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PROTEUS2: A Web Server for Comprehensive Protein Structure Prediction and Structure-Based Annotation
Download2008
Shrivistava, S., Berjanskii, M., Wishart, D.S., Cruz, J.A., Arndt, D., Montgomerie, S.
PROTEUS2 is a web server designed to support comprehensive protein structure prediction and structure-based annotation. PROTEUS2 accepts either single sequences (for directed studies) or multiple sequences (for whole proteome annotation) and predicts the secondary and, if possible, tertiary...
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Spatiotemporal integration of molecular and anatomical data in virtual reality using semantic mapping
Download2009
Janzen, R.P., Dong, X., Gordon, P.M., Soh, J., Wishart, D.S., Sabhaney, A., Turinsky, A.L., Sensen, C.W., Chang, J., Hau, D., Xia, J., Trinh, Q.M.
We have developed a computational framework for spatiotemporal integration of molecular and anatomical datasets in a virtual reality environment. Using two case studies involving gene expression data and pharmacokinetic data, respectively, we demonstrate how existing knowledge bases for molecular...
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2004
Maiti, R., Van Domselaar, G.H., Wishart, D.S., Zhang, H.
The SuperPose web server rapidly and robustly calculates both pairwise and multiple protein structure superpositions using a modified quaternion eigenvalue approach. SuperPose generates sequence alignments, structure alignments,PDB(Protein Data Bank) coordinates andRMSDstatistics, as well as...
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The CyberCell Database (CCDB): A comprehensive, self-updating relational database to coordinate and facilitate in silico modeling of Escherichia coli
Download2004
Stothard, P., Rouani, M., Sundararaj, S., Wishart, D.S., Nazhad, B.H., Guo, A., Ellison, M.
The CyberCell Database (CCDB: http://redpoll. pharmacy.ualberta.ca/CCDB) is a comprehensive, web-accessible database designed to support and coordinate international efforts in modeling an Escherichia coli cell on a computer. The CCDB brings together both observed and derived quantitative data...
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2003
Monzavi, H., Willard, L., Zhang, H., Boyko, R.F., Ranjan, A., Wishart, D.S., Sykes, B.D.
VADAR (Volume Area Dihedral Angle Reporter) is a comprehensive web server for quantitative protein structure evaluation. It accepts Protein Data Bank (PDB) formatted files or PDB accession numbers as input and calculates, identifies, graphs, reports and/ or evaluates a large number (>30) of key...