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  1. Article: Biochemical functional predictions for protein structures of unknown or uncertain function.

    Mills, Caitlyn L / Beuning, Penny J / Ondrechen, Mary Jo

    Computational and structural biotechnology journal

    2015  Volume 13, Page(s) 182–191

    Abstract: ... information and better predictions of function for proteins of unknown function. Global initiatives, including ... three-dimensional-structure-based methods for protein function prediction have been reviewed previously ... the function of proteins of unknown function. These initiatives and global collaborations will increase ...

    Abstract With the exponential growth in the determination of protein sequences and structures via genome sequencing and structural genomics efforts, there is a growing need for reliable computational methods to determine the biochemical function of these proteins. This paper reviews the efforts to address the challenge of annotating the function at the molecular level of uncharacterized proteins. While sequence- and three-dimensional-structure-based methods for protein function prediction have been reviewed previously, the recent trends in local structure-based methods have received less attention. These local structure-based methods are the primary focus of this review. Computational methods have been developed to predict the residues important for catalysis and the local spatial arrangements of these residues can be used to identify protein function. In addition, the combination of different types of methods can help obtain more information and better predictions of function for proteins of unknown function. Global initiatives, including the Enzyme Function Initiative (EFI), COMputational BRidges to EXperiments (COMBREX), and the Critical Assessment of Function Annotation (CAFA), are evaluating and testing the different approaches to predicting the function of proteins of unknown function. These initiatives and global collaborations will increase the capability and reliability of methods to predict biochemical function computationally and will add substantial value to the current volume of structural genomics data by reducing the number of absent or inaccurate functional annotations.
    Language English
    Publishing date 2015-02-18
    Publishing country Netherlands
    Document type Journal Article ; Review
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2015.02.003
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Biochemical functional predictions for protein structures of unknown or uncertain function

    Caitlyn L. Mills / Penny J. Beuning / Mary Jo Ondrechen

    Computational and Structural Biotechnology Journal, Vol 13, Iss C, Pp 182-

    2015  Volume 191

    Abstract: ... information and better predictions of function for proteins of unknown function. Global initiatives, including ... three-dimensional-structure-based methods for protein function prediction have been reviewed previously ... the function of proteins of unknown function. These initiatives and global collaborations will increase ...

    Abstract With the exponential growth in the determination of protein sequences and structures via genome sequencing and structural genomics efforts, there is a growing need for reliable computational methods to determine the biochemical function of these proteins. This paper reviews the efforts to address the challenge of annotating the function at the molecular level of uncharacterized proteins. While sequence- and three-dimensional-structure-based methods for protein function prediction have been reviewed previously, the recent trends in local structure-based methods have received less attention. These local structure-based methods are the primary focus of this review. Computational methods have been developed to predict the residues important for catalysis and the local spatial arrangements of these residues can be used to identify protein function. In addition, the combination of different types of methods can help obtain more information and better predictions of function for proteins of unknown function. Global initiatives, including the Enzyme Function Initiative (EFI), COMputational BRidges to EXperiments (COMBREX), and the Critical Assessment of Function Annotation (CAFA), are evaluating and testing the different approaches to predicting the function of proteins of unknown function. These initiatives and global collaborations will increase the capability and reliability of methods to predict biochemical function computationally and will add substantial value to the current volume of structural genomics data by reducing the number of absent or inaccurate functional annotations.
    Keywords Structural genomics ; Protein function prediction ; Local structure methods ; Computational chemistry ; Biotechnology ; TP248.13-248.65
    Language English
    Publishing date 2015-01-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article: Biochemical functional predictions for protein structures of unknown or uncertain function

    Mills, Caitlyn L / Mary Jo Ondrechen / Penny J. Beuning

    Computational and Structural Biotechnology Journal. 2015, v. 13

    2015  

    Abstract: ... information and better predictions of function for proteins of unknown function. Global initiatives, including ... three-dimensional-structure-based methods for protein function prediction have been reviewed previously ... the function of proteins of unknown function. These initiatives and global collaborations will increase ...

    Abstract With the exponential growth in the determination of protein sequences and structures via genome sequencing and structural genomics efforts, there is a growing need for reliable computational methods to determine the biochemical function of these proteins. This paper reviews the efforts to address the challenge of annotating the function at the molecular level of uncharacterized proteins. While sequence- and three-dimensional-structure-based methods for protein function prediction have been reviewed previously, the recent trends in local structure-based methods have received less attention. These local structure-based methods are the primary focus of this review. Computational methods have been developed to predict the residues important for catalysis and the local spatial arrangements of these residues can be used to identify protein function. In addition, the combination of different types of methods can help obtain more information and better predictions of function for proteins of unknown function. Global initiatives, including the Enzyme Function Initiative (EFI), COMputational BRidges to EXperiments (COMBREX), and the Critical Assessment of Function Annotation (CAFA), are evaluating and testing the different approaches to predicting the function of proteins of unknown function. These initiatives and global collaborations will increase the capability and reliability of methods to predict biochemical function computationally and will add substantial value to the current volume of structural genomics data by reducing the number of absent or inaccurate functional annotations.
    Keywords amino acid sequences ; biotechnology ; catalytic activity ; genomics ; prediction ; proteins ; sequence analysis
    Language English
    Size p. 182-191.
    Publishing place Elsevier B.V.
    Document type Article
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2015.02.003
    Database NAL-Catalogue (AGRICOLA)

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  4. Article ; Online: Local structure based method for prediction of the biochemical function of proteins: Applications to glycoside hydrolases.

    Parasuram, Ramya / Mills, Caitlyn L / Wang, Zhouxi / Somasundaram, Saroja / Beuning, Penny J / Ondrechen, Mary Jo

    Methods (San Diego, Calif.)

    2016  Volume 93, Page(s) 51–63

    Abstract: Thousands of protein structures of unknown or uncertain function have been reported as a result ... for limited sets of SG proteins, the biochemical functions for most SG proteins are still unknown or uncertain ... Therefore, computational methods for the reliable prediction of protein function from structure can add tremendous value ...

    Abstract Thousands of protein structures of unknown or uncertain function have been reported as a result of high-throughput structure determination techniques developed by Structural Genomics (SG) projects. However, many of the putative functional assignments of these SG proteins in the Protein Data Bank (PDB) are incorrect. While high-throughput biochemical screening techniques have provided valuable functional information for limited sets of SG proteins, the biochemical functions for most SG proteins are still unknown or uncertain. Therefore, computational methods for the reliable prediction of protein function from structure can add tremendous value to the existing SG data. In this article, we show how computational methods may be used to predict the function of SG proteins, using examples from the six-hairpin glycosidase (6-HG) and the concanavalin A-like lectin/glucanase (CAL/G) superfamilies. Using a set of predicted functional residues, obtained from computed electrostatic and chemical properties for each protein structure, it is shown that these superfamilies may be sorted into functional families according to biochemical function. Within these superfamilies, a total of 18 SG proteins were analyzed according to their predicted, local functional sites: 13 from the 6-HG superfamily, five from the CAL/G superfamily. Within the 6-HG superfamily, an uncharacterized protein BACOVA_03626 from Bacteroides ovatus (PDB 3ON6) and a hypothetical protein BT3781 from Bacteroides thetaiotaomicron (PDB 2P0V) are shown to have very strong active site matches with exo-α-1,6-mannosidases, thus likely possessing this function. Also in this superfamily, it is shown that protein BH0842, a putative glycoside hydrolase from Bacillus halodurans (PDB 2RDY), has a predicted active site that matches well with a known α-L-galactosidase. In the CAL/G superfamily, an uncharacterized glycosyl hydrolase family 16 protein from Mycobacterium smegmatis (PDB 3RQ0) is shown to have local structural similarity at the predicted active site with the known members of the GH16 family, with the closest match to the endoglucanase subfamily. The method discussed herein can predict whether an SG protein is correctly or incorrectly annotated and can sometimes provide a reliable functional annotation. Examples of application of the method across folds, comparing active sites between two proteins of different structural folds, are also given.
    MeSH term(s) Computational Biology/methods ; Databases, Protein ; Forecasting ; Glycoside Hydrolases/chemistry ; Glycoside Hydrolases/physiology ; Protein Structure, Secondary ; Proteins/chemistry ; Proteins/physiology
    Chemical Substances Proteins ; Glycoside Hydrolases (EC 3.2.1.-)
    Language English
    Publishing date 2016-01-15
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1066584-5
    ISSN 1095-9130 ; 1046-2023
    ISSN (online) 1095-9130
    ISSN 1046-2023
    DOI 10.1016/j.ymeth.2015.11.010
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3239: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

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  5. Article: Local structure based method for prediction of the biochemical function of proteins: Applications to glycoside hydrolases

    Parasuram, Ramya / Caitlyn L. Mills / Mary Jo Ondrechen / Penny J. Beuning / Saroja Somasundaram / Zhouxi Wang

    Methods. 2016 Jan. 15, v. 93

    2016  

    Abstract: Thousands of protein structures of unknown or uncertain function have been reported as a result ... for limited sets of SG proteins, the biochemical functions for most SG proteins are still unknown or uncertain ... Therefore, computational methods for the reliable prediction of protein function from structure can add tremendous value ...

    Abstract Thousands of protein structures of unknown or uncertain function have been reported as a result of high-throughput structure determination techniques developed by Structural Genomics (SG) projects. However, many of the putative functional assignments of these SG proteins in the Protein Data Bank (PDB) are incorrect. While high-throughput biochemical screening techniques have provided valuable functional information for limited sets of SG proteins, the biochemical functions for most SG proteins are still unknown or uncertain. Therefore, computational methods for the reliable prediction of protein function from structure can add tremendous value to the existing SG data. In this article, we show how computational methods may be used to predict the function of SG proteins, using examples from the six-hairpin glycosidase (6-HG) and the concanavalin A-like lectin/glucanase (CAL/G) superfamilies. Using a set of predicted functional residues, obtained from computed electrostatic and chemical properties for each protein structure, it is shown that these superfamilies may be sorted into functional families according to biochemical function. Within these superfamilies, a total of 18 SG proteins were analyzed according to their predicted, local functional sites: 13 from the 6-HG superfamily, five from the CAL/G superfamily. Within the 6-HG superfamily, an uncharacterized protein BACOVA_03626 from Bacteroides ovatus (PDB 3ON6) and a hypothetical protein BT3781 from Bacteroides thetaiotaomicron (PDB 2P0V) are shown to have very strong active site matches with exo-α-1,6-mannosidases, thus likely possessing this function. Also in this superfamily, it is shown that protein BH0842, a putative glycoside hydrolase from Bacillus halodurans (PDB 2RDY), has a predicted active site that matches well with a known α-l-galactosidase. In the CAL/G superfamily, an uncharacterized glycosyl hydrolase family 16 protein from Mycobacterium smegmatis (PDB 3RQ0) is shown to have local structural similarity at the predicted active site with the known members of the GH16 family, with the closest match to the endoglucanase subfamily. The method discussed herein can predict whether an SG protein is correctly or incorrectly annotated and can sometimes provide a reliable functional annotation. Examples of application of the method across folds, comparing active sites between two proteins of different structural folds, are also given.
    Keywords active sites ; Bacillus halodurans ; Bacteroides ovatus ; Bacteroides thetaiotaomicron ; databases ; endo-1,4-beta-glucanase ; genomics ; glycosides ; lectins ; Mycobacterium smegmatis ; physicochemical properties ; prediction ; protein structure ; screening
    Language English
    Dates of publication 2016-0115
    Size p. 51-63.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 1066584-5
    ISSN 1095-9130 ; 1046-2023
    ISSN (online) 1095-9130
    ISSN 1046-2023
    DOI 10.1016/j.ymeth.2015.11.010
    Database NAL-Catalogue (AGRICOLA)

    Full text online

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 3239: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

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