The Experts below are selected from a list of 1290 Experts worldwide ranked by ideXlab platform
Yang Zhang - One of the best experts on this subject based on the ideXlab platform.
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Y: COFACTOR: An accurate comparative algorithm for structure-based protein function annotation. Nucleic Acids Res 2012, 40(Web Server issue):W471-W477. doi:10.1186/1471-2105-14-S17-A10 Cite this article as: Kapadia and Rinehart: Ab Initio prediction
2016Co-Authors: A Roy, Jianyi Yang, Yang ZhangAbstract:We have developed a new COFACTOR webserver for automated structure-based protein function annotation. Starting from a structural model, given by either experimental determination or computa-tional modeling, COFACTOR first identifies template proteins of similar folds and functional sites by threading the target structure through three representative template libraries that have known protein–ligand binding interactions, Enzyme Commission Number or Gene Ontology terms. The biological function insights in these three aspects are then deduced from the functional templates, the confidence of which is evaluated by a scoring function that combines both global and local structural similarities. The algorithm has been extensively benchmarked by large-scale bench-marking tests and demonstrated significant advan-tages compared to traditional sequence-based methods. In the recent community-wide CASP9 experiment, COFACTOR was ranked as the best method for protein–ligand binding site predictions. The COFACTOR sever and the template libraries are freely available a
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protein structure and function prediction using i tasser
Current protocols in human genetics, 2015Co-Authors: Jianyi Yang, Yang ZhangAbstract:I-TASSER is a hierarchical protocol for automated protein structure prediction and structure-based function annotation. Starting from the amino acid sequence of target proteins, I-TASSER first generates full-length atomic structural models from multiple threading alignments and iterative structural assembly simulations followed by atomic-level structure refinement. The biological functions of the protein, including ligand-binding sites, Enzyme Commission Number, and gene ontology terms, are then inferred from known protein function databases based on sequence and structure profile comparisons. I-TASSER is freely available as both an on-line server and a stand-alone package. This unit describes how to use the I-TASSER protocol to generate structure and function prediction and how to interpret the prediction results, as well as alternative approaches for further improving the I-TASSER modeling quality for distant-homologous and multi-domain protein targets.
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Current Protocols in Bioinformatics - Protein Structure and Function Prediction Using I‐TASSER
Current protocols in bioinformatics, 2015Co-Authors: Jianyi Yang, Yang ZhangAbstract:I-TASSER is a hierarchical protocol for automated protein structure prediction and structure-based function annotation. Starting from the amino acid sequence of target proteins, I-TASSER first generates full-length atomic structural models from multiple threading alignments and iterative structural assembly simulations followed by atomic-level structure refinement. The biological functions of the protein, including ligand-binding sites, Enzyme Commission Number, and gene ontology terms, are then inferred from known protein function databases based on sequence and structure profile comparisons. I-TASSER is freely available as both an on-line server and a stand-alone package. This unit describes how to use the I-TASSER protocol to generate structure and function prediction and how to interpret the prediction results, as well as alternative approaches for further improving the I-TASSER modeling quality for distant-homologous and multi-domain protein targets.
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cofactor an accurate comparative algorithm for structure based protein function annotation
Nucleic Acids Research, 2012Co-Authors: A Roy, Jianyi Yang, Yang ZhangAbstract:We have developed a new COFACTOR webserver for automated structure-based protein function annotation. Starting from a structural model, given by either experimental determination or computational modeling, COFACTOR first identifies template proteins of similar folds and functional sites by threading the target structure through three representative template libraries that have known protein-ligand binding interactions, Enzyme Commission Number or Gene Ontology terms. The biological function insights in these three aspects are then deduced from the functional templates, the confidence of which is evaluated by a scoring function that combines both global and local structural similarities. The algorithm has been extensively benchmarked by large-scale benchmarking tests and demonstrated significant advantages compared to traditional sequence-based methods. In the recent community-wide CASP9 experiment, COFACTOR was ranked as the best method for protein-ligand binding site predictions. The COFACTOR sever and the template libraries are freely available at http://zhanglab.ccmb.med.umich.edu/COFACTOR.
Jianyi Yang - One of the best experts on this subject based on the ideXlab platform.
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Y: COFACTOR: An accurate comparative algorithm for structure-based protein function annotation. Nucleic Acids Res 2012, 40(Web Server issue):W471-W477. doi:10.1186/1471-2105-14-S17-A10 Cite this article as: Kapadia and Rinehart: Ab Initio prediction
2016Co-Authors: A Roy, Jianyi Yang, Yang ZhangAbstract:We have developed a new COFACTOR webserver for automated structure-based protein function annotation. Starting from a structural model, given by either experimental determination or computa-tional modeling, COFACTOR first identifies template proteins of similar folds and functional sites by threading the target structure through three representative template libraries that have known protein–ligand binding interactions, Enzyme Commission Number or Gene Ontology terms. The biological function insights in these three aspects are then deduced from the functional templates, the confidence of which is evaluated by a scoring function that combines both global and local structural similarities. The algorithm has been extensively benchmarked by large-scale bench-marking tests and demonstrated significant advan-tages compared to traditional sequence-based methods. In the recent community-wide CASP9 experiment, COFACTOR was ranked as the best method for protein–ligand binding site predictions. The COFACTOR sever and the template libraries are freely available a
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protein structure and function prediction using i tasser
Current protocols in human genetics, 2015Co-Authors: Jianyi Yang, Yang ZhangAbstract:I-TASSER is a hierarchical protocol for automated protein structure prediction and structure-based function annotation. Starting from the amino acid sequence of target proteins, I-TASSER first generates full-length atomic structural models from multiple threading alignments and iterative structural assembly simulations followed by atomic-level structure refinement. The biological functions of the protein, including ligand-binding sites, Enzyme Commission Number, and gene ontology terms, are then inferred from known protein function databases based on sequence and structure profile comparisons. I-TASSER is freely available as both an on-line server and a stand-alone package. This unit describes how to use the I-TASSER protocol to generate structure and function prediction and how to interpret the prediction results, as well as alternative approaches for further improving the I-TASSER modeling quality for distant-homologous and multi-domain protein targets.
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Current Protocols in Bioinformatics - Protein Structure and Function Prediction Using I‐TASSER
Current protocols in bioinformatics, 2015Co-Authors: Jianyi Yang, Yang ZhangAbstract:I-TASSER is a hierarchical protocol for automated protein structure prediction and structure-based function annotation. Starting from the amino acid sequence of target proteins, I-TASSER first generates full-length atomic structural models from multiple threading alignments and iterative structural assembly simulations followed by atomic-level structure refinement. The biological functions of the protein, including ligand-binding sites, Enzyme Commission Number, and gene ontology terms, are then inferred from known protein function databases based on sequence and structure profile comparisons. I-TASSER is freely available as both an on-line server and a stand-alone package. This unit describes how to use the I-TASSER protocol to generate structure and function prediction and how to interpret the prediction results, as well as alternative approaches for further improving the I-TASSER modeling quality for distant-homologous and multi-domain protein targets.
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cofactor an accurate comparative algorithm for structure based protein function annotation
Nucleic Acids Research, 2012Co-Authors: A Roy, Jianyi Yang, Yang ZhangAbstract:We have developed a new COFACTOR webserver for automated structure-based protein function annotation. Starting from a structural model, given by either experimental determination or computational modeling, COFACTOR first identifies template proteins of similar folds and functional sites by threading the target structure through three representative template libraries that have known protein-ligand binding interactions, Enzyme Commission Number or Gene Ontology terms. The biological function insights in these three aspects are then deduced from the functional templates, the confidence of which is evaluated by a scoring function that combines both global and local structural similarities. The algorithm has been extensively benchmarked by large-scale benchmarking tests and demonstrated significant advantages compared to traditional sequence-based methods. In the recent community-wide CASP9 experiment, COFACTOR was ranked as the best method for protein-ligand binding site predictions. The COFACTOR sever and the template libraries are freely available at http://zhanglab.ccmb.med.umich.edu/COFACTOR.
John R Finnerty - One of the best experts on this subject based on the ideXlab platform.
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Production of a reference transcriptome and transcriptomic database (EdwardsiellaBase) for the lined sea anemone, Edwardsiella lineata, a parasitic cnidarian
BMC Genomics, 2014Co-Authors: Derek J Stefanik, Tristan J Lubinski, Brian R Granger, Allyson L Byrd, Adam M Reitzel, Lukas Defilippo, Allison Lorenc, John R FinnertyAbstract:Background The lined sea anemone Edwardsiella lineata is an informative model system for evolutionary-developmental studies of parasitism. In this species, it is possible to compare alternate developmental pathways leading from a larva to either a free-living polyp or a vermiform parasite that inhabits the mesoglea of a ctenophore host. Additionally, E. lineata is confamilial with the model cnidarian Nematostella vectensis , providing an opportunity for comparative genomic, molecular and organismal studies. Description We generated a reference transcriptome for E. lineata via high-throughput sequencing of RNA isolated from five developmental stages (parasite; parasite-to-larva transition; larva; larva-to-adult transition; adult). The transcriptome comprises 90,440 contigs assembled from >15 billion nucleotides of DNA sequence. Using a molecular clock approach, we estimated the divergence between E. lineata and N. vectensis at 215–364 million years ago. Based on gene ontology and metabolic pathway analyses and gene family surveys (bHLH-PAS, deiodinases, Fox genes, LIM homeodomains, minicollagens, nuclear receptors, Sox genes, and Wnts), the transcriptome of E. lineata is comparable in depth and completeness to N. vectensis . Analyses of protein motifs and revealed extensive conservation between the proteins of these two edwardsiid anemones, although we show the NF-κB protein of E. lineata reflects the ancestral structure, while the NF-κB protein of N. vectensis has undergone a split that separates the DNA-binding domain from the inhibitory domain. All contigs have been deposited in a public database (EdwardsiellaBase), where they may be searched according to contig ID, gene ontology, protein family motif (Pfam), Enzyme Commission Number, and BLAST. The alignment of the raw reads to the contigs can also be visualized via JBrowse. Conclusions The transcriptomic data and database described here provide a platform for studying the evolutionary developmental genomics of a derived parasitic life cycle. In addition, these data from E. lineata will aid in the interpretation of evolutionary novelties in gene sequence or structure that have been reported for the model cnidarian N. vectensis ( e.g ., the split NF-κB locus). Finally, we include custom computational tools to facilitate the annotation of a transcriptome based on high-throughput sequencing data obtained from a “non-model system.”
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production of a reference transcriptome and transcriptomic database edwardsiellabase for the lined sea anemone edwardsiella lineata a parasitic cnidarian
BMC Genomics, 2014Co-Authors: Derek J Stefanik, Tristan J Lubinski, Brian R Granger, Allyson L Byrd, Adam M Reitzel, Lukas Defilippo, Allison Lorenc, John R FinnertyAbstract:The lined sea anemone Edwardsiella lineata is an informative model system for evolutionary-developmental studies of parasitism. In this species, it is possible to compare alternate developmental pathways leading from a larva to either a free-living polyp or a vermiform parasite that inhabits the mesoglea of a ctenophore host. Additionally, E. lineata is confamilial with the model cnidarian Nematostella vectensis, providing an opportunity for comparative genomic, molecular and organismal studies. We generated a reference transcriptome for E. lineata via high-throughput sequencing of RNA isolated from five developmental stages (parasite; parasite-to-larva transition; larva; larva-to-adult transition; adult). The transcriptome comprises 90,440 contigs assembled from >15 billion nucleotides of DNA sequence. Using a molecular clock approach, we estimated the divergence between E. lineata and N. vectensis at 215–364 million years ago. Based on gene ontology and metabolic pathway analyses and gene family surveys (bHLH-PAS, deiodinases, Fox genes, LIM homeodomains, minicollagens, nuclear receptors, Sox genes, and Wnts), the transcriptome of E. lineata is comparable in depth and completeness to N. vectensis. Analyses of protein motifs and revealed extensive conservation between the proteins of these two edwardsiid anemones, although we show the NF-κB protein of E. lineata reflects the ancestral structure, while the NF-κB protein of N. vectensis has undergone a split that separates the DNA-binding domain from the inhibitory domain. All contigs have been deposited in a public database (EdwardsiellaBase), where they may be searched according to contig ID, gene ontology, protein family motif (Pfam), Enzyme Commission Number, and BLAST. The alignment of the raw reads to the contigs can also be visualized via JBrowse. The transcriptomic data and database described here provide a platform for studying the evolutionary developmental genomics of a derived parasitic life cycle. In addition, these data from E. lineata will aid in the interpretation of evolutionary novelties in gene sequence or structure that have been reported for the model cnidarian N. vectensis (e.g., the split NF-κB locus). Finally, we include custom computational tools to facilitate the annotation of a transcriptome based on high-throughput sequencing data obtained from a “non-model system.”
Derek J Stefanik - One of the best experts on this subject based on the ideXlab platform.
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Production of a reference transcriptome and transcriptomic database (EdwardsiellaBase) for the lined sea anemone, Edwardsiella lineata, a parasitic cnidarian
BMC Genomics, 2014Co-Authors: Derek J Stefanik, Tristan J Lubinski, Brian R Granger, Allyson L Byrd, Adam M Reitzel, Lukas Defilippo, Allison Lorenc, John R FinnertyAbstract:Background The lined sea anemone Edwardsiella lineata is an informative model system for evolutionary-developmental studies of parasitism. In this species, it is possible to compare alternate developmental pathways leading from a larva to either a free-living polyp or a vermiform parasite that inhabits the mesoglea of a ctenophore host. Additionally, E. lineata is confamilial with the model cnidarian Nematostella vectensis , providing an opportunity for comparative genomic, molecular and organismal studies. Description We generated a reference transcriptome for E. lineata via high-throughput sequencing of RNA isolated from five developmental stages (parasite; parasite-to-larva transition; larva; larva-to-adult transition; adult). The transcriptome comprises 90,440 contigs assembled from >15 billion nucleotides of DNA sequence. Using a molecular clock approach, we estimated the divergence between E. lineata and N. vectensis at 215–364 million years ago. Based on gene ontology and metabolic pathway analyses and gene family surveys (bHLH-PAS, deiodinases, Fox genes, LIM homeodomains, minicollagens, nuclear receptors, Sox genes, and Wnts), the transcriptome of E. lineata is comparable in depth and completeness to N. vectensis . Analyses of protein motifs and revealed extensive conservation between the proteins of these two edwardsiid anemones, although we show the NF-κB protein of E. lineata reflects the ancestral structure, while the NF-κB protein of N. vectensis has undergone a split that separates the DNA-binding domain from the inhibitory domain. All contigs have been deposited in a public database (EdwardsiellaBase), where they may be searched according to contig ID, gene ontology, protein family motif (Pfam), Enzyme Commission Number, and BLAST. The alignment of the raw reads to the contigs can also be visualized via JBrowse. Conclusions The transcriptomic data and database described here provide a platform for studying the evolutionary developmental genomics of a derived parasitic life cycle. In addition, these data from E. lineata will aid in the interpretation of evolutionary novelties in gene sequence or structure that have been reported for the model cnidarian N. vectensis ( e.g ., the split NF-κB locus). Finally, we include custom computational tools to facilitate the annotation of a transcriptome based on high-throughput sequencing data obtained from a “non-model system.”
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production of a reference transcriptome and transcriptomic database edwardsiellabase for the lined sea anemone edwardsiella lineata a parasitic cnidarian
BMC Genomics, 2014Co-Authors: Derek J Stefanik, Tristan J Lubinski, Brian R Granger, Allyson L Byrd, Adam M Reitzel, Lukas Defilippo, Allison Lorenc, John R FinnertyAbstract:The lined sea anemone Edwardsiella lineata is an informative model system for evolutionary-developmental studies of parasitism. In this species, it is possible to compare alternate developmental pathways leading from a larva to either a free-living polyp or a vermiform parasite that inhabits the mesoglea of a ctenophore host. Additionally, E. lineata is confamilial with the model cnidarian Nematostella vectensis, providing an opportunity for comparative genomic, molecular and organismal studies. We generated a reference transcriptome for E. lineata via high-throughput sequencing of RNA isolated from five developmental stages (parasite; parasite-to-larva transition; larva; larva-to-adult transition; adult). The transcriptome comprises 90,440 contigs assembled from >15 billion nucleotides of DNA sequence. Using a molecular clock approach, we estimated the divergence between E. lineata and N. vectensis at 215–364 million years ago. Based on gene ontology and metabolic pathway analyses and gene family surveys (bHLH-PAS, deiodinases, Fox genes, LIM homeodomains, minicollagens, nuclear receptors, Sox genes, and Wnts), the transcriptome of E. lineata is comparable in depth and completeness to N. vectensis. Analyses of protein motifs and revealed extensive conservation between the proteins of these two edwardsiid anemones, although we show the NF-κB protein of E. lineata reflects the ancestral structure, while the NF-κB protein of N. vectensis has undergone a split that separates the DNA-binding domain from the inhibitory domain. All contigs have been deposited in a public database (EdwardsiellaBase), where they may be searched according to contig ID, gene ontology, protein family motif (Pfam), Enzyme Commission Number, and BLAST. The alignment of the raw reads to the contigs can also be visualized via JBrowse. The transcriptomic data and database described here provide a platform for studying the evolutionary developmental genomics of a derived parasitic life cycle. In addition, these data from E. lineata will aid in the interpretation of evolutionary novelties in gene sequence or structure that have been reported for the model cnidarian N. vectensis (e.g., the split NF-κB locus). Finally, we include custom computational tools to facilitate the annotation of a transcriptome based on high-throughput sequencing data obtained from a “non-model system.”
Robert N. Goldberg - One of the best experts on this subject based on the ideXlab platform.
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Thermodynamics of Enzyme-Catalyzed Reactions: Part 7—2007 Update
Journal of Physical and Chemical Reference Data, 2007Co-Authors: Robert N. Goldberg, Yadu B. Tewari, Talapady N. BhatAbstract:This review serves to update previously published evaluations of equilibrium constants and enthalpy changes for Enzyme-catalyzed reactions. For each reaction, the following information is given: the reference for the data, the reaction studied, the name of the Enzyme used and its Enzyme Commission Number, the method of measurement, the conditions of measurement [temperature, pH, ionic strength, and the buffer(s) and cofactor(s) used], the data and their evaluation, and, sometimes, commentary on the data and on any corrections which have been applied to the data or any calculations for which the data have been used. The review contains data from 119 references which have been examined and evaluated. Chemical Abstract Service registry Numbers are given for the substances involved in these various reactions. There is also a cross reference between the substances and the Enzyme Commission Numbers of the Enzymes used to catalyze the reactions in which the substances participate.This review serves to update previously published evaluations of equilibrium constants and enthalpy changes for Enzyme-catalyzed reactions. For each reaction, the following information is given: the reference for the data, the reaction studied, the name of the Enzyme used and its Enzyme Commission Number, the method of measurement, the conditions of measurement [temperature, pH, ionic strength, and the buffer(s) and cofactor(s) used], the data and their evaluation, and, sometimes, commentary on the data and on any corrections which have been applied to the data or any calculations for which the data have been used. The review contains data from 119 references which have been examined and evaluated. Chemical Abstract Service registry Numbers are given for the substances involved in these various reactions. There is also a cross reference between the substances and the Enzyme Commission Numbers of the Enzymes used to catalyze the reactions in which the substances participate.
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Thermodynamics of Enzyme-Catalyzed Reactions: Part 6—1999 Update
Journal of Physical and Chemical Reference Data, 1999Co-Authors: Robert N. GoldbergAbstract:This review serves to update previously published evaluations of equilibrium constants and enthalpy changes for Enzyme-catalyzed reactions. For each reaction the following information is given: the reference for the data; the reaction studied; the name of the Enzyme used and its Enzyme Commission Number; the method of measurement; the conditions of measurement [temperature, pH, ionic strength, and the buffer(s) and cofactor(s) used]; the data and an evaluation of it; and, sometimes, commentary on the data and on any corrections which have been applied to it or any calculations for which the data have been used. The data from 96 references have been examined and evaluated. Chemical Abstract Service registry Numbers are given for the substances involved in these various reactions. There is also a cross reference between the substances and the Enzyme Commission Numbers of the Enzymes used to catalyze the reactions in which the substances participate.
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Thermodynamics of Enzyme‐Catalyzed Reactions: Part 5. Isomerases and Ligases
Journal of Physical and Chemical Reference Data, 1995Co-Authors: Robert N. Goldberg, Yadu B. TewariAbstract:Equilibrium constants and enthalpy changes for reactions catalyzed by the isomerase and ligase classes of Enzymes have been compiled. For each reaction the following information is given: the reference for the data; the reaction studied; the name of the Enzyme used and its Enzyme Commission Number; the method of measurement; the conditions of measurement (temperature, pH, ionic strength, and the buffer(s) and cofactor(s) used); the data and an evaluation of it; and, sometimes, commentary on the data and on any corrections which have been applied to it or any calculations for which the data have been used. The data from 176 references have been examined and evaluated. Chemical Abstract Service registry Numbers are given for the substances involved in these various reactions. There is a cross reference between the substances and the Enzyme Commission Numbers of the Enzymes used to catalyze the reactions in which the substances participate.
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Thermodynamics of Enzyme‐Catalyzed Reactions: Part 4. Lyases
Journal of Physical and Chemical Reference Data, 1994Co-Authors: Robert N. Goldberg, Yadu B. TewariAbstract:Equilibrium constants and enthalpy changes for reactions catalyzed by the hydrolase class of Enzymes have been compiled. For each reaction the following information is given: The reference for the data; the reaction studied; the name of the Enzyme used and its Enzyme Commission Number; the method of measurement; the conditions of measurement [temperature, pH, ionic strength, and the buffer(s) and cofactor(s) used]; the data and an evaluation of it; and, sometimes, commentary on the data and on any corrections which have been applied to it or any calculations for which the data have been used. The data from 145 references have been examined and evaluated. Chemical Abstract Service registry Numbers are given for the substances involved in these various reactions. There is a cross reference between the substances and the Enzyme Commission Numbers of the Enzymes used to catalyze the reactions in which the substances participate.
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Thermodynamics of Enzyme‐Catalyzed Reactions: Part 2. Transferases
Journal of Physical and Chemical Reference Data, 1994Co-Authors: Robert N. Goldberg, Yadu B. TewariAbstract:Equilibrium constants and enthalpy changes for reactions catalyzed by the transferase class of Enzymes have been compiled. For each reaction the following information is given: the reference for the data; the reaction studied; the name of the Enzyme used and its Enzyme Commission Number; the method of measurement; the conditions of measurement [temperature, pH, ionic strength, and the buffer(s) and cofactor(s) used]; the data and an evaluation of it; and, sometimes, commentary on the data and on any corrections which have been applied to it or any calculations for which the data have been used. The data from 285 references have been examined and evaluated. Chemical Abstract Service registry Numbers are given for the substances involved in these various reactions. There is a cross reference between the substances and the Enzyme Commission Numbers of the Enzymes used to catalyze the reactions in which the substances participate.