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Skip to Search Results- 23Biological Sciences, Department of
- 23Biological Sciences, Department of/Journal Articles (Biological Sciences)
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- 1Educational Psychology, Department of/Journal Articles (Educational Psychology)
- 1Roy Berg Kinsella Research Ranch
- 1Roy Berg Kinsella Research Ranch/Journal Articles (Kinsella Ranch)
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2005
Stothard, P., Van Domselaar, G., Cruz, J., Wishart, D.S., Shrivistava, S., Guo, A.C., O'Neill, B., Ellison, M.J.
BacMap is an interactive visual database containing fully labeled, zoomable and searchable chromosome maps from more than 170 bacterial (archaebacterial and eubacterial) species. It uses a recently developed visualization tool (CGView) to generate highresolution circular genome maps from sequence...
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2005
Stothard, P., Lu, P., Cruz, J.A., Szafron, D., Van Domselaar, G.H., Shrivistava, S., Guo, A., Dong, X., Grenier, R., Wishart, D.S.
BASys (Bacterial Annotation System) is a web server that supports automated, in-depth annotation of bacterial genomic (chromosomal and plasmid) sequences. It accepts raw DNA sequence data and an optional list of gene identification information and provides extensive textual annotation and...
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CS23D: A web server for rapid protein structure generation using NMR chemical shifts and sequence data
Download2008
Wishart, D.S., Berjanskii, M., Arndt, D., Lin, G., Tang, P., Zhou, J.
CS23D (chemical shift to 3D structure) is a web server for rapidly generating accurate 3D protein structures using only assigned nuclear magnetic resonance (NMR) chemical shifts and sequence data as input. Unlike conventional NMR methods, CS23D requires no NOE and/or J-coupling data to perform...
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2006
Hassanali, M., Stothard, P., Knox, C., Wishart, D.S., Shrivastava, S., Guo, A., Woolsey, J.
DrugBank is a unique bioinformatics/cheminformatics resource that combines detailed drug (i.e. chemical) data with comprehensive drug target (i.e. protein) information. The database contains .4100 drug entries including .800 FDA approved small molecule and biotech drugs as well as .3200...
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2006
Berlyn, M.K., Plunkett, G., Wishart, D.S., Nori, H., Riley, M., Rudd, K.E., Glasner, J.D., Arnaud, M.B., Abe, T., Thomson, N.R., Wanner, B.L., Pernas, N.T., Blattner, F.R., Serres, M.H., Thomas, G.H., Horiuchi, T., Kosuge, T., Keseler, I.M., Chaudhuri, R.R.
The goal of this group project has been to coordinate and bring up-to-date information on all genes of Escherichia coli K-12. Annotation of the genome of an organism entails identification of genes, the boundaries of genes in terms of precise start and end sites, and description of the gene...
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2009
Bassett, E., Wishart, D.S., Lu, P., MacDonnell, C., Berjanskii, M., Zhou, J., Liang, J., Zhou, Y., Cruz, J.A., Lin, G., Tang, P.
GeNMR (GEnerate NMR structures) is a web server for rapidly generating accurate 3D protein structures using sequence data, NOE-based distance restraints and/or NMR chemical shifts as input. GeNMR accepts distance restraints in XPLOR or CYANA format as well as chemical shift files in either SHIFTY...
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Genomic sequence and activity of KS10, a transposable phage of the Burkholderia cepacia complex
Download2008
Seed, K.D., Lynch, K.H., Dennis, J.J., Goudie, A.D., Wishart, D.S., Shrivastava, S., Stothard, P.
Background: The Burkholderia cepacia complex (BCC) is a versatile group of Gram negative organisms that can be found throughout the environment in sources such as soil, water, and plants. While BCC bacteria can be involved in beneficial interactions with plants, they are also considered...
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2009
Lewis, A., Wishart, D.S., Guo, A.C., Gautam, B., Tzur, D., Sobsey, C.A., Shaykhutdinov, R., Fradette, R., De Souza, A., Cruz, J.A., Xiong, Y., Bouatra, S., Mandal, R., Psychogios, N., Sinelnikov, I., Vogel, H.J., Fang, L., Peng, J., Xia, J., Li, L., Knox, C., Shrivastava, S., Clements, M., Lim, E., Eisner, R., Cheng, D., Dawe, M., Zuniga, A., Young, N., Jia, L., Grenier, R., Hau, D.D., Huang, P., Nazyrova, A., Liu, P., Forsythe, I., Dong, E., Clive, D.
The Human Metabolome Database (HMDB, http:// www.hmdb.ca (http://www.hmdb.ca)) is a richly annotated resource that is designed to address the broad needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists and members of the metabolomics community. Since its first...
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Improving the accuracy of protein secondary structure prediction using structural alignment
Download2006
Gallin, W.J., Wishart, D.S., Montgomerie, S., Sundararaj, S.
Background: The accuracy of protein secondary structure prediction has steadily improved over the past 30 years. Now many secondary structure prediction methods routinely achieve an accuracy (Q3) of about 75%. We believe this accuracy could be further improved by including structure (as opposed...