Bioinformatics (Oxford, England)

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Relational patterns of gene expression via non-metric multidimensional scaling analysis
Bioinformatics (Oxford, England) - Tập 21 Số 6 - Trang 730-740 - 2005
Y‐h. Taguchi, Y. Oono
Abstract Motivation: Microarray experiments result in large-scale data sets that require extensive mining and refining to extract useful information. We demonstrate the usefulness of (non-metric) multidimensional scaling (MDS) method in analyzing a large number of genes. Applying MDS to the microarray data is certainly not new, but the existing works...... hiện toàn bộ
Modelling cellular systems with PySCeS
Bioinformatics (Oxford, England) - Tập 21 Số 4 - Trang 560-561 - 2005
Brett G. Olivier, Johann M. Rohwer, Jan‐Hendrik S. Hofmeyr
Abstract Summary: The Python Simulator for Cellular Systems (PySCeS) is an extendable research tool for the numerical analysis and investigation of cellular systems. Availability: PySCeS is distributed as Open Source Software under the GNU General Public Licence and is available for download from http://pysces.sourceforge.net
PySCeSToolbox: a collection of metabolic pathway analysis tools
Bioinformatics (Oxford, England) - Tập 34 Số 1 - Trang 124-125 - 2018
Carl D. Christensen, Jan‐Hendrik S. Hofmeyr, Johann M. Rohwer
Abstract Summary PySCeSToolbox is an extension to the Python Simulator for Cellular Systems (PySCeS) that includes tools for performing generalized supply–demand analysis, symbolic metabolic control analysis, and a framework for investigating the kinetic and thermodynamic aspects...... hiện toàn bộ
Causal analysis approaches in Ingenuity Pathway Analysis
Bioinformatics (Oxford, England) - Tập 30 Số 4 - Trang 523-530 - 2014
A. Krämer, Jeff Green, Jack Pollard, Stuart Tugendreich
Abstract Motivation: Prior biological knowledge greatly facilitates the meaningful interpretation of gene-expression data. Causal networks constructed from individual relationships curated from the literature are particularly suited for this task, since they create mechanistic hypotheses that explain the expression changes observed in datasets.... hiện toàn bộ
pyDockWEB: a web server for rigid-body protein–protein docking using electrostatics and desolvation scoring
Bioinformatics (Oxford, England) - Tập 29 Số 13 - Trang 1698-1699 - 2013
Brian Jiménez‐García, Carles Pons, Juan Fernández‐Recio
Abstract Summary: pyDockWEB is a web server for the rigid-body docking prediction of protein–protein complex structures using a new version of the pyDock scoring algorithm. We use here a new custom parallel FTDock implementation, with adjusted grid size for optimal FFT calculations, and a new version of pyDock, which dramatically speeds up calculatio...... hiện toàn bộ
ZDOCK server: interactive docking prediction of protein–protein complexes and symmetric multimers
Bioinformatics (Oxford, England) - Tập 30 Số 12 - Trang 1771-1773 - 2014
Brian G. Pierce, Kevin Wiehe, Bong‐Hyun Kim, Thom Vreven, Zhiping Weng
Abstract Summary: Protein–protein interactions are essential to cellular and immune function, and in many cases, because of the absence of an experimentally determined structure of the complex, these interactions must be modeled to obtain an understanding of their molecular basis. We present a user-friendly protein docking server, based on the rigid-...... hiện toàn bộ
InterProSurf: a web server for predicting interacting sites on protein surfaces
Bioinformatics (Oxford, England) - Tập 23 Số 24 - Trang 3397-3399 - 2007
Surendra S. Negi, Catherine H. Schein, Numan Oezguen, Trevor D. Power, Werner Braun
AbstractSummary: A new web server, InterProSurf, predicts interacting amino acid residues in proteins that are most likely to interact with other proteins, given the 3D structures of subunits of a protein complex. The prediction method is based on solvent accessible surface area of residues in the isolated subunits, a propensity scale for interface residues and a c...... hiện toàn bộ
A multi-algorithm, multi-timescale method for cell simulation
Bioinformatics (Oxford, England) - Tập 20 Số 4 - Trang 538-546 - 2004
Kouichi Takahashi, Kazunari Kaizu, Bin Hu, Masaru Tomita
Abstract Motivation: Many important problems in cell biology require the dense nonlinear interactions between functional modules to be considered. The importance of computer simulation in understanding cellular processes is now widely accepted, and a variety of simulation algorithms useful for studying certain subsystems have been designed. Many of t...... hiện toàn bộ
E-CELL: software environment for whole-cell simulation.
Bioinformatics (Oxford, England) - Tập 15 Số 1 - Trang 72-84 - 1999
Masaru Tomita, Kazuaki Hashimoto, Kazutoshi Takahashi, Toshio Shimizu, Yumi Matsuzaki, Fumito Miyoshi, Kanako Saito, Sakura Tanida, Katsuyuki Yugi, J. Craig Venter, Clyde A. Hutchison
Abstract MOTIVATION: Genome sequencing projects and further systematic functional analyses of complete gene sets are producing an unprecedented mass of molecular information for a wide range of model organisms. This provides us with a detailed account of the cell with which we may begin to build models for simulating intracellular molecular processes...... hiện toàn bộ
InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data
Bioinformatics (Oxford, England) - Tập 28 Số 23 - Trang 3163-3165 - 2012
Richard Smith, J. Aleksić, Daniela Butano, Adrian R. Carr, Sergio Contrino, Fengyuan Hu, Mike Lyne, Rachel Lyne, Alex Kalderimis, Kim Rutherford, Radek Štěpán, Julie Sullivan, Matthew N. Wakeling, Xavier Watkins, Gos Micklem
Abstract Summary: InterMine is an open-source data warehouse system that facilitates the building of databases with complex data integration requirements and a need for a fast customizable query facility. Using InterMine, large biological databases can be created from a range of heterogeneous data sources, and the extensible data model allows for eas...... hiện toàn bộ
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