Pathway editor

Pathway Editor is a tool to visualize a sequence of structures in a multistep reaction or a metabolic pathway. 

The Case Western Reserve University s Pathways Database System [Ozsoyoglu, Nadeau, and Ozsoyoglu 2003] comes with a sample set of metabolic and signaling pathways, most drawn from Michal s Biochemical Pathways [Michal 1999], It consists of a suite of tools, including query interfaces, viewers, and a pathway editor. 

Cee M L and M Page 1993. Computing Reaction Pathways on Molecular Potential Energy Surfaces. In Lipkowitz K B and D B Boyd (Editors). Reviews in Computational Chemistry Volume 4. New York, VCH Publishers, pp. 35-65. 

Smith WL, Fitzpatrick FA The eicosanoids Cyclooxygenase, lipoxygenase, and epoxygenase pathways. In Biochemistry of Lipids, Lipoproteins and Membranes. Vance DE, Vance JE (editors). Elsevier, 1996. 

Marusak RA, Mears CF. 1995. Exploration of selected pathways for metabolic oxidative ring opening of benzene based on estimates of molecular energetics In Valentine JS, Foote CS, Greenberg A, Liebman JE, editors. Active Oxygen in Biochemistry. New York Chapman and Hall. p. 336. 

Lindvall O., Bjorklund A. (1982). Neuroanatomy of central dopamine pathways review of recent progress. In M Real, editor. Advances in Dopamine Research. Oxford and New York Pergamon Press pp. 297-311. 

Herbes, S.E., Southworth, G.R., Shaeffer, D.L., Griest, W.H., Maskarinec, M.P (1980) Critical pathways of polycyclic aromatic hydrocarbons in aquatic environments. In The Scientific Basis of Toxicity Assessment. Witschi, H. Editor, pp. 113-128, Elsevier/North-Holland Biomedical Press, Amsterdam. 

Isherwood, F. A. Bio.synthesis of Lignin. In Pridham, J. B., and T. Swain (Editors) Biosynthetic Pathways in Higher Plants. Academic Press, London-New York, 1965. 

Drake HL. 1994. Acetogenesis, acetogenic bacteria, and the acetyl-CoA Wood/ Ljungdahl pathway past and current perspectives. In Drake HL, editor. Acetogenesis. New York Chapman Hall. 

Michal G, editor. Biochemical pathways an atlas of biochemistry and molecular biology. New York Wiley, 1999. 

Biosynthesis of catecholamines. The rate-limiting step, conversion of tyrosine to dopa, can be inhibited by metyrosine ( -methyltyrosine). The alternative pathways shown by the dashed arrows have not been found to be of physiologic significance in humans. However, tyramine and octopamine may accumulate in patients treated with monoamine oxidase inhibitors. (Reproduced, with permission, from Greenspan FS, Gardner DG (editors) Basic and Clinical Endocrinology,... 

In 1970, scientists from the Pharmaceutical Analysis Section of the Academy of Pharmaceutical Sciences began to plan a cooperative venture to compile and publish a series of volumes entitled the Analytical Profiles of Drug Substances. The aim of the series was to provide information not available in the official compendial monograph of a drug substance, such as physical or chemical data, methods of synthesis, and pathways of physical or biological degradation and metabolism. Klaus Florey became the first editor of the series, and between 1972 and 1991 he edited the first 20 volumes in the Analytical Profiles series. 

P Volume 1,1991,283 pp. 109.50/ 69.50 ISBN 1-55938-180-9 CONTENTS Introduction to the Series An Editor s Foreword, Albert Padwa. Preface, Brian Halton. Strain in Organic Chemistry A Perspective, Brian Halton. Gem-Dihalocyclopropanes in Chemical Synthesis, Martin G. Banwell and Monica E. Re-um. 1-Halo- and 1, 2-Dihalocyclopropenes Useful Synthetic Intermediates, Mark S. Baird. Cyciization and Cycloaddition Reactions of Cyclopropenes, Albert Padwa and Glen E. Fryx-ell. New Synthetic Pathways From Cyclobutanones, Edward Lee-Ruff. Cyclic Alkynes, Enynes and Dienynes A Synthetic Challenge, Herbert Meier. Index. 

Pathway Hole Filler can then be applied to predict likely genes to fill holes (missing steps) in predicted pathways. Thereafter, the Pathway Tools Navigator and Editor functions let users visualize, analyze, access, and update the database. Thus, by using PathoLogic and encyclopedias such as MetaCyc, an initial fast reconstruction can be developed automatically, and then, using the other units of Pathway Tools, a detailed manual update, curation, and verification step is possible. 

Merigan WH, Maunsell JHR. 1993. How parallel are the primate visual pathways Annual Review of Neuroscience. Cowan WM, Shooter EM, Stevens CF, Thompson RF, editors. Palo Alto, CA Annual Reviews, Inc. pp. 369-402. 

Lewis, B.G., 1976. Selenium in biological systems, and pathways for its volatilization in higher plants. In J.O. Nriagu (Editor), Environmental Biogeochemistry, Vol. 1. Ann Arbor Science, Ann Arbor, pp. 389—409., ... 

Mechalas, B.J., 1974. Pathways and environmental requirements for biogenic gas production in the ocean. In I.R. Kaplan (Editor), Natural Gases in Marine Sediments. Plenum, New York, NY, pp. 11—25. 

Siegel, L.M., 1975. Biochemistry of the sulfur cycle. In D.M. Greenberg (Editor), Metabolic Pathways, Vol. 7, Metabolism of Sulfur Compounds. Academic, New York, NY, pp. 217-286. 

At a cellular level, the purported sorafenib editors should be assayed using the renal cancer cell line RCC-786-O and NRVMs (neonatal rat ventricular monocytes). In RCCs, the sorafenib/WBZ 4 combination yields agonistic synergy, marked by an increased inhibition of cell proliferation when compared to sorafenib-alone levels at equivalent bulk concentrations (Fig. 12.5a) The dose-dependent inhibition is greater than the Loewe-additive values [20, 21] (Fig. 12.5b). By contrast, the sorafenib-induced recruitment of the pro-apoptotic pathway in cardiomyocytes should be impaired by the downstream interference of WBZ 4 through JNK inhibition (Fig. 12.3a). Consequently, cytosolic release of... 

T. Roberts (Ed.), Metabolic Pathways of Agrochemicals. Part 1. Flerbicides and Plant Growth Regulators, Royal Society of Chemistry Information Services, Cambridge, 1998. (Contributing editors on title page, D. H. Hutson, P. W. Lee, P. H. Nicholls and J. R. Plimmer.)... 

During the investigation of a biotransformation pathway of a lead drug compound, many different types of data accumulate, such as documents, images, chromatograms, mass spectra, NMR spectra, structures, substructures, generic structures, and result tables. A study editor module serves as the main user interface for the... 

Metacore (table 7.1) is a suite of software oriented toward understanding the function of gene sets discovered by expression analysis. It includes a database of annotated metabolic, signaling, and regulatory pathways and a graphical pathway display/editor. 

Pathways Laboratory Automation focuses on the development of a work-flow to capture and automate best practices for laboratory procedures. To achieve this, the product consists of four distinct tools, a. The Workshop Configuration Editor is used to define and organize the procedures that the laboratory supports. This model of lab capabilities details a set of unit processes with inputs and outputs in terms of... 

ANDERS, M.W. (editor) (1985) Bioactivation of Foreign Compounds (New York Academic Press). BAKKE, J. and GUSTAFSSON, J.A. (1984) Mercapturic acid pathway metabolites and xenobiotics ... 

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