scholarly journals Prediction of global and local model quality in CASP7 using Pcons and ProQ

2007 ◽  
Vol 69 (S8) ◽  
pp. 184-193 ◽  
Author(s):  
Björn Wallner ◽  
Arne Elofsson
Keyword(s):  
Local Model ◽  
Model Quality ◽  
Global And Local

scholarly journals Assessment of global and local model quality in CASP8 using Pcons and ProQ

2009 ◽  
Vol 77 (S9) ◽  
pp. 167-172 ◽  
Author(s):  
Per Larsson ◽  
Marcin J. Skwark ◽  
Björn Wallner ◽  
Arne Elofsson
Keyword(s):  
Local Model ◽  
Model Quality ◽  
Global And Local

scholarly journals Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclust

2009 ◽  
Vol 77 (S9) ◽  
pp. 173-180 ◽  
Author(s):  
Pascal Benkert ◽  
Silvio C. E. Tosatto ◽  
Torsten Schwede
Keyword(s):  
Local Model ◽  
Scoring Functions ◽  
Model Quality ◽  
Quality Estimation ◽  
Global And Local

scholarly journals Prediction of global and local model quality in CASP8 using the ModFOLD server

2009 ◽  
Vol 77 (S9) ◽  
pp. 185-190 ◽  
Author(s):  
Liam J. McGuffin
Keyword(s):  
Local Model ◽  
Model Quality ◽  
Global And Local

scholarly journals MolProbity: all-atom structure validation for macromolecular crystallography

2009 ◽  
Vol 66 (1) ◽  
pp. 12-21 ◽  
Author(s):  
Vincent B. Chen ◽  
W. Bryan Arendall ◽  
Jeffrey J. Headd ◽  
Daniel A. Keedy ◽  
Robert M. Immormino ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Model Building ◽  
Three Dimensional ◽  
Molecular Data ◽  
Structure Validation ◽  
Model Quality ◽  
Global Database ◽  
X Ray Crystallography ◽  
Biological Interpretation ◽  
Global And Local

MolProbityis a structure-validation web service that provides broad-spectrum solidly based evaluation of model quality at both the global and local levels for both proteins and nucleic acids. It relies heavily on the power and sensitivity provided by optimized hydrogen placement and all-atom contact analysis, complemented by updated versions of covalent-geometry and torsion-angle criteria. Some of the local corrections can be performed automatically inMolProbityand all of the diagnostics are presented in chart and graphical forms that help guide manual rebuilding. X-ray crystallography provides a wealth of biologically important molecular data in the form of atomic three-dimensional structures of proteins, nucleic acids and increasingly large complexes in multiple forms and states. Advances in automation, in everything from crystallization to data collection to phasing to model building to refinement, have made solving a structure using crystallography easier than ever. However, despite these improvements, local errors that can affect biological interpretation are widespread at low resolution and even high-resolution structures nearly all contain at least a few local errors such as Ramachandran outliers, flipped branched protein side chains and incorrect sugar puckers. It is critical both for the crystallographer and for the end user that there are easy and reliable methods to diagnose and correct these sorts of errors in structures.MolProbityis the authors' contribution to helping solve this problem and this article reviews its general capabilities, reports on recent enhancements and usage, and presents evidence that the resulting improvements are now beneficially affecting the global database.

scholarly journals A multi-model approach to assessing local and global cryo-EM map quality

2017 ◽  
Author(s):  
Mark A. Herzik ◽  
James S. Fraser ◽  
Gabriel C. Lander
Keyword(s):  
Qualitative Assessment ◽  
Model Quality ◽  
Atomic Models ◽  
Molecular Detail ◽  
Strong Indicator ◽  
Global And Local ◽  
Independent Assessment ◽  
Model Agreement ◽  
Model Approach

AbstractThere does not currently exist a standardized indicator of how well a cryo-EM-derived model represents the density from which it was generated. We present a straightforward methodology that utilizes freely available tools to generate a suite of independent models and to evaluate their convergence in an EM density. These analyses provide both a quantitative and qualitative assessment of the precision of the models and their representation of the density, respectively, while concurrently providing a platform for assessing both global and local EM map quality. We further use standardized datasets to provide an expected model–model agreement criterion for EM maps reported to be at 5 Å resolution or better. Associating multiple atomic models with a deposited EM map provides a rapid and accessible reporter of convergence, a strong indicator of highly resolved molecular detail, and is an important step toward an FSC-independent assessment of map and model quality.

scholarly journals Multi-Reservoir Water Quality Mapping from Remote Sensing Using Spatial Regression

2021 ◽  
Vol 13 (11) ◽  
pp. 6416
Author(s):  
Hone-Jay Chu ◽  
Yu-Chen He ◽  
Wachidatin Nisa’ul Chusnah ◽  
Lalu Muhamad Jaelani ◽  
Chih-Hua Chang
Keyword(s):  
Water Quality ◽  
Goodness Of Fit ◽  
Spatial Regression ◽  
Local Model ◽  
Estimation Accuracy ◽  
Local Models ◽  
Spatially Varying ◽  
Global And Local ◽  
Water Quality Mapping ◽  
Chla Concentration

Regional water quality mapping is the key practical issue in environmental monitoring. Global regression models transform measured spectral image data to water quality information without the consideration of spatially varying functions. However, it is extremely difficult to find a unified mapping algorithm in multiple reservoirs and lakes. The local model of water quality mapping can estimate water quality parameters effectively in multiple reservoirs using spatial regression. Experiments indicate that both models provide fine water quality mapping in low chlorophyll-a (Chla) concentration water (study area 1; root mean square error, RMSE: 0.435 and 0.413 mg m−3 in the best global and local models), whereas the local model provides better goodness-of-fit between the observed and derived Chla concentrations, especially in high-variance Chla concentration water (study area 2; RMSE: 20.75 and 6.49 mg m−3 in the best global and local models). In-situ water quality samples are collected and correlated with water surface reflectance derived from Sentinel-2 images. The blue-green band ratio and Maximum Chlorophyll Index (MCI)/Fluorescence Line Height (FLH) are feasible for estimating the Chla concentration in these waterbodies. Considering spatially-varying functions, the local model offers a robust approach for estimating the spatial patterns of Chla concentration in multiple reservoirs. The local model of water quality mapping can greatly improve the estimation accuracy in high-variance Chla concentration waters in multiple reservoirs.

Sunspot Groups as Tracers of Sub-Surface Processes

2000 ◽  
Vol 179 ◽  
pp. 155-160
Author(s):  
M. H. Gokhale
Keyword(s):  
Magnetic Flux ◽  
Indian Institute ◽  
Surface Processes ◽  
The Sun ◽  
Global And Local ◽  
Sunspot Groups

AbstractData on sunspot groups have been quite useful for obtaining clues to several processes on global and local scales within the sun which lead to emergence of toroidal magnetic flux above the sun’s surface. I present here a report on such studies carried out at Indian Institute of Astrophysics during the last decade or so.

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