USDA software

MS and MS/MS ASCII files were uploaded to their respective databases in the USDA software [18]. 

All the in silico fragment ion files were then batch uploaded to their respective database in the USDA software. 

In silico sequence files having N-terminal methionine removal (but no sequence files with signal peptides) were uploaded to the in silico database of the USDA software. 

Pigure 25.5 is a graphical user interface (GUI) image (as displayed in the USDA software) of the centroided (ASCII) MS/MS spectrum shown in Pigure 25.3. 

FIGURE 25 A graphical user interface (GUI) image as shown in the USDA software of the processed and centroided MS/ MS spectrum shown in Figure 25.3. A limited number of the m/z versus absolute intensity of MS/MS fragment ions are displayed in the sidebar. 

Ralph, S. A. Landucci, L. L. Ralph, J. Available at http //ars.usda.gov/Services/docs. htm ldocid— 10429 (previously http //www.dfrc.ars.usda.gov/software.h1ml), updated at... 

Simunek, X Sejna, M. van Genuchten, M. Th. (1999) The HYDRUS-2D Software Package for Simulating the Two-Dimensional Movement of Water, Heat, and Multiple Solutes in Variably-Saturated Media, Version 2.0, U. S. Salinity Laboratory, USDA, ARS. 

Katritzky et al. (2008PNAS7359) successfully developed classification ANN QSAR for 200 compounds used as repellents against mosquitoes. Mosquito repellent activities from USDA archives of N-acylpiperidines were extracted and modeled using molecular descriptors calculated by CODESSA PRO software. The ANN model was used for the correlation of these archival repellent activities and used to predict the activities of novel compounds of similar structures. The outcome of this QSAR led to a selection of 34 promising mosquito N-acylpiperidine repellent candidates which were synthesized by reactions of acylbenzotriazoles with piperidines. These synthesized compounds were screened as topical mosquito repellents by... 

This chapter describes a step-by-step protocol for top-down proteomic identification of protein biomarkers of bacterial food-borne pathogens using matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry (MALDI-TOF-TOF-MS/MS) and web-based software developed at the Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture (USDA). 

Researchers have used 3D quantitative structural activity relationship (QSAR) of deet and related analogs to construct pharmacophores to better understand the structural basis that leads to repellency by these amide compounds."- Their model was constructed primarily from the protection time data of Suryanarayana and others. Ma and others" showed that one could predict repellent duration based on compound structure and specifically that the amide group and attached substituents played a significant role in the experimentally determined repellent efficacy. Using the same data set, Katritzky and others applied Codessa Pro software to develop a QSAR model for the prediction of complete protection time (CPT) from descriptors related to the structural and electronic properties of deet analogs. This work is the foundation for current projects that involve the examination of repellency and toxicity data for subsets of compounds within the U.S. Department of Agriculture (USDA) archive. 

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