Computational Method

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The Experts below are selected from a list of 588900 Experts worldwide ranked by ideXlab platform

Jean-luc Bozet - One of the best experts on this subject based on the ideXlab platform.

Christophe Servais - One of the best experts on this subject based on the ideXlab platform.

Ruiling Liu - One of the best experts on this subject based on the ideXlab platform.

  • A novel Computational Method for the identification of plant alternative splice sites
    Biochemical and Biophysical Research Communications, 2013
    Co-Authors: Ying Cui, Jiuqiang Han, Dexing Zhong, Ruiling Liu
    Abstract:

    Alternative splicing (AS) increases protein diversity by generating multiple transcript isoforms from a single gene in higher eukaryotes. Up to 48% of plant genes exhibit alternative splicing, which has proven to be involved in some important plant functions such as the stress response. A hybrid feature extraction approach which combing the position weight matrix (PWM) with the increment of diversity (ID) was proposed to represent the base conservative level (BCL) near splice sites and the similarity level of two datasets, respectively. Using the extracted features, the support vector machine (SVM) was applied to classify alternative and constitutive splice sites. By the proposed algorithm, 80.8% of donor sites and 85.4% of acceptor sites were correctly classified. It is anticipated that the novel Computational Method is promising for the identification of AS sites in plants.

Benoit Roux - One of the best experts on this subject based on the ideXlab platform.

  • a rapid coarse residue based Computational Method for x ray solution scattering characterization of protein folds and multiple conformational states of large protein complexes
    Biophysical Journal, 2009
    Co-Authors: Sichun Yang, Sanghyun Park, Lee Makowski, Benoit Roux
    Abstract:

    We present a coarse residue-based Computational Method to rapidly compute the solution scattering profile from a protein with dynamical fluctuations. The Method is built upon a coarse-grained (CG) representation of the protein. This CG representation takes advantage of the intrinsic low-resolution and CG nature of solution scattering data. It allows rapid scattering determination from a large number of conformations that can be extracted from CG simulations to obtain scattering characterization of protein conformations. The Method includes several important elements, effective residue structure factors derived from the Protein Data Bank, explicit treatment of water molecules in the hydration layer at the surface of the protein, and an ensemble average of scattering from a variety of appropriate conformations to account for macromolecular flexibility. This simplified Method is calibrated and illustrated to accurately reproduce the experimental scattering curve of Hen egg white lysozyme. We then illustrated the applications of this CG Method by computing the solution scattering patterns of several representative protein folds and multiple conformational states. The results suggest that solution scattering data, when combined with the reliable Computational Method that we developed, show great potential for a better structural description of multidomain complexes in different functional states, and for recognizing structural folds when sequence similarity to a protein of known structure is low.

Ying Cui - One of the best experts on this subject based on the ideXlab platform.

  • ASCC - An effective Computational Method for human splice sites identification
    2013 9th Asian Control Conference (ASCC), 2013
    Co-Authors: Jiuqiang Han, Ying Cui, Jun Liu, Xinman Zhang
    Abstract:

    Owing to the vast amount of DNA sequence data, the prediction of the complete structure of genes from the genomic DNA sequence becomes an important issue. For the eukaryotes, especially for the human genome, the splice sites identification plays a crucial role in gene structure prediction. A hybrid feature extraction approach which combing the position weight matrix (PWM) with the increment of diversity (ID) was proposed. Based on the extracted features, the support vector machine (SVM) was applied to classify authentic and false splice sites. The new algorithm was shown to be effective and simple. By the proposed algorithm, 92.98% of donor sites and 90.46% of acceptor sites were correctly classified. It is anticipated that the novel Computational Method is promising for the identification of splice sites in human genome.

  • A novel Computational Method for the identification of plant alternative splice sites
    Biochemical and Biophysical Research Communications, 2013
    Co-Authors: Ying Cui, Jiuqiang Han, Dexing Zhong, Ruiling Liu
    Abstract:

    Alternative splicing (AS) increases protein diversity by generating multiple transcript isoforms from a single gene in higher eukaryotes. Up to 48% of plant genes exhibit alternative splicing, which has proven to be involved in some important plant functions such as the stress response. A hybrid feature extraction approach which combing the position weight matrix (PWM) with the increment of diversity (ID) was proposed to represent the base conservative level (BCL) near splice sites and the similarity level of two datasets, respectively. Using the extracted features, the support vector machine (SVM) was applied to classify alternative and constitutive splice sites. By the proposed algorithm, 80.8% of donor sites and 85.4% of acceptor sites were correctly classified. It is anticipated that the novel Computational Method is promising for the identification of AS sites in plants.