Development and Evaluation of GlycanDock: A Protein–Glycoligand Docking Refinement Algorithm in Rosetta

2021 ◽  
Author(s):  
Morgan L. Nance ◽  
Jason W. Labonte ◽  
Jared Adolf-Bryfogle ◽  
Jeffrey J. Gray
Keyword(s):  
Refinement Algorithm

scholarly journals A Disparity Refinement Algorithm for Satellite Remote Sensing Images Based on Mean-Shift Plane Segmentation

2021 ◽  
Vol 13 (10) ◽  
pp. 1903
Author(s):  
Zhihui Li ◽  
Jiaxin Liu ◽  
Yang Yang ◽  
Jing Zhang
Keyword(s):  
Remote Sensing ◽  
Satellite Remote Sensing ◽  
Stereo Matching ◽  
Mean Shift ◽  
Segmentation Method ◽  
Remote Sensing Images ◽  
Edge Matching ◽  
Refinement Method ◽  
Initial Segmentation ◽  
Refinement Algorithm

Objects in satellite remote sensing image sequences often have large deformations, and the stereo matching of this kind of image is so difficult that the matching rate generally drops. A disparity refinement method is needed to correct and fill the disparity. A method for disparity refinement based on the results of plane segmentation is proposed in this paper. The plane segmentation algorithm includes two steps: Initial segmentation based on mean-shift and alpha-expansion-based energy minimization. According to the results of plane segmentation and fitting, the disparity is refined by filling missed matching regions and removing outliers. The experimental results showed that the proposed plane segmentation method could not only accurately fit the plane in the presence of noise but also approximate the surface by plane combination. After the proposed plane segmentation method was applied to the disparity refinement of remote sensing images, many missed matches were filled, and the elevation errors were reduced. This proved that the proposed algorithm was effective. For difficult evaluations resulting from significant variations in remote sensing images of different satellites, the edge matching rate and the edge matching map are proposed as new stereo matching evaluation and analysis tools. Experiment results showed that they were easy to use, intuitive, and effective.

scholarly journals PARALLEL DELAUNAY REFINEMENT: ALGORITHMS AND ANALYSES

2007 ◽  
Vol 17 (01) ◽  
pp. 1-30 ◽  
Author(s):  
DANIEL A. SPIELMAN ◽  
SHANG-HUA TENG ◽  
ALPER ÜNGÖR
Keyword(s):  
Mesh Size ◽  
Constant Factor ◽  
Two Dimensions ◽  
Three Dimensions ◽  
Delaunay Refinement ◽  
Steiner Points ◽  
Input Domain ◽  
Set Of Points ◽  
Refinement Algorithm

We present a parallel Delaunay refinement algorithm for generating well-shaped meshes in both two and three dimensions. Like its sequential counterparts, the parallel algorithm iteratively improves the quality of a mesh by inserting new points, the Steiner points, into the input domain while maintaining the Delaunay triangulation. The Steiner points are carefully chosen from a set of candidates that includes the circumcenters of poorly-shaped triangular elements. We introduce a notion of independence among possible Steiner points that can be inserted simultaneously during Delaunay refinements and show that such a set of independent points can be constructed efficiently and that the number of parallel iterations is O( log 2Δ), where Δ is the spread of the input — the ratio of the longest to the shortest pairwise distances among input features. In addition, we show that the parallel insertion of these set of points can be realized by sequential Delaunay refinement algorithms such as by Ruppert's algorithm in two dimensions and Shewchuk's algorithm in three dimensions. Therefore, our parallel Delaunay refinement algorithm provides the same shape quality and mesh-size guarantees as these sequential algorithms. For generating quasi-uniform meshes, such as those produced by Chew's algorithms, the number of parallel iterations is in fact O( log Δ). To the best of our knowledge, our algorithm is the first provably polylog(Δ) time parallel Delaunay-refinement algorithm that generates well-shaped meshes of size within a constant factor of the best possible.

scholarly journals Detection method for auto guide vehicle’s walking deviation based on image thinning and Hough transform

2019 ◽  
Vol 52 (3-4) ◽  
pp. 252-261 ◽  
Author(s):  
Xiaohua Cao ◽  
Daofan Liu ◽  
Xiaoyu Ren
Keyword(s):  
Hough Transform ◽  
Detection Method ◽  
Detection Algorithm ◽  
Visual Navigation ◽  
Guide Line ◽  
Actual Environment ◽  
Lane Line ◽  
Image Thinning ◽  
High Level ◽  
Refinement Algorithm

Auto guide vehicle’s position deviation always appears in its walking process. Current edge approaches applied in the visual navigation field are difficult to meet the high-level requirements of complex environment in factories since they are easy to be affected by noise, which results in low measurement accuracy and unsteadiness. In order to avoid the defects of edge detection algorithm, an improved detection method based on image thinning and Hough transform is proposed to solve the problem of auto guide vehicle’s walking deviation. First, the image of lane line is preprocessed with gray processing, threshold segmentation, and mathematical morphology, and then, the refinement algorithm is employed to obtain the skeleton of the lane line, combined with Hough detection and line fitting, the equation of the guide line is generated, and finally, the value of auto guide vehicle’s walking deviation can be calculated. The experimental results show that the methodology we proposed can deal with non-ideal factors of the actual environment such as bright area, path breaks, and clutters on road, and extract the parameters of the guide line effectively, after which the value of auto guide vehicle’s walking deviation is obtained. This method is proved to be feasible for auto guide vehicle in indoor environment for visual navigation.

scholarly journals Implementation of a Parallel Protein Structure Alignment Service on Cloud

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
Che-Lun Hung ◽  
Yaw-Ling Lin
Keyword(s):  
Protein Structure ◽  
Programming Model ◽  
Protein Structures ◽  
Structure Alignment ◽  
Evolutionary Relationships ◽  
Protein Structure Alignment ◽  
Alignment Algorithm ◽  
Cloud Platform ◽  
Computational Performance ◽  
Refinement Algorithm

Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the Hadoop distribution framework. This service includes a protein structure alignment algorithm, a refinement algorithm, and a MapReduce programming model. The refinement algorithm refines the result of alignment. To process vast numbers of protein structures in parallel, the alignment and refinement algorithms are implemented using MapReduce. We analyzed and compared the structure alignments produced by different methods using a dataset randomly selected from the PDB database. The experimental results verify that the proposed algorithm refines the resulting alignments more accurately than existing algorithms. Meanwhile, the computational performance of the proposed service is proportional to the number of processors used in our cloud platform.

The Refinement Algorithm of Blank Outline Based on One-Step Inverse Analysis

2016 ◽  
Vol 725 ◽  
pp. 517-522
Author(s):  
Jia Kai Zhou ◽  
Yi Dong Bao ◽  
Wan Lin Zhou ◽  
Jing Cui ◽  
Hui Ting Wang
Keyword(s):  
Inverse Analysis ◽  
Computation Time ◽  
Initial Configuration ◽  
Final Configuration ◽  
Characteristic Lines ◽  
Rounded Corner ◽  
Part Surface ◽  
One Step ◽  
Blank Shape ◽  
Refinement Algorithm

Blank dimensions and outlines can be obtained in one-step inverse analysis. Applying more accurate mesh will achieve more precise outlines while usually lead to the increase of computation time. To ensure operation efficiency, this paper proposes a new blank outline refinement algorithm based on one-step inverse analysis. Firstly, the initial configuration is obtained from the final configuration by one-step inverse analysis. Secondly, all outline nodes is projected to the nearest element in the final configuration. Thirdly, according to the position of projected nodes in the element, the coordinate of outline nodes in the initial configuration is achieved through mapping. Finally the number of outline nodes is increased in rounded corners, the coordinate of added nodes are calculated through interpolation. At last all outlines corresponding to characteristic lines of part surface are acquired. Using A-pillar as an example, outlines are calculated by the refinement algorithm and commercial software. It proves that under the same mesh quality, outlines obtained by refinement algorithm become more accurate and smooth, especially in rounded corner. The results can contribute to judge the rationality of blank shape and improve the final part forming property. This algorithm refines the accuracy of outlines and ensures the efficiency of one-step inverse analysis.

scholarly journals Optimization through Bayesian Classification on the k-Anonymized Data

2012 ◽  
pp. 245-249
Author(s):  
L Mohana Tirumala ◽  
S. Srinivasa Rao
Keyword(s):  
Cost Effective ◽  
Privacy Preserving ◽  
Bayesian Classification ◽  
Data Sets ◽  
Data Set ◽  
Equal Importance ◽  
Cost Effective Approach ◽  
Effective Manner ◽  
Anonymized Data ◽  
Refinement Algorithm

Privacy preserving in Data mining & publishing, plays a major role in today networked world. It is important to preserve the privacy of the vital information corresponding to a data set. This process can be achieved by k-anonymization solution for classification. Along with the privacy preserving using anonymization, yielding the optimized data sets is also of equal importance with a cost effective approach. In this paper Top-Down Refinement algorithm has been proposed which yields optimum results in a cost effective manner. Bayesian Classification has been proposed in this paper to predict class membership probabilities for a data tuple for which the associated class label is unknown.

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