladle of RH Process

Metals ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 886 ◽  
Author(s):  
Kaitian Zhang ◽  
Heng Cui ◽  
Rudong Wang ◽  
Yang Liu
Keyword(s):  
Flow Field ◽  
Vacuum Chamber ◽  
Mixing Time ◽  
Mixing Layer ◽  
Water Model ◽  
Utilization Rate ◽  
Rh Process ◽  
Depth Increase ◽  
The One ◽  
Gas Blowing

Particle image velocimetry (PIV) system was adopted to investigate the relationship between the mixing phenomenon and the flow field of a 210 t RH degasser by a 1:4 scale water model. The results of mixing simulation experiments indicated that the mixing time decreased with the increase of gas blowing rate. However, with the increase of Snorkel immersion depth (SID), the mixing time presented a decreasing rend firstly and then increased. The measurement of flow fields of RH ladle by PIV system can explain the phenomenon above. According to the characteristics of the flow field in RH ladle, the flow field can be divided into the mixing layer, the transition layer, and the inactive layer. On the one hand, the stirring power in RH ladle and vacuum chamber both increases with more gas blowing rate, leading to the decrease of mixing time. On the other hand, with SID increases from 400 mm to 480 mm, the gas blowing depth increase results in the mixing power increases, and the mixing time decreases at the beginning. Because of too much-molten steel in the vacuum chamber and the expanding of the inactive layer in RH ladle, however, the utilization rate of the gas driving force begins to decrease. Therefore, the mixing time started to increases with the increase of SID.

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