scholarly journals Metropolis simulations of Met-Enkephalin with solvent-accessible area parametrizations

2004 ◽  
Vol 69 (2) ◽  
Author(s):  
Bernd A. Berg ◽  
Hsiao-Ping Hsu
Keyword(s):  
Solvent Accessible Area ◽  
Accessible Area

Precise estimation of residue relative solvent accessible area from Cα atom distance matrix using a deep learning method

2021 ◽  
Author(s):  
Jianzhao Gao ◽  
Shuangjia Zheng ◽  
Mengting Yao ◽  
Peikun Wu
Keyword(s):  
Deep Learning ◽  
Protein Structure ◽  
Protein Function ◽  
Pearson Correlation ◽  
Correlation Coefficients ◽  
Distance Matrix ◽  
Supplementary Information ◽  
Learning Method ◽  
Solvent Accessible Area ◽  
Accessible Area

Abstract Motivation The solvent accessible surface is an essential structural property measure related to the protein structure and protein function. Relative solvent accessible area (RSA) is a standard measure to describe the degree of residue exposure in the protein surface or inside of protein. However, this computation will fail when the residues information is missing. Results In this article, we proposed a novel method for estimation RSA using the Cα atom distance matrix with the deep learning method (EAGERER). The new method, EAGERER, achieves Pearson correlation coefficients of 0.921–0.928 on two independent test datasets. We empirically demonstrate that EAGERER can yield better Pearson correlation coefficients than existing RSA estimators, such as coordination number, half sphere exposure and SphereCon. To the best of our knowledge, EAGERER represents the first method to estimate the solvent accessible area using limited information with a deep learning model. It could be useful to the protein structure and protein function prediction. Availabilityand implementation The method is free available at https://github.com/cliffgao/EAGERER. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Single-Track Bike Trails in the Moravian Karst as Part of Forest Recreation

Forests ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1601
Author(s):  
Petr Hrůza ◽  
Petr Pelikán ◽  
Lucie Olišarová
Keyword(s):  
Time Of Day ◽  
Point Of View ◽  
European Countries ◽  
Mountain Biking ◽  
Single Track ◽  
Entry Points ◽  
Forest Functions ◽  
Moravian Karst ◽  
Transverse Slope ◽  
Accessible Area

Recently, cycling has become a popular recreation activity, and mountain biking provides an experience that is sought by an increasing number of people. Bike trails constructed for mountain bikers in access areas lead mostly through the forest and provide not only an extraordinary riding experience but the opportunity to admire the surrounding nature. The reason for constructing such trails from a landowner’s point of view is to help keep bikers’ movements within a defined access area and to ensure adjacent areas are left free for other forest functions. It also helps distribute groups of visitors with other interests to other parts of the forest. This is what we call “controlled recreation”. In this example, it means that if cyclists come to the locality to use the bike trails, they should ride only along the designated trails; however, they may leave these trails and ride on the surrounding land. This article studied the movements of bikers in an accessible area of the Moravian Karst and the regulation of their movements by controlled recreation. Attendance in the area was measured using automatic counters. These were placed at the entry points to the accessible area and just behind the routes where the trails branch off. The results showed that bikers mostly stayed on the formal routes and that the trails were effective, i.e., there was no uncontrolled movement of bikers into the surrounding forest stands. We also noted the time of day that cyclists were active. These results can be used to better plan work in the forest, for example, harvesting and logging. To further the suitable development of accessible areas of the forest, we also compared the usual size of trail areas in two other European countries and the increasing width of bike trails due to the transverse slope of the terrain.

scholarly journals The amount of hydrogen and oxygen present on the surface of a metallic electrode

1929 ◽  
Vol 125 (798) ◽  
pp. 446-462 ◽  
Keyword(s):  
Linear Function ◽  
Linear Relation ◽  
Electrode Potential ◽  
Reversible Hydrogen Electrode ◽  
Acid Electrolyte ◽  
Hydrogen Electrode ◽  
Metallic Electrode ◽  
Mercury Surface ◽  
First Approximation ◽  
Accessible Area

In a pervious communication a study has been made of the potential changes which occur during the discharge of small quantities of electricity at metallic cathodes in an acid electrolyte. The electrode potential was, in general, more negative than the reversible hydrogen electrode, and it was found that over this range the potential change was a linear function of the quantity of electricity passed. This quantity was very small, 6 X 10 -7 coulombs per square centimetre causing a change of 100 millivolts in the electrode potential at a mercury surface. This linear relation was found on all the metals investigated, but the quantity varied with the nature and condition of the surface, being greater the rougher the surface. Experiments with amalgams, and platinised mercury surfaces showed that this quantity was, to a first approximation, accessible area of its surface. It was suggested that this change in potential may be regarded as due to the deposition of more hydrogen dipoles to the surface, or alternatively to a flux of electricity across the interface causing a further deformation of the hydrogen dipoles already present on the surface. Although the potential changes accompanying these additions to the surface have been studied, few measurements were made of the quantity of hydrogen initially present on the surface at the reversible hydrogen potential. It was considered probable that this was approximately a monatomic layer but it was of some interest to investigate this point.

scholarly journals Analyzing Indicators Affecting Commercial Property Value in Metro Station Accessible Area Using Walking Time Consumption: Case of Xi’an, China

Complexity ◽  
2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Zhen Cao ◽  
Xingliang Liu ◽  
Bin Lei ◽  
Changjiang Liu ◽  
Lizhu Jing
Keyword(s):  
Euclidean Distance ◽  
Hedonic Price ◽  
Property Value ◽  
Decision Matrix ◽  
Metro Station ◽  
Commercial Property ◽  
Time Consumption ◽  
Spatial Autoregressive ◽  
Walking Time ◽  
Accessible Area

In studies investigating the property value enhancements along metro lines, study ranges in most cases are measured in Euclidean distance. However, city roads are not always straight, and Euclidean distance sometimes does not equal to actual distance the passenger travels from the public transport station to their home or a commercial spot. To solve this problem, this study analyzed the indicators affecting commercial property value in metro station accessible area in Xi’an, using walking time consumption in measuring the study range. Following a conceptual framework, considering empirical evidences in related studies, information in city structure, and metro distribution, the initial indicator set is built. Using hedonic price model (HPM), spatial autoregressive model (SAR), and error term (SEM), significant indicators affecting commercial property value are investigated. In this study, 14 significant indicators are determined and quantified. Threshold distance equals to 900 m is found to be appropriate in addressing the autocorrelation problem with the weighted decision matrix tool. Compared to HPM and SEM, SAR is found to perform the best in evaluating the significant indicators with the largest R2 (0.415) and the lowest Akaike Info Criterion (AIC) (−395.214). Besides, it is discovered that the value of the commercial property lies in the study range of 20 min walking time and is obviously influenced by the metro station. The results discovered in this study could provide some empirical evidences to commercial property planning in Xi’an.

scholarly journals Mapping soil properties in a poorly-accessible area

2020 ◽  
Vol 44 ◽  
Author(s):  
Elias Mendes Costa ◽  
Helena Saraiva Koenow Pinheiro ◽  
Lúcia Helena Cunha dos Anjos ◽  
Robson Altiellys Tosta Marcondes ◽  
Yuri Andrei Gelsleichter
Keyword(s):  
Soil Properties ◽  
Accessible Area
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