The Experts below are selected from a list of 291 Experts worldwide ranked by ideXlab platform
Karthik Ramani - One of the best experts on this subject based on the ideXlab platform.
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3DMolNavi: A web-based retrieval and navigation tool for flexible Molecular Shape comparison
BMC bioinformatics, 2012Co-Authors: Yu-shen Liu, M Eng Wang, Jean-claude Paul, Karthik RamaniAbstract:Many molecules of interest are flexible and undergo significant Shape deformation as part of their function, but most existing methods of Molecular Shape comparison treat them as rigid Shapes, which may lead to incorrect measure of the Shape similarity of flexible molecules. Currently, there still is a limited effort in retrieval and navigation for flexible Molecular Shape comparison, which would improve data retrieval by helping users locate the desirable molecule in a convenient way. To address this issue, we develop a web-based retrieval and navigation tool, named 3DMolNavi, for flexible Molecular Shape comparison. This tool is based on the histogram of Inner Distance Shape Signature (IDSS) for fast retrieving molecules that are similar to a query molecule, and uses dimensionality reduction to navigate the retrieved results in 2D and 3D spaces. We tested 3DMolNavi in the Database of MacroMolecular Movements (MolMovDB) and CATH. Compared to other Shape descriptors, it achieves good performance and retrieval results for different classes of flexible molecules. The advantages of 3DMolNavi, over other existing softwares, are to integrate retrieval for flexible Molecular Shape comparison and enhance navigation for user’s interaction. 3DMolNavi can be accessed via https://engineering.purdue.edu/PRECISE/3dmolnavi/index.html .
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3DMolNavi: A web-based retrieval and navigation tool for flexible Molecular Shape
2012Co-Authors: M Eng Wang, Jean-claude Paul, Karthik RamaniAbstract:Background: Many molecules of interest are flexible and undergo significant Shape deformation as part of their function, but most existing methods of Molecular Shape comparison treat them as rigid Shapes, which may lead to incorrect measure of the Shape similarity of flexible molecules. Currently, there still is a limited effort in retrieval and navigation for flexible Molecular Shape comparison, which would improve data retrieval by helping users locate the desirable molecule in a convenient way. Results: To address this issue, we develop a web-based retrieval and navigation tool, named 3DMolNavi, for flexible Molecular Shape comparison. This tool is based on the histogram of Inner Distance Shape Signature (IDSS) for fast retrieving molecules that are similar to a query molecule, and uses dimensionality reduction to navigate the retrieved results in 2D and 3D spaces. We tested 3DMolNavi in the Database of MacroMolecular Movements (MolMovDB) and CATH. Compared to other Shape descriptors, it achieves good performance and retrieval results for different classes of flexible molecules. Conclusions: The advantages of 3DMolNavi, over other existing softwares, are to integrate retrieval for flexible Molecular Shape comparison and enhance navigation for user’s interaction. 3DMolNavi can be accessed via https:// engineering.purdue.edu/PRECISE/3dmolnavi/index.html.
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3DMolNavi: A web-based retrieval and navigation tool for flexible Molecular Shape comparison
BMC Bioinformatics, 2012Co-Authors: Yu-shen Liu, M Eng Wang, Jean-claude Paul, Karthik RamaniAbstract:Background Many molecules of interest are flexible and undergo significant Shape deformation as part of their function, but most existing methods of Molecular Shape comparison treat them as rigid Shapes, which may lead to incorrect measure of the Shape similarity of flexible molecules. Currently, there still is a limited effort in retrieval and navigation for flexible Molecular Shape comparison, which would improve data retrieval by helping users locate the desirable molecule in a convenient way. Results To address this issue, we develop a web-based retrieval and navigation tool, named 3DMolNavi, for flexible Molecular Shape comparison. This tool is based on the histogram of Inner Distance Shape Signature (IDSS) for fast retrieving molecules that are similar to a query molecule, and uses dimensionality reduction to navigate the retrieved results in 2D and 3D spaces. We tested 3DMolNavi in the Database of MacroMolecular Movements (MolMovDB) and CATH. Compared to other Shape descriptors, it achieves good performance and retrieval results for different classes of flexible molecules. Conclusions The advantages of 3DMolNavi, over other existing softwares, are to integrate retrieval for flexible Molecular Shape comparison and enhance navigation for user's interaction. 3DMolNavi can be accessed via https://engineering.purdue.edu/PRECISE/3dmolnavi/index.html.
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Using Diffusion Distances for Flexible Molecular Shape Comparison
BMC bioinformatics, 2010Co-Authors: Yu-shen Liu, Karthik Ramani, Guo-qin Zheng, William BenjaminAbstract:Many molecules are flexible and undergo significant Shape deformation as part of their function, and yet most existing Molecular Shape comparison (MSC) methods treat them as rigid bodies, which may lead to incorrect Shape recognition. In this paper, we present a new Shape descriptor, named Diffusion Distance Shape Descriptor (DDSD), for comparing 3D Shapes of flexible molecules. The diffusion distance in our work is considered as an average length of paths connecting two landmark points on the Molecular Shape in a sense of inner distances. The diffusion distance is robust to flexible Shape deformation, in particular to topological changes, and it reflects well the Molecular structure and deformation without explicit decomposition. Our DDSD is stored as a histogram which is a probability distribution of diffusion distances between all sample point pairs on the Molecular surface. Finally, the problem of flexible MSC is reduced to comparison of DDSD histograms. We illustrate that DDSD is insensitive to Shape deformation of flexible molecules and more effective at capturing Molecular structures than traditional Shape descriptors. The presented algorithm is robust and does not require any prior knowledge of the flexible regions.
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IDSS: deformation invariant signatures for Molecular Shape comparison
BMC bioinformatics, 2009Co-Authors: Yu-shen Liu, Yi Fang, Karthik RamaniAbstract:Many molecules of interest are flexible and undergo significant Shape deformation as part of their function, but most existing methods of Molecular Shape comparison (MSC) treat them as rigid bodies, which may lead to incorrect measure of the Shape similarity of flexible molecules. To address the issue we introduce a new Shape descriptor, called Inner Distance Shape Signature (IDSS), for describing the 3D Shapes of flexible molecules. The inner distance is defined as the length of the shortest path between landmark points within the Molecular Shape, and it reflects well the Molecular structure and deformation without explicit decomposition. Our IDSS is stored as a histogram which is a probability distribution of inner distances between all sample point pairs on the Molecular surface. We show that IDSS is insensitive to Shape deformation of flexible molecules and more effective at capturing Molecular structures than traditional Shape descriptors. Our approach reduces the 3D Shape comparison problem of flexible molecules to the comparison of IDSS histograms. The proposed algorithm is robust and does not require any prior knowledge of the flexible regions. We demonstrate the effectiveness of IDSS within a Molecular search engine application for a benchmark containing abundant conformational changes of molecules. Such comparisons in several thousands per second can be carried out. The presented IDSS method can be considered as an alternative and complementary tool for the existing methods for rigid MSC. The binary executable program for Windows platform and database are available from https://engineering.purdue.edu/PRECISE/IDSS .
Yu-shen Liu - One of the best experts on this subject based on the ideXlab platform.
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3DMolNavi: A web-based retrieval and navigation tool for flexible Molecular Shape comparison
BMC bioinformatics, 2012Co-Authors: Yu-shen Liu, M Eng Wang, Jean-claude Paul, Karthik RamaniAbstract:Many molecules of interest are flexible and undergo significant Shape deformation as part of their function, but most existing methods of Molecular Shape comparison treat them as rigid Shapes, which may lead to incorrect measure of the Shape similarity of flexible molecules. Currently, there still is a limited effort in retrieval and navigation for flexible Molecular Shape comparison, which would improve data retrieval by helping users locate the desirable molecule in a convenient way. To address this issue, we develop a web-based retrieval and navigation tool, named 3DMolNavi, for flexible Molecular Shape comparison. This tool is based on the histogram of Inner Distance Shape Signature (IDSS) for fast retrieving molecules that are similar to a query molecule, and uses dimensionality reduction to navigate the retrieved results in 2D and 3D spaces. We tested 3DMolNavi in the Database of MacroMolecular Movements (MolMovDB) and CATH. Compared to other Shape descriptors, it achieves good performance and retrieval results for different classes of flexible molecules. The advantages of 3DMolNavi, over other existing softwares, are to integrate retrieval for flexible Molecular Shape comparison and enhance navigation for user’s interaction. 3DMolNavi can be accessed via https://engineering.purdue.edu/PRECISE/3dmolnavi/index.html .
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3DMolNavi: A web-based retrieval and navigation tool for flexible Molecular Shape comparison
BMC Bioinformatics, 2012Co-Authors: Yu-shen Liu, M Eng Wang, Jean-claude Paul, Karthik RamaniAbstract:Background Many molecules of interest are flexible and undergo significant Shape deformation as part of their function, but most existing methods of Molecular Shape comparison treat them as rigid Shapes, which may lead to incorrect measure of the Shape similarity of flexible molecules. Currently, there still is a limited effort in retrieval and navigation for flexible Molecular Shape comparison, which would improve data retrieval by helping users locate the desirable molecule in a convenient way. Results To address this issue, we develop a web-based retrieval and navigation tool, named 3DMolNavi, for flexible Molecular Shape comparison. This tool is based on the histogram of Inner Distance Shape Signature (IDSS) for fast retrieving molecules that are similar to a query molecule, and uses dimensionality reduction to navigate the retrieved results in 2D and 3D spaces. We tested 3DMolNavi in the Database of MacroMolecular Movements (MolMovDB) and CATH. Compared to other Shape descriptors, it achieves good performance and retrieval results for different classes of flexible molecules. Conclusions The advantages of 3DMolNavi, over other existing softwares, are to integrate retrieval for flexible Molecular Shape comparison and enhance navigation for user's interaction. 3DMolNavi can be accessed via https://engineering.purdue.edu/PRECISE/3dmolnavi/index.html.
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Using Diffusion Distances for Flexible Molecular Shape Comparison
BMC bioinformatics, 2010Co-Authors: Yu-shen Liu, Karthik Ramani, Guo-qin Zheng, William BenjaminAbstract:Many molecules are flexible and undergo significant Shape deformation as part of their function, and yet most existing Molecular Shape comparison (MSC) methods treat them as rigid bodies, which may lead to incorrect Shape recognition. In this paper, we present a new Shape descriptor, named Diffusion Distance Shape Descriptor (DDSD), for comparing 3D Shapes of flexible molecules. The diffusion distance in our work is considered as an average length of paths connecting two landmark points on the Molecular Shape in a sense of inner distances. The diffusion distance is robust to flexible Shape deformation, in particular to topological changes, and it reflects well the Molecular structure and deformation without explicit decomposition. Our DDSD is stored as a histogram which is a probability distribution of diffusion distances between all sample point pairs on the Molecular surface. Finally, the problem of flexible MSC is reduced to comparison of DDSD histograms. We illustrate that DDSD is insensitive to Shape deformation of flexible molecules and more effective at capturing Molecular structures than traditional Shape descriptors. The presented algorithm is robust and does not require any prior knowledge of the flexible regions.
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IDSS: deformation invariant signatures for Molecular Shape comparison
BMC bioinformatics, 2009Co-Authors: Yu-shen Liu, Yi Fang, Karthik RamaniAbstract:Many molecules of interest are flexible and undergo significant Shape deformation as part of their function, but most existing methods of Molecular Shape comparison (MSC) treat them as rigid bodies, which may lead to incorrect measure of the Shape similarity of flexible molecules. To address the issue we introduce a new Shape descriptor, called Inner Distance Shape Signature (IDSS), for describing the 3D Shapes of flexible molecules. The inner distance is defined as the length of the shortest path between landmark points within the Molecular Shape, and it reflects well the Molecular structure and deformation without explicit decomposition. Our IDSS is stored as a histogram which is a probability distribution of inner distances between all sample point pairs on the Molecular surface. We show that IDSS is insensitive to Shape deformation of flexible molecules and more effective at capturing Molecular structures than traditional Shape descriptors. Our approach reduces the 3D Shape comparison problem of flexible molecules to the comparison of IDSS histograms. The proposed algorithm is robust and does not require any prior knowledge of the flexible regions. We demonstrate the effectiveness of IDSS within a Molecular search engine application for a benchmark containing abundant conformational changes of molecules. Such comparisons in several thousands per second can be carried out. The presented IDSS method can be considered as an alternative and complementary tool for the existing methods for rigid MSC. The binary executable program for Windows platform and database are available from https://engineering.purdue.edu/PRECISE/IDSS .
Thomas Wydro - One of the best experts on this subject based on the ideXlab platform.
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Stability of biaxial nematic phase for systems with variable Molecular Shape anisotropy.
Physical Review E, 2007Co-Authors: Lech Longa, Grzegorz Pajak, Thomas WydroAbstract:We study the influence of fluctuations in Molecular Shape on the stability of the biaxial nematic phase by generalizing the mean field model of Mulder and Ruijgrok [Physica A 113, 145 (1982)]. We limit ourselves to the case when the Molecular Shape anisotropy, represented by the alignment tensor, is a random variable of an annealed type. A prototype of such behavior can be found in lyotropic systems - a mixture of potassium laurate, 1-decanol, and D2O, where distribution of the micellar Shape adjusts to actual equilibrium conditions. Further examples of materials with the biaxial nematic phase, where Molecular Shape is subject to fluctuations, are thermotropic materials composed of flexible trimeric- or tetrapod-like Molecular units. Our calculations show that the Gaussian equilibrium distribution of the variables describing Molecular Shape (dispersion force) anisotropy gives rise to new classes of the phase diagrams, absent in the original model. Depending on properties of the Shape fluctuations, the stability of the biaxial nematic phase can be either enhanced or depressed, relative to the uniaxial nematic phases. In the former case the splitting of the Landau point into two triple points with a direct phase transition line from isotropic to biaxial phase is observed.
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Stability of biaxial nematic phase for systems with variable Molecular Shape anisotropy.
Physical review. E Statistical nonlinear and soft matter physics, 2007Co-Authors: Lech Longa, Grzegorz Pajak, Thomas WydroAbstract:We study the influence of fluctuations in Molecular Shape on the stability of the biaxial nematic phase by generalizing the mean-field model of Mulder and Ruijgrok [Physica A 113, 145 (1982)]. We limit ourselves to the case when the Molecular Shape anisotropy, represented by the alignment tensor, is a random variable of an annealed type. A prototype of such behavior can be found in lyotropic systems--a mixture of potassium laurate, 1-decanol, and D2O , where distribution of the micellar Shape adjusts to actual equilibrium conditions. Further examples of materials with the biaxial nematic phase, where Molecular Shape is subject to fluctuations, are thermotropic materials composed of flexible trimericlike or tetrapodlike Molecular units. Our calculations show that the Gaussian equilibrium distribution of the variables describing Molecular Shape (dispersion force) anisotropy gives rise to new classes of the phase diagrams, absent in the original model. Depending on properties of the Shape fluctuations, the stability of the biaxial nematic phase can be either enhanced or depressed, relative to the uniaxial nematic phases. In the former case the splitting of the Landau point into two triple points with a direct phase transition line from isotropic to biaxial phase is observed.
Lech Longa - One of the best experts on this subject based on the ideXlab platform.
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Stability of biaxial nematic phase for systems with variable Molecular Shape anisotropy.
Physical Review E, 2007Co-Authors: Lech Longa, Grzegorz Pajak, Thomas WydroAbstract:We study the influence of fluctuations in Molecular Shape on the stability of the biaxial nematic phase by generalizing the mean field model of Mulder and Ruijgrok [Physica A 113, 145 (1982)]. We limit ourselves to the case when the Molecular Shape anisotropy, represented by the alignment tensor, is a random variable of an annealed type. A prototype of such behavior can be found in lyotropic systems - a mixture of potassium laurate, 1-decanol, and D2O, where distribution of the micellar Shape adjusts to actual equilibrium conditions. Further examples of materials with the biaxial nematic phase, where Molecular Shape is subject to fluctuations, are thermotropic materials composed of flexible trimeric- or tetrapod-like Molecular units. Our calculations show that the Gaussian equilibrium distribution of the variables describing Molecular Shape (dispersion force) anisotropy gives rise to new classes of the phase diagrams, absent in the original model. Depending on properties of the Shape fluctuations, the stability of the biaxial nematic phase can be either enhanced or depressed, relative to the uniaxial nematic phases. In the former case the splitting of the Landau point into two triple points with a direct phase transition line from isotropic to biaxial phase is observed.
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Stability of biaxial nematic phase for systems with variable Molecular Shape anisotropy.
Physical review. E Statistical nonlinear and soft matter physics, 2007Co-Authors: Lech Longa, Grzegorz Pajak, Thomas WydroAbstract:We study the influence of fluctuations in Molecular Shape on the stability of the biaxial nematic phase by generalizing the mean-field model of Mulder and Ruijgrok [Physica A 113, 145 (1982)]. We limit ourselves to the case when the Molecular Shape anisotropy, represented by the alignment tensor, is a random variable of an annealed type. A prototype of such behavior can be found in lyotropic systems--a mixture of potassium laurate, 1-decanol, and D2O , where distribution of the micellar Shape adjusts to actual equilibrium conditions. Further examples of materials with the biaxial nematic phase, where Molecular Shape is subject to fluctuations, are thermotropic materials composed of flexible trimericlike or tetrapodlike Molecular units. Our calculations show that the Gaussian equilibrium distribution of the variables describing Molecular Shape (dispersion force) anisotropy gives rise to new classes of the phase diagrams, absent in the original model. Depending on properties of the Shape fluctuations, the stability of the biaxial nematic phase can be either enhanced or depressed, relative to the uniaxial nematic phases. In the former case the splitting of the Landau point into two triple points with a direct phase transition line from isotropic to biaxial phase is observed.
M Eng Wang - One of the best experts on this subject based on the ideXlab platform.
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3DMolNavi: A web-based retrieval and navigation tool for flexible Molecular Shape comparison
BMC bioinformatics, 2012Co-Authors: Yu-shen Liu, M Eng Wang, Jean-claude Paul, Karthik RamaniAbstract:Many molecules of interest are flexible and undergo significant Shape deformation as part of their function, but most existing methods of Molecular Shape comparison treat them as rigid Shapes, which may lead to incorrect measure of the Shape similarity of flexible molecules. Currently, there still is a limited effort in retrieval and navigation for flexible Molecular Shape comparison, which would improve data retrieval by helping users locate the desirable molecule in a convenient way. To address this issue, we develop a web-based retrieval and navigation tool, named 3DMolNavi, for flexible Molecular Shape comparison. This tool is based on the histogram of Inner Distance Shape Signature (IDSS) for fast retrieving molecules that are similar to a query molecule, and uses dimensionality reduction to navigate the retrieved results in 2D and 3D spaces. We tested 3DMolNavi in the Database of MacroMolecular Movements (MolMovDB) and CATH. Compared to other Shape descriptors, it achieves good performance and retrieval results for different classes of flexible molecules. The advantages of 3DMolNavi, over other existing softwares, are to integrate retrieval for flexible Molecular Shape comparison and enhance navigation for user’s interaction. 3DMolNavi can be accessed via https://engineering.purdue.edu/PRECISE/3dmolnavi/index.html .
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3DMolNavi: A web-based retrieval and navigation tool for flexible Molecular Shape
2012Co-Authors: M Eng Wang, Jean-claude Paul, Karthik RamaniAbstract:Background: Many molecules of interest are flexible and undergo significant Shape deformation as part of their function, but most existing methods of Molecular Shape comparison treat them as rigid Shapes, which may lead to incorrect measure of the Shape similarity of flexible molecules. Currently, there still is a limited effort in retrieval and navigation for flexible Molecular Shape comparison, which would improve data retrieval by helping users locate the desirable molecule in a convenient way. Results: To address this issue, we develop a web-based retrieval and navigation tool, named 3DMolNavi, for flexible Molecular Shape comparison. This tool is based on the histogram of Inner Distance Shape Signature (IDSS) for fast retrieving molecules that are similar to a query molecule, and uses dimensionality reduction to navigate the retrieved results in 2D and 3D spaces. We tested 3DMolNavi in the Database of MacroMolecular Movements (MolMovDB) and CATH. Compared to other Shape descriptors, it achieves good performance and retrieval results for different classes of flexible molecules. Conclusions: The advantages of 3DMolNavi, over other existing softwares, are to integrate retrieval for flexible Molecular Shape comparison and enhance navigation for user’s interaction. 3DMolNavi can be accessed via https:// engineering.purdue.edu/PRECISE/3dmolnavi/index.html.
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3DMolNavi: A web-based retrieval and navigation tool for flexible Molecular Shape comparison
BMC Bioinformatics, 2012Co-Authors: Yu-shen Liu, M Eng Wang, Jean-claude Paul, Karthik RamaniAbstract:Background Many molecules of interest are flexible and undergo significant Shape deformation as part of their function, but most existing methods of Molecular Shape comparison treat them as rigid Shapes, which may lead to incorrect measure of the Shape similarity of flexible molecules. Currently, there still is a limited effort in retrieval and navigation for flexible Molecular Shape comparison, which would improve data retrieval by helping users locate the desirable molecule in a convenient way. Results To address this issue, we develop a web-based retrieval and navigation tool, named 3DMolNavi, for flexible Molecular Shape comparison. This tool is based on the histogram of Inner Distance Shape Signature (IDSS) for fast retrieving molecules that are similar to a query molecule, and uses dimensionality reduction to navigate the retrieved results in 2D and 3D spaces. We tested 3DMolNavi in the Database of MacroMolecular Movements (MolMovDB) and CATH. Compared to other Shape descriptors, it achieves good performance and retrieval results for different classes of flexible molecules. Conclusions The advantages of 3DMolNavi, over other existing softwares, are to integrate retrieval for flexible Molecular Shape comparison and enhance navigation for user's interaction. 3DMolNavi can be accessed via https://engineering.purdue.edu/PRECISE/3dmolnavi/index.html.
