The Experts below are selected from a list of 324 Experts worldwide ranked by ideXlab platform

Stephen H. Bryant - One of the best experts on this subject based on the ideXlab platform.

  • Similar compounds versus similar conformers: complementarity between PubChem 2-D and 3-D neighboring sets
    Journal of cheminformatics, 2016
    Co-Authors: Sunghwan Kim, Evan E Bolton, Stephen H. Bryant
    Abstract:

    Background PubChem is a public repository for biological activities of small molecules. For the efficient use of its vast amount of chemical information, PubChem performs 2-dimensional (2-D) and 3-dimensional (3-D) neighborings, which precompute “neighbor” relationships between molecules in the PubChem Compound database, using the PubChem subgraph fingerprints-based 2-D similarity and the Gaussian-shape overlay-based 3-D similarity, respectively. These neighborings allow PubChem to provide the user with immediate access to the list of 2-D and 3-D neighbors (also called “Similar Compounds” and “Similar Conformers”, respectively) for each compound in PubChem. However, because 3-D neighboring is much more time-consuming than 2-D neighboring, how different the results of the two neighboring schemes are is an important question, considering limited computational resources.

  • PubChem3D: Similar conformers.
    Journal of cheminformatics, 2011
    Co-Authors: Evan E Bolton, Sunghwan Kim, Stephen H. Bryant
    Abstract:

    Background PubChem is a free and open public resource for the biological activities of small molecules. With many tens of millions of both chemical structures and biological test results, PubChem is a sizeable system with an uneven degree of available information. Some chemical structures in PubChem include a great deal of biological annotation, while others have little to none. To help users, PubChem pre-computes "neighboring" relationships to relate similar chemical structures, which may have similar biological function. In this work, we introduce a "Similar Conformers" neighboring relationship to identify compounds with similar 3-D shape and similar 3-D orientation of functional groups typically used to define pharmacophore features.

Evan E Bolton - One of the best experts on this subject based on the ideXlab platform.

  • Similar compounds versus similar conformers: complementarity between PubChem 2-D and 3-D neighboring sets
    Journal of cheminformatics, 2016
    Co-Authors: Sunghwan Kim, Evan E Bolton, Stephen H. Bryant
    Abstract:

    Background PubChem is a public repository for biological activities of small molecules. For the efficient use of its vast amount of chemical information, PubChem performs 2-dimensional (2-D) and 3-dimensional (3-D) neighborings, which precompute “neighbor” relationships between molecules in the PubChem Compound database, using the PubChem subgraph fingerprints-based 2-D similarity and the Gaussian-shape overlay-based 3-D similarity, respectively. These neighborings allow PubChem to provide the user with immediate access to the list of 2-D and 3-D neighbors (also called “Similar Compounds” and “Similar Conformers”, respectively) for each compound in PubChem. However, because 3-D neighboring is much more time-consuming than 2-D neighboring, how different the results of the two neighboring schemes are is an important question, considering limited computational resources.

  • PubChem3D: Similar conformers.
    Journal of cheminformatics, 2011
    Co-Authors: Evan E Bolton, Sunghwan Kim, Stephen H. Bryant
    Abstract:

    Background PubChem is a free and open public resource for the biological activities of small molecules. With many tens of millions of both chemical structures and biological test results, PubChem is a sizeable system with an uneven degree of available information. Some chemical structures in PubChem include a great deal of biological annotation, while others have little to none. To help users, PubChem pre-computes "neighboring" relationships to relate similar chemical structures, which may have similar biological function. In this work, we introduce a "Similar Conformers" neighboring relationship to identify compounds with similar 3-D shape and similar 3-D orientation of functional groups typically used to define pharmacophore features.

F C G A Nicolleau - One of the best experts on this subject based on the ideXlab platform.

  • a self similar field theory for 1d linear elastic continua and self similar diffusion problem
    arXiv: Mathematical Physics, 2011
    Co-Authors: Thomas M Michelitsch, Gerard A Maugin, Rahman Mujibur, Shahram Derogar, Andrzej F Nowakowski, F C G A Nicolleau
    Abstract:

    This paper is devoted to the analysis of some fundamental problems of linear elasticity in 1D continua with self-similar interparticle interactions. We introduce a self-similar continuous field approach where the self-similarity is reflected by equations of motion which are spatially non-local convolutions with power-function kernels (fractional integrals). We obtain closed-form expressions for the static displacement Green's function due to a unit $\delta$-force. In the dynamic framework we derive the solution of the {\it Cauchy problem} and the retarded Green's function. We deduce the distribution of a self-similar variant of diffusion problem with Levi-stable distributions as solutions with infinite mean fluctuations describing the statistics Levi-flights. We deduce a hierarchy of solutions for the self-similar Poisson's equation which we call "self-similar potentials". These non-local singular potentials are in a sense self-similar analogues to the 1D-Dirac's $\delta$-function. The approach can be the starting point to tackle a variety of scale invariant interdisciplinary problems.

  • A self-similar field theory for 1D linear elastic continua and self-similar diffusion problem
    2011
    Co-Authors: Thomas M Michelitsch, Gerard A Maugin, Rahman Mujibur, Shahram Derogar, Andrzej Nowakowski, F C G A Nicolleau
    Abstract:

    This paper is devoted to the analysis of some fundamental problems of linear elasticity in 1D continua with self-similar interparticle interactions. We introduce a self-similar continuous field approach where the self-similarity is reflected by equations of motion which are spatially non-local convolutions with power-function kernels (fractional integrals). We obtain closed-form expressions for the static displacement Green's function due to a unit $\delta$-force. In the dynamic framework we derive the solution of the {\it Cauchy problem} and the retarded Green's function. We deduce the distribution of a self-similar variant of diffusion problem with Lévi-stable distributions as solutions with infinite mean fluctuations describing the statistics Lévi-flights. We deduce a hierarchy of solutions for the self-similar Poisson's equation which we call "self-similar potentials". These non-local singular potentials are in a sense self-similar analogues to the 1D-Dirac's $\delta$-function. The approach can be the starting point to tackle a variety of scale invariant interdisciplinary problems.

Sunghwan Kim - One of the best experts on this subject based on the ideXlab platform.

  • Similar compounds versus similar conformers: complementarity between PubChem 2-D and 3-D neighboring sets
    Journal of cheminformatics, 2016
    Co-Authors: Sunghwan Kim, Evan E Bolton, Stephen H. Bryant
    Abstract:

    Background PubChem is a public repository for biological activities of small molecules. For the efficient use of its vast amount of chemical information, PubChem performs 2-dimensional (2-D) and 3-dimensional (3-D) neighborings, which precompute “neighbor” relationships between molecules in the PubChem Compound database, using the PubChem subgraph fingerprints-based 2-D similarity and the Gaussian-shape overlay-based 3-D similarity, respectively. These neighborings allow PubChem to provide the user with immediate access to the list of 2-D and 3-D neighbors (also called “Similar Compounds” and “Similar Conformers”, respectively) for each compound in PubChem. However, because 3-D neighboring is much more time-consuming than 2-D neighboring, how different the results of the two neighboring schemes are is an important question, considering limited computational resources.

  • PubChem3D: Similar conformers.
    Journal of cheminformatics, 2011
    Co-Authors: Evan E Bolton, Sunghwan Kim, Stephen H. Bryant
    Abstract:

    Background PubChem is a free and open public resource for the biological activities of small molecules. With many tens of millions of both chemical structures and biological test results, PubChem is a sizeable system with an uneven degree of available information. Some chemical structures in PubChem include a great deal of biological annotation, while others have little to none. To help users, PubChem pre-computes "neighboring" relationships to relate similar chemical structures, which may have similar biological function. In this work, we introduce a "Similar Conformers" neighboring relationship to identify compounds with similar 3-D shape and similar 3-D orientation of functional groups typically used to define pharmacophore features.

Beate Blenneman - One of the best experts on this subject based on the ideXlab platform.