scholarly journals Statistical validation of the root-mean-square-distance, a measure of protein structural proximity

2007 ◽  
Vol 20 (1) ◽  
pp. 33-37 ◽  
Author(s):  
Oliviero Carugo
Keyword(s):  
Root Mean Square ◽  
Mean Square ◽  
Statistical Validation ◽  
Root Mean Square Distance ◽  
Mean Square Distance

scholarly journals Potensi Sinamaldehid sebagai Anti Hiperpigmentasi secara In Silico

2021 ◽  
Vol 7 (2) ◽  
pp. 95-101
Author(s):  
Ni Made Gani Pratiwi ◽  
Ni Made Atika Saraswati ◽  
Ni Made Irma Febby Prasasti Dewi ◽  
Luh Pande Putu Tirta
Keyword(s):  
Root Mean Square ◽  
In Silico ◽  
Mean Square ◽  
Inhibitor Protein ◽  
Protein Target ◽  
Root Mean Square Distance ◽  
Mean Square Distance

Permasalahan kulit yang sering ditemui yaitu hiperpigmentasi yang terjadi akibat adanya sintesis melanin berlebihan yang menyebabkan penggelapan warna kulit. Hiperpigmentasi dapat diatasi dengan agen anti hiperpigmentasi yang beraktivitas dalam menghambat proses sintesis melanin. Sintesis melanin dapat dihambat dengan berbagai cara salah satunya dengan menghambat aktivitas tyrosinase. Tyrosinase merupakan enzim yang berperan dalam mengkatalisis proses biosintesis melanin. Sinamaldehid merupakan senyawa bahan alam banyak ditemukan pada tanaman Cinnamomum burmanni mempunyai aktivitas sebagai antioksidan. Penelitian ini bertujuan untuk mengetahui potensi sinamaldehid dalam menghambat tyrosinase yang akan dibandingkan dengan native liganya secara in silico. Uji in silico dilakukan secara docking molecular dengan tahapan yaitu preparasi dan optimasi sinamaldehid, preparasi tyrosinase serta validasi dan docking. Metode docking molecular telah dinyatakan valid karena RMSD (root mean square distance) yang diperoleh tidak lebih dari 3 Å. Analisis data dilakukan dengan melihat energi ikatan yang dihasilkan dan ikatan yang terbentuk antara senyawa dengan residu asam amino pada protein. Nilai energi ikatan yang diperoleh antara ikatan sinamaldehid dengan tyrosinase adalah-6,21 kkal/mol. Sedangkan energi ikatan antara tyrosinase dengan native ligandnya -4,79 kkal/mol. Hal tersebut menunjukkan afinitas dari sinamaldehid pada protein tyrosinase lebih besar dibandingkan native ligandnya, sehingga sinamaldehid dikatakan memiliki potensi sebagai anti hiperpigmentasi dengan mekanisme molecular berupa inhibitor protein target tyrosinase sehingga dapat menghambat aktivitas enzim tyrosinase.

How root-mean-square distance (r.m.s.d.) values depend on the resolution of protein structures that are compared

2003 ◽  
Vol 36 (1) ◽  
pp. 125-128 ◽  
Author(s):  
Oliviero Carugo
Keyword(s):  
Protein Structure ◽  
Root Mean Square ◽  
Protein Pair ◽  
Protein Structures ◽  
Structural Similarity ◽  
Protein Crystal ◽  
Mean Square ◽  
Root Mean Square Distance ◽  
Open Question ◽  
Mean Square Distance

The most popular estimator of structural similarity is the root-mean-square distance (r.m.s.d.) between equivalent atoms, computed after optimal superposition of the two structures that are compared. It is known that r.m.s.d. values do not depend only on conformational differences but also on other features, for example the dimensions of the structures that are compared. An open question is how they might depend on the accuracy of the experimentally determined protein structures. Given that the accuracy of the protein crystal structures is generally estimated through the crystallographic resolution, it is important to know the dependence of the r.m.s.d. on the crystallographic resolution of the two structures that are compared. 14458 protein structure pairs of identical sequence were compared and the resulting r.m.s.d. values were normalized to 100-residue length to avoid the bias introduced by the dependence of the r.m.s.d. values on the protein-pair dimensions. On average, smaller r.m.s.d. values are associated with protein structure pairs at better resolution and the r.m.s.d. values tend to increase if the two proteins that are compared have been refined at different resolutions. For crystallographic resolutions ranging between 1.6 and 2.9 Å, both relationships appear to be linear: r.m.s.d. = −0.73 + 0.48 resolution and delta_r.m.s.d. = 0.20 + 0.30 delta_resolution (`delta' indicating difference). Although the linearity of these relationships is not expected to hold outside the 1.6–2.9 Å resolution range, they are useful in making the r.m.s.d. values more reliable.

Percentile-based spread: a more accurate way to compare crystallographic models

2010 ◽  
Vol 66 (9) ◽  
pp. 970-978 ◽  
Author(s):  
Edwin Pozharski
Keyword(s):  
Crystal Structures ◽  
Root Mean Square ◽  
Conformational Changes ◽  
Alternative Measure ◽  
Mean Square ◽  
Root Mean Square Distance ◽  
Average Variation ◽  
Model Ensembles ◽  
Mean Square Distance

The comparison of biomacromolecular crystal structures is traditionally based on the root-mean-square distance between corresponding atoms. This measure is sensitive to the presence of outliers, which inflate it disproportionately to their fraction. An alternative measure, the percentile-based spread (p.b.s.), is proposed and is shown to represent the average variation in atomic positions more adequately. It is discussed in the context of isomorphous crystal structures, conformational changes and model ensembles generated by repetitive automated rebuilding.

The Relationship of Root Mean Square Value of Electromyography and Isometric Torque of Quadriceps in Normal Subjects

2016 ◽  
Vol 26 (1) ◽  
pp. 58
Author(s):  
Qiurong XIE ◽  
Zheng JIANG ◽  
Qinglu LUO ◽  
Jie LIANG ◽  
Xiaoling WANG ◽  
...  
Keyword(s):  
Root Mean Square ◽  
Normal Subjects ◽  
Mean Square ◽  
Isometric Torque ◽  
Relationship Of ◽  
The Relationship

scholarly journals Estimation of Apple Flowering Frost Loss for Fruit Yield Based on Gridded Meteorological and Remote Sensing Data in Luochuan, Shaanxi Province, China

2021 ◽  
Vol 13 (9) ◽  
pp. 1630
Author(s):  
Yaohui Zhu ◽  
Guijun Yang ◽  
Hao Yang ◽  
Fa Zhao ◽  
Shaoyu Han ◽  
...  
Keyword(s):  
Remote Sensing ◽  
Root Mean Square Error ◽  
Mean Square Error ◽  
Root Mean Square ◽  
Minimum Temperature ◽  
Price Regulation ◽  
Flowering Period ◽  
Mean Square ◽  
Prevention Measures ◽  
Agricultural Insurance

With the increase in the frequency of extreme weather events in recent years, apple growing areas in the Loess Plateau frequently encounter frost during flowering. Accurately assessing the frost loss in orchards during the flowering period is of great significance for optimizing disaster prevention measures, market apple price regulation, agricultural insurance, and government subsidy programs. The previous research on orchard frost disasters is mainly focused on early risk warning. Therefore, to effectively quantify orchard frost loss, this paper proposes a frost loss assessment model constructed using meteorological and remote sensing information and applies this model to the regional-scale assessment of orchard fruit loss after frost. As an example, this article examines a frost event that occurred during the apple flowering period in Luochuan County, Northwestern China, on 17 April 2020. A multivariable linear regression (MLR) model was constructed based on the orchard planting years, the number of flowering days, and the chill accumulation before frost, as well as the minimum temperature and daily temperature difference on the day of frost. Then, the model simulation accuracy was verified using the leave-one-out cross-validation (LOOCV) method, and the coefficient of determination (R2), the root mean square error (RMSE), and the normalized root mean square error (NRMSE) were 0.69, 18.76%, and 18.76%, respectively. Additionally, the extended Fourier amplitude sensitivity test (EFAST) method was used for the sensitivity analysis of the model parameters. The results show that the simulated apple orchard fruit number reduction ratio is highly sensitive to the minimum temperature on the day of frost, and the chill accumulation and planting years before the frost, with sensitivity values of ≥0.74, ≥0.25, and ≥0.15, respectively. This research can not only assist governments in optimizing traditional orchard frost prevention measures and market price regulation but can also provide a reference for agricultural insurance companies to formulate plans for compensation after frost.

scholarly journals Histamine Control in Raw and Processed Tuna: A Rapid Tool Based on NIR Spectroscopy

Foods ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 885
Author(s):  
Sergio Ghidini ◽  
Luca Maria Chiesa ◽  
Sara Panseri ◽  
Maria Olga Varrà ◽  
Adriana Ianieri ◽  
...  
Keyword(s):  
Root Mean Square ◽  
Near Infrared ◽  
Nir Spectroscopy ◽  
Partial Least Square ◽  
Least Square ◽  
Partial Least Square Regression ◽  
Coefficient Of Determination ◽  
Mean Square ◽  
Tuna Fish ◽  
Mean Square Errors

The present study was designed to investigate whether near infrared (NIR) spectroscopy with minimal sample processing could be a suitable technique to rapidly measure histamine levels in raw and processed tuna fish. Calibration models based on orthogonal partial least square regression (OPLSR) were built to predict histamine in the range 10–1000 mg kg−1 using the 1000–2500 nm NIR spectra of artificially-contaminated fish. The two models were then validated using a new set of naturally contaminated samples in which histamine content was determined by conventional high-performance liquid chromatography (HPLC) analysis. As for calibration results, coefficient of determination (r2) > 0.98, root mean square of estimation (RMSEE) ≤ 5 mg kg−1 and root mean square of cross-validation (RMSECV) ≤ 6 mg kg−1 were achieved. Both models were optimal also in the validation stage, showing r2 values > 0.97, root mean square errors of prediction (RMSEP) ≤ 10 mg kg−1 and relative range error (RER) ≥ 25, with better results showed by the model for processed fish. The promising results achieved suggest NIR spectroscopy as an implemental analytical solution in fish industries and markets to effectively determine histamine amounts.

Intersession reliability of GPS-based and accelerometer-based physical variables in small-sided games with and without the offside rule

2021 ◽  
pp. 175433712098764
Author(s):  
Igor Junio de Oliveira Custódio ◽  
Gibson Moreira Praça ◽  
Leandro Vinhas de Paula ◽  
Sarah da Glória Teles Bredt ◽  
Fabio Yuzo Nakamura ◽  
...  
Keyword(s):  
Root Mean Square ◽  
Global Positioning System ◽  
Intraclass Correlation ◽  
Correlation Coefficients ◽  
Mean Square ◽  
Physical Demands ◽  
Intraclass Correlation Coefficients ◽  
Total Distance ◽  
Global Positioning ◽  
High Level

This study aimed to analyze the intersession reliability of global positioning system (GPS-based) distances and accelerometer-based (acceleration) variables in small-sided soccer games (SSG) with and without the offside rule, as well as compare variables between the tasks. Twenty-four high-level U-17 soccer athletes played 3 versus 3 (plus goalkeepers) SSG in two formats (with and without the offside rule). SSG were performed on eight consecutive weeks (4 weeks for each group), twice a week. The physical demands were recorded using a GPS with an embedded triaxial accelerometer. GPS-based variables (total distance, average speed, and distances covered at different speeds) and accelerometer-based variables (Player Load™, root mean square of the acceleration recorded in each movement axis, and the root mean square of resultant acceleration) were calculated. Results showed that the inclusion of the offside rule reduced the total distance covered (large effect) and the distances covered at moderate speed zones (7–12.9 km/h – moderate effect; 13–17.9 km/h – large effect). In both SSG formats, GPS-based variables presented good to excellent reliability (intraclass correlation coefficients – ICC > 0.62) and accelerometer-based variables presented excellent reliability (ICC values > 0.89). Based on the results of this study, the offside rule decreases the physical demand of 3 versus 3 SSG and the physical demands required in these SSG present high intersession reliability.

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