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WISHARTLAB.COM
Welcome to the Wishart Research Group home page. Dr. David Wishart (PhD Yale, 1991) is a Professor in the Departments of Biological Sciences and Computing Science at the University of Alberta. ABOUT - WISHART RESEARCH GROUP - WISHARTLAB.COM About. Welcome to the Wishart Research Group home page. Dr. David Wishart (PhD Yale, 1991) is a Professor in the Departments of Biological Sciences and Computing Science at the University of Alberta. He is also a senior research officer and the director of the Nano Life Science program at the NRC’s National Institute for Nanotechnology (NINT).SUPERPOSE
SuperPose can look for structurally similar and dissimilar regions between aligned protein chains. This is useful in identifying hinge motions, mobile segments, etc. If SuperPose finds structurally dissimilar regions, it will superpose the structures based on the single longest structurally similar region shared byVADAR
Single (or Multiple) Model Protein Structure Analysis. VADAR (Volume, Area, Dihedral Angle Reporter) is a compilation of more than 15 different algorithms and programs for analyzing and assessing peptide and protein structures from their PDB coordinate data.CFM-ID
CFM-ID 3.0 is an improved version of CFM-ID, a freely available tool for MS-spectra prediction, MS-spectra annotation, and MS-based compound identification. The improvements to CFM-ID’s performance and speed include: the implementation of a rule-based fragmentation approach for lipid MS/MS spectral prediction, which greatly improves the speed and accuracy of CFM-ID;PHAST
PHAST(PHAge Search Tool) is a web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids.It accepts either raw DNA sequence data or partially annotated GenBank formatted data and rapidly performs a number of database comparisons as well as phage “cornerstone” feature identification steps to locate CLASSYFIRE: RUN CLASSIFICATION ClassyFire is a web-based application for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire provides a hierarchical chemical classification of chemical entities (mostly small molecules and short peptide sequences), as well as a structure-based textualBACMAP
Arthrobacter chlorophenolicus (strain A6) is a Gram-positive actinobacterium capable of mineralizing several substituted phenols such as 4-chlorophenol (4-CP), 4-nitrophenol (4-NP) and phenol as a sole source of carbon and energy under mesophilic (28 1 degrees Celsius) as well as under psychrophilic (5 1 degrees Celsius)conditions.
BACMAP
Pseudomonas stutzeri A1501. Pseudomonas stutzeri (strain A1501) is an aerobic bacterium phylogenetically associated with the gamma subdivision of the Proteobacteria. This strain was isolated from rice roots that had been inoculated with strain A15 in a rice paddy in China. It is considered wild-type, has been studied for thenitrogen-fixation
BACMAP
Bacillus clausii KSM-K16. Bacillus clausii KSM-K16 is an alkaliphilic bacterium used for production of a high-alkaline protease (M-protease) used in laundry detergents. It grows as spore-forming motile rods, with cream-white colonies that form a filamentous margin. Growth was observed in the temperature range of 15-50 degrees C and from pH7-10.5.
WISHARTLAB.COM
Welcome to the Wishart Research Group home page. Dr. David Wishart (PhD Yale, 1991) is a Professor in the Departments of Biological Sciences and Computing Science at the University of Alberta. ABOUT - WISHART RESEARCH GROUP - WISHARTLAB.COM About. Welcome to the Wishart Research Group home page. Dr. David Wishart (PhD Yale, 1991) is a Professor in the Departments of Biological Sciences and Computing Science at the University of Alberta. He is also a senior research officer and the director of the Nano Life Science program at the NRC’s National Institute for Nanotechnology (NINT).SUPERPOSE
SuperPose can look for structurally similar and dissimilar regions between aligned protein chains. This is useful in identifying hinge motions, mobile segments, etc. If SuperPose finds structurally dissimilar regions, it will superpose the structures based on the single longest structurally similar region shared byVADAR
Single (or Multiple) Model Protein Structure Analysis. VADAR (Volume, Area, Dihedral Angle Reporter) is a compilation of more than 15 different algorithms and programs for analyzing and assessing peptide and protein structures from their PDB coordinate data.CFM-ID
CFM-ID 3.0 is an improved version of CFM-ID, a freely available tool for MS-spectra prediction, MS-spectra annotation, and MS-based compound identification. The improvements to CFM-ID’s performance and speed include: the implementation of a rule-based fragmentation approach for lipid MS/MS spectral prediction, which greatly improves the speed and accuracy of CFM-ID;PHAST
PHAST(PHAge Search Tool) is a web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids.It accepts either raw DNA sequence data or partially annotated GenBank formatted data and rapidly performs a number of database comparisons as well as phage “cornerstone” feature identification steps to locate CLASSYFIRE: RUN CLASSIFICATION ClassyFire is a web-based application for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire provides a hierarchical chemical classification of chemical entities (mostly small molecules and short peptide sequences), as well as a structure-based textualBACMAP
Arthrobacter chlorophenolicus (strain A6) is a Gram-positive actinobacterium capable of mineralizing several substituted phenols such as 4-chlorophenol (4-CP), 4-nitrophenol (4-NP) and phenol as a sole source of carbon and energy under mesophilic (28 1 degrees Celsius) as well as under psychrophilic (5 1 degrees Celsius)conditions.
BACMAP
Pseudomonas stutzeri A1501. Pseudomonas stutzeri (strain A1501) is an aerobic bacterium phylogenetically associated with the gamma subdivision of the Proteobacteria. This strain was isolated from rice roots that had been inoculated with strain A15 in a rice paddy in China. It is considered wild-type, has been studied for thenitrogen-fixation
BACMAP
Bacillus clausii KSM-K16. Bacillus clausii KSM-K16 is an alkaliphilic bacterium used for production of a high-alkaline protease (M-protease) used in laundry detergents. It grows as spore-forming motile rods, with cream-white colonies that form a filamentous margin. Growth was observed in the temperature range of 15-50 degrees C and from pH7-10.5.
MEMBERS - WISHART RESEARCH GROUP - WISHARTLAB.COM Reza Jafari. Manager, CRIO. © Wishart Research Group 1996 — 2021BACMAP
Kocuria rhizophila DC2201. Kocuria rhizophila (strain ATCC 9341 / NBRC 12708 / DC2201) is a coccoid, halotolerant (tolerated up to 10% NaCl in growth media), phenol-degrading Gram-positive bacterium isolated from the rhizosphere of narrowleaf cattail (Typha angustifolia). Members of the genus Kocuria were isolated from a wide variety ofnatural
BACMAP
Names: Arthrobacter chlorophenolicus A6: Accession numbers: NC_011879, NC_011881, NC_011886: Background: Arthrobacter chlorophenolicus (strain A6) is a Gram-positive actinobacterium capable of mineralizing several substituted phenols such as 4-chlorophenol (4-CP), 4-nitrophenol (4-NP) and phenol as a sole source of carbon and energy under mesophilic (28 1 degrees Celsius) as well as underBACMAP
In the human colon, Clostridium cluster XIVa is 1 of 2 abundantly represented clusters of Firmicutes.Eubacterium spp., members of Clostridium closter XIVa, are a group of anaerobic Gram-positive nonspore-forming rods; strain ATCC 27750 is a human-gut derived bacterium. Little is yet known about the niche this bacterium occupiesin the human gut.
BACMAP
Enterococci are regular inhabitants of the bowel. The genome of E. faecalis is more than 25% exogenously acquired DNA. Enterococci are the leading cause of hospital-acquired secondary infections.The genome of Enterococcus faecalis was recently sequenced. The main chromosome is 3,218,031 bp long with 3,182 open-reading frames, and the threeBACMAP
Strain DSM 20547, the type strain, is a free-living, nonmotile, Gram-positive bacterium, originally isolated from a marine environment in about 1944. It grows as spherical/coccoid and occurs predominantly in tetrads which can be arranged in cubical packets. It is non-encapsulated and does not form endospores, is strictly aerobic andCFM-ID
CFM-ID can be used for: Spectra Prediction: Predicting the spectra for a given chemical structure. This task predicts low/10 eV, medium/20 eV, and high/40 eV energy MS/MS spectra for an input structure provided in SMILES or InChI format. Spectra are predicted using combinatorial fragmentation, except in the case of selected lipids,polyphenols
CFM-ID
CFM-ID provides a method for accurately and efficiently identifying metabolites in spectra generated by electrospray tandem mass spectrometry (ESI-MS/MS). The program uses Competitive Fragmentation Modeling to produce a probabilistic generative model for the MS/MS fragmentation process and machine learning techniques to adapt the model parameters from data.BACMAP
Acidilobus saccharovorans (strain DSM 16705 / VKM B-2471 / 345-15) is an obligate anaerobic, organotrophic, thermoacidophilic crenarchaeon isolated from a hot spring of Uzon Caldera, Kamchatka, Russia. It grows with a range of pH from 2.5 to 5.8 with an optimum at 3.5 to 4 and a temperature range from 60 to 90 degrees Celsius with an optimumat
CGVIEW MAP - BACMAP.WISHARTLAB.COM This is a fully expanded view. Displayed PNG file size: 56 kb; SVG file size: 113 kb. Valid XHTML 1.0; Valid CSS. Centered on base 2,220,000; Zoom = 36.WISHARTLAB.COM
Welcome to the Wishart Research Group home page. Dr. David Wishart (PhD Yale, 1991) is a Professor in the Departments of Biological Sciences and Computing Science at the University of Alberta. ABOUT - WISHART RESEARCH GROUP - WISHARTLAB.COM About. Welcome to the Wishart Research Group home page. Dr. David Wishart (PhD Yale, 1991) is a Professor in the Departments of Biological Sciences and Computing Science at the University of Alberta. He is also a senior research officer and the director of the Nano Life Science program at the NRC’s National Institute for Nanotechnology (NINT).SUPERPOSE
SuperPose can look for structurally similar and dissimilar regions between aligned protein chains. This is useful in identifying hinge motions, mobile segments, etc. If SuperPose finds structurally dissimilar regions, it will superpose the structures based on the single longest structurally similar region shared byVADAR
Single (or Multiple) Model Protein Structure Analysis. VADAR (Volume, Area, Dihedral Angle Reporter) is a compilation of more than 15 different algorithms and programs for analyzing and assessing peptide and protein structures from their PDB coordinate data.CFM-ID
CFM-ID 3.0 is an improved version of CFM-ID, a freely available tool for MS-spectra prediction, MS-spectra annotation, and MS-based compound identification. The improvements to CFM-ID’s performance and speed include: the implementation of a rule-based fragmentation approach for lipid MS/MS spectral prediction, which greatly improves the speed and accuracy of CFM-ID;PHAST
PHAST(PHAge Search Tool) is a web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids.It accepts either raw DNA sequence data or partially annotated GenBank formatted data and rapidly performs a number of database comparisons as well as phage “cornerstone” feature identification steps to locate CLASSYFIRE: RUN CLASSIFICATION ClassyFire is a web-based application for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire provides a hierarchical chemical classification of chemical entities (mostly small molecules and short peptide sequences), as well as a structure-based textualBACMAP
Arthrobacter chlorophenolicus (strain A6) is a Gram-positive actinobacterium capable of mineralizing several substituted phenols such as 4-chlorophenol (4-CP), 4-nitrophenol (4-NP) and phenol as a sole source of carbon and energy under mesophilic (28 1 degrees Celsius) as well as under psychrophilic (5 1 degrees Celsius)conditions.
BACMAP
Pseudomonas stutzeri A1501. Pseudomonas stutzeri (strain A1501) is an aerobic bacterium phylogenetically associated with the gamma subdivision of the Proteobacteria. This strain was isolated from rice roots that had been inoculated with strain A15 in a rice paddy in China. It is considered wild-type, has been studied for thenitrogen-fixation
BACMAP
Bacillus clausii KSM-K16. Bacillus clausii KSM-K16 is an alkaliphilic bacterium used for production of a high-alkaline protease (M-protease) used in laundry detergents. It grows as spore-forming motile rods, with cream-white colonies that form a filamentous margin. Growth was observed in the temperature range of 15-50 degrees C and from pH7-10.5.
WISHARTLAB.COM
Welcome to the Wishart Research Group home page. Dr. David Wishart (PhD Yale, 1991) is a Professor in the Departments of Biological Sciences and Computing Science at the University of Alberta. ABOUT - WISHART RESEARCH GROUP - WISHARTLAB.COM About. Welcome to the Wishart Research Group home page. Dr. David Wishart (PhD Yale, 1991) is a Professor in the Departments of Biological Sciences and Computing Science at the University of Alberta. He is also a senior research officer and the director of the Nano Life Science program at the NRC’s National Institute for Nanotechnology (NINT).SUPERPOSE
SuperPose can look for structurally similar and dissimilar regions between aligned protein chains. This is useful in identifying hinge motions, mobile segments, etc. If SuperPose finds structurally dissimilar regions, it will superpose the structures based on the single longest structurally similar region shared byVADAR
Single (or Multiple) Model Protein Structure Analysis. VADAR (Volume, Area, Dihedral Angle Reporter) is a compilation of more than 15 different algorithms and programs for analyzing and assessing peptide and protein structures from their PDB coordinate data.CFM-ID
CFM-ID 3.0 is an improved version of CFM-ID, a freely available tool for MS-spectra prediction, MS-spectra annotation, and MS-based compound identification. The improvements to CFM-ID’s performance and speed include: the implementation of a rule-based fragmentation approach for lipid MS/MS spectral prediction, which greatly improves the speed and accuracy of CFM-ID;PHAST
PHAST(PHAge Search Tool) is a web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids.It accepts either raw DNA sequence data or partially annotated GenBank formatted data and rapidly performs a number of database comparisons as well as phage “cornerstone” feature identification steps to locate CLASSYFIRE: RUN CLASSIFICATION ClassyFire is a web-based application for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire provides a hierarchical chemical classification of chemical entities (mostly small molecules and short peptide sequences), as well as a structure-based textualBACMAP
Arthrobacter chlorophenolicus (strain A6) is a Gram-positive actinobacterium capable of mineralizing several substituted phenols such as 4-chlorophenol (4-CP), 4-nitrophenol (4-NP) and phenol as a sole source of carbon and energy under mesophilic (28 1 degrees Celsius) as well as under psychrophilic (5 1 degrees Celsius)conditions.
BACMAP
Pseudomonas stutzeri A1501. Pseudomonas stutzeri (strain A1501) is an aerobic bacterium phylogenetically associated with the gamma subdivision of the Proteobacteria. This strain was isolated from rice roots that had been inoculated with strain A15 in a rice paddy in China. It is considered wild-type, has been studied for thenitrogen-fixation
BACMAP
Bacillus clausii KSM-K16. Bacillus clausii KSM-K16 is an alkaliphilic bacterium used for production of a high-alkaline protease (M-protease) used in laundry detergents. It grows as spore-forming motile rods, with cream-white colonies that form a filamentous margin. Growth was observed in the temperature range of 15-50 degrees C and from pH7-10.5.
MEMBERS - WISHART RESEARCH GROUP - WISHARTLAB.COM Reza Jafari. Manager, CRIO. © Wishart Research Group 1996 — 2021BACMAP
Kocuria rhizophila DC2201. Kocuria rhizophila (strain ATCC 9341 / NBRC 12708 / DC2201) is a coccoid, halotolerant (tolerated up to 10% NaCl in growth media), phenol-degrading Gram-positive bacterium isolated from the rhizosphere of narrowleaf cattail (Typha angustifolia). Members of the genus Kocuria were isolated from a wide variety ofnatural
BACMAP
Names: Arthrobacter chlorophenolicus A6: Accession numbers: NC_011879, NC_011881, NC_011886: Background: Arthrobacter chlorophenolicus (strain A6) is a Gram-positive actinobacterium capable of mineralizing several substituted phenols such as 4-chlorophenol (4-CP), 4-nitrophenol (4-NP) and phenol as a sole source of carbon and energy under mesophilic (28 1 degrees Celsius) as well as underBACMAP
In the human colon, Clostridium cluster XIVa is 1 of 2 abundantly represented clusters of Firmicutes.Eubacterium spp., members of Clostridium closter XIVa, are a group of anaerobic Gram-positive nonspore-forming rods; strain ATCC 27750 is a human-gut derived bacterium. Little is yet known about the niche this bacterium occupiesin the human gut.
BACMAP
Enterococci are regular inhabitants of the bowel. The genome of E. faecalis is more than 25% exogenously acquired DNA. Enterococci are the leading cause of hospital-acquired secondary infections.The genome of Enterococcus faecalis was recently sequenced. The main chromosome is 3,218,031 bp long with 3,182 open-reading frames, and the threeBACMAP
Strain DSM 20547, the type strain, is a free-living, nonmotile, Gram-positive bacterium, originally isolated from a marine environment in about 1944. It grows as spherical/coccoid and occurs predominantly in tetrads which can be arranged in cubical packets. It is non-encapsulated and does not form endospores, is strictly aerobic andCFM-ID
CFM-ID can be used for: Spectra Prediction: Predicting the spectra for a given chemical structure. This task predicts low/10 eV, medium/20 eV, and high/40 eV energy MS/MS spectra for an input structure provided in SMILES or InChI format. Spectra are predicted using combinatorial fragmentation, except in the case of selected lipids,polyphenols
CFM-ID
CFM-ID provides a method for accurately and efficiently identifying metabolites in spectra generated by electrospray tandem mass spectrometry (ESI-MS/MS). The program uses Competitive Fragmentation Modeling to produce a probabilistic generative model for the MS/MS fragmentation process and machine learning techniques to adapt the model parameters from data.BACMAP
Acidilobus saccharovorans (strain DSM 16705 / VKM B-2471 / 345-15) is an obligate anaerobic, organotrophic, thermoacidophilic crenarchaeon isolated from a hot spring of Uzon Caldera, Kamchatka, Russia. It grows with a range of pH from 2.5 to 5.8 with an optimum at 3.5 to 4 and a temperature range from 60 to 90 degrees Celsius with an optimumat
CGVIEW MAP - BACMAP.WISHARTLAB.COM This is a fully expanded view. Displayed PNG file size: 56 kb; SVG file size: 113 kb. Valid XHTML 1.0; Valid CSS. Centered on base 2,220,000; Zoom = 36. Toggle navigation Wishart Research Group* Members
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WELCOME TO THE WISHART RESEARCH GROUP University of Alberta, Edmonton, CanadaLearn more
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Welcome to the Wishart Research Group home page. Dr. David Wishart (PhD Yale, 1991) is a Professor in the Departments of Biological Sciences and Computing Science at the University of Alberta. He is also a senior research officer and the director of the Nano Life Science program at the NRC’s National Institute for Nanotechnology (NINT) . He has been with the University of Alberta since 1995. Dr. Wishart has active research programs in structural biology, nanobiology, synthetic biology, prion biology, bioinformatics and metabolomics. Some of his lab's most significant contributions have been in the area of protein chemical shift analysis and the prediction of protein structure. More about our group . Wishart Research Group 1996 — 2020Details
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