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  1. Book ; Online: Protein Structure

    Faraggi, Eshel

    2012  

    Keywords Biochemistry
    Size 1 electronic resource (410 pages)
    Publisher IntechOpen
    Document type Book ; Online
    Note English ; Open Access
    HBZ-ID HT021045530
    ISBN 9789535152781 ; 9535152785
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  2. Book: Prediction of protein secondary structure

    Zhou, Yaoqi / Kloczkowski, Andrzej / Faraggi, Eshel / Yang, Yuedong

    (Methods in molecular biology ; 1484 ; Springer protocols)

    2017  

    Author's details edited by Yaoqi Zhou, Andrzej Kloczkowski, Eshel Faraggi, Yuedong Yang
    Series title Methods in molecular biology ; 1484
    Springer protocols
    Collection
    Keywords 1D structural properties of proteins ; 3D structure ; Backbone torsion angles ; Model building ; One-dimensional functional properties ; Protein backbone structure
    Language English
    Size xi, 313 Seiten, Illustrationen, Diagramme, 25.4 cm x 17.8 cm, 0 g
    Publisher Humana Press
    Publishing place New York
    Publishing country United States
    Document type Book
    HBZ-ID HT019084917
    ISBN 978-1-4939-6404-8 ; 9781493964062 ; 1-4939-6404-6 ; 1493964062
    DOI 10.1007/978-1-4939-6406-2
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    Zs A 7042 -1484- verfügbar in Königswinter Königswinter

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  3. Article ; Online: A Hybrid Levenberg-Marquardt Algorithm on a Recursive Neural Network for Scoring Protein Models.

    Faraggi, Eshel / Jernigan, Robert L / Kloczkowski, Andrzej

    Methods in molecular biology (Clifton, N.J.)

    2020  Volume 2190, Page(s) 307–316

    Abstract: We have studied the ability of three types of neural networks to predict the closeness of a given protein model to the native structure associated with its sequence. We show that a partial combination of the Levenberg-Marquardt algorithm and the back- ... ...

    Abstract We have studied the ability of three types of neural networks to predict the closeness of a given protein model to the native structure associated with its sequence. We show that a partial combination of the Levenberg-Marquardt algorithm and the back-propagation algorithm produced the best results, giving the lowest error and largest Pearson correlation coefficient. We also find, as previous studies, that adding associative memory to a neural network improves its performance. Additionally, we find that the hybrid method we propose was the most robust in the sense that other configurations of it experienced less decline in comparison to the other methods. We find that the hybrid networks also undergo more fluctuations on the path to convergence. We propose that these fluctuations allow for better sampling. Overall we find it may be beneficial to treat different parts of a neural network with varied computational approaches during optimization.
    MeSH term(s) Algorithms ; Neural Networks, Computer ; Proteins/chemistry
    Chemical Substances Proteins
    Language English
    Publishing date 2020-09-10
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-0826-5_15
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Accurate Prediction of One-Dimensional Protein Structure Features Using SPINE-X.

    Faraggi, Eshel / Kloczkowski, Andrzej

    Methods in molecular biology (Clifton, N.J.)

    2017  Volume 1484, Page(s) 45–53

    Abstract: Accurate prediction of protein secondary structure and other one-dimensional structure features is essential for accurate sequence alignment, three-dimensional structure modeling, and function prediction. SPINE-X is a software package to predict ... ...

    Abstract Accurate prediction of protein secondary structure and other one-dimensional structure features is essential for accurate sequence alignment, three-dimensional structure modeling, and function prediction. SPINE-X is a software package to predict secondary structure as well as accessible surface area and dihedral angles ϕ and ψ. For secondary structure SPINE-X achieves an accuracy of between 81 and 84 % depending on the dataset and choice of tests. The Pearson correlation coefficient for accessible surface area prediction is 0.75 and the mean absolute error from the ϕ and ψ dihedral angles are 20
    Language English
    Publishing date 2017
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-6406-2_5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Computational Ways to Enhance Protein Inhibitor Design.

    Jernigan, Robert L / Sankar, Kannan / Jia, Kejue / Faraggi, Eshel / Kloczkowski, Andrzej

    Frontiers in molecular biosciences

    2021  Volume 7, Page(s) 607323

    Abstract: Two new computational approaches are described to aid in the design of new peptide-based drugs by evaluating ensembles of protein structures from their dynamics and through the assessing of structures using empirical contact potential. These approaches ... ...

    Abstract Two new computational approaches are described to aid in the design of new peptide-based drugs by evaluating ensembles of protein structures from their dynamics and through the assessing of structures using empirical contact potential. These approaches build on the concept that conformational variability can aid in the binding process and, for disordered proteins, can even facilitate the binding of more diverse ligands. This latter consideration indicates that such a design process should be less restrictive so that multiple inhibitors might be effective. The example chosen here focuses on proteins/peptides that bind to hemagglutinin (HA) to block the large-scale conformational change for activation. Variability in the conformations is considered from sets of experimental structures, or as an alternative, from their simple computed dynamics; the set of designe peptides/small proteins from the David Baker lab designed to bind to hemagglutinin, is the large set considered and is assessed with the new empirical contact potentials.
    Language English
    Publishing date 2021-02-03
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2814330-9
    ISSN 2296-889X
    ISSN 2296-889X
    DOI 10.3389/fmolb.2020.607323
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Computational Ways to Enhance Protein Inhibitor Design

    Robert L. Jernigan / Kannan Sankar / Kejue Jia / Eshel Faraggi / Andrzej Kloczkowski

    Frontiers in Molecular Biosciences, Vol

    2021  Volume 7

    Abstract: Two new computational approaches are described to aid in the design of new peptide-based drugs by evaluating ensembles of protein structures from their dynamics and through the assessing of structures using empirical contact potential. These approaches ... ...

    Abstract Two new computational approaches are described to aid in the design of new peptide-based drugs by evaluating ensembles of protein structures from their dynamics and through the assessing of structures using empirical contact potential. These approaches build on the concept that conformational variability can aid in the binding process and, for disordered proteins, can even facilitate the binding of more diverse ligands. This latter consideration indicates that such a design process should be less restrictive so that multiple inhibitors might be effective. The example chosen here focuses on proteins/peptides that bind to hemagglutinin (HA) to block the large-scale conformational change for activation. Variability in the conformations is considered from sets of experimental structures, or as an alternative, from their simple computed dynamics; the set of designe peptides/small proteins from the David Baker lab designed to bind to hemagglutinin, is the large set considered and is assessed with the new empirical contact potentials.
    Keywords protein design ; peptide design ; computational design ; protein ensemble ; protein potentials ; Biology (General) ; QH301-705.5
    Subject code 612
    Language English
    Publishing date 2021-02-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options.

    Basu, Sushmita / Zhao, Bi / Biró, Bálint / Faraggi, Eshel / Gsponer, Jörg / Hu, Gang / Kloczkowski, Andrzej / Malhis, Nawar / Mirdita, Milot / Söding, Johannes / Steinegger, Martin / Wang, Duolin / Wang, Kui / Xu, Dong / Zhang, Jian / Kurgan, Lukasz

    Nucleic acids research

    2023  Volume 52, Issue D1, Page(s) D426–D433

    Abstract: The DescribePROT database of amino acid-level descriptors of protein structures and functions was substantially expanded since its release in 2020. This expansion includes substantial increase in the size, scope, and quality of the underlying data, the ... ...

    Abstract The DescribePROT database of amino acid-level descriptors of protein structures and functions was substantially expanded since its release in 2020. This expansion includes substantial increase in the size, scope, and quality of the underlying data, the addition of experimental structural information, the inclusion of new data download options, and an upgraded graphical interface. DescribePROT currently covers 19 structural and functional descriptors for proteins in 273 reference proteomes generated by 11 accurate and complementary predictive tools. Users can search our resource in multiple ways, interact with the data using the graphical interface, and download data at various scales including individual proteins, entire proteomes, and whole database. The annotations in DescribePROT are useful for a broad spectrum of studies that include investigations of protein structure and function, development and validation of predictive tools, and to support efforts in understanding molecular underpinnings of diseases and development of therapeutics. DescribePROT can be freely accessed at http://biomine.cs.vcu.edu/servers/DESCRIBEPROT/.
    MeSH term(s) Proteome/chemistry ; Databases, Factual ; Amino Acids
    Chemical Substances Proteome ; Amino Acids
    Language English
    Publishing date 2023-11-07
    Publishing country England
    Document type Journal Article
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkad985
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1067: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  8. Article: Entropy, Fluctuations, and Disordered Proteins.

    Faraggi, Eshel / Dunker, A Keith / Jernigan, Robert L / Kloczkowski, Andrzej

    Entropy (Basel, Switzerland)

    2019  Volume 21, Issue 8

    Abstract: Entropy should directly reflect the extent of disorder in proteins. By clustering structurally related proteins and studying the multiple-sequence-alignment of the sequences of these clusters, we were able to link between sequence, structure, and ... ...

    Abstract Entropy should directly reflect the extent of disorder in proteins. By clustering structurally related proteins and studying the multiple-sequence-alignment of the sequences of these clusters, we were able to link between sequence, structure, and disorder information. We introduced several parameters as measures of fluctuations at a given MSA site and used these as representative of the sequence and structure entropy at that site. In general, we found a tendency for negative correlations between disorder and structure, and significant positive correlations between disorder and the fluctuations in the system. We also found evidence for residue-type conservation for those residues proximate to potentially disordered sites. Mutation at the disorder site itself appear to be allowed. In addition, we found positive correlation for disorder and accessible surface area, validating that disordered residues occur in exposed regions of proteins. Finally, we also found that fluctuations in the dihedral angles at the original mutated residue and disorder are positively correlated while dihedral angle fluctuations in spatially proximal residues are negatively correlated with disorder. Our results seem to indicate permissible variability in the disordered site, but greater rigidity in the parts of the protein with which the disordered site interacts. This is another indication that disordered residues are involved in protein function.
    Language English
    Publishing date 2019-08-06
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2014734-X
    ISSN 1099-4300
    ISSN 1099-4300
    DOI 10.3390/e21080764
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Book ; Online: Symmetrical charge-charge interactions in ionic solutions

    Faraggi, Eshel

    implications for biological interactions

    2012  

    Abstract: As is well known in electrolyte theory, electrostatic fields are attenuated by the presence of mobile charges in the solution. This seems to limit the possibility of an electrostatic repulsion model of biological interactions such as cell division. Here, ...

    Abstract As is well known in electrolyte theory, electrostatic fields are attenuated by the presence of mobile charges in the solution. This seems to limit the possibility of an electrostatic repulsion model of biological interactions such as cell division. Here, a system of two charges in an ionic solution is considered. It is found that in the context of the symmetries of the system, the electrostatic repulsion between the two is considerably increased as compared to the electrostatic repulsion between two bare charges in a dielectric. This increase in repulsion, directly resulting from interactions between the symmetrical parts of the system, was found to be dependent on the magnitude of the charges and the separation between them. It was also found that this increases reaches a steady state for separation greater than a solvent determined length scale related to the Debye length. These findings strongly suggest that electrostatic interactions can play a crucial part in the physical forces that are involved in biological interactions.

    Comment: 5 Pages, 3 figures. Submitted to the Phys. Rev. Lett. 2009, PNAS-USA 2010, J. of Appl. Phys. 2011
    Keywords Physics - Biological Physics ; Quantitative Biology - Cell Behavior
    Subject code 612
    Publishing date 2012-01-02
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Fast and Accurate Accessible Surface Area Prediction Without a Sequence Profile.

    Faraggi, Eshel / Kouza, Maksim / Zhou, Yaoqi / Kloczkowski, Andrzej

    Methods in molecular biology (Clifton, N.J.)

    2017  Volume 1484, Page(s) 127–136

    Abstract: A fast accessible surface area (ASA) predictor is presented. In this new approach no residue mutation profiles generated by multiple sequence alignments are used as inputs. Instead, we use only single sequence information and global features such as ... ...

    Abstract A fast accessible surface area (ASA) predictor is presented. In this new approach no residue mutation profiles generated by multiple sequence alignments are used as inputs. Instead, we use only single sequence information and global features such as single-residue and two-residue compositions of the chain. The resulting predictor is both highly more efficient than sequence alignment based predictors and of comparable accuracy to them. Introduction of the global inputs significantly helps achieve this comparable accuracy. The predictor, termed ASAquick, is found to perform similarly well for so-called easy and hard cases indicating generalizability and possible usability for de-novo protein structure prediction. The source code and a Linux executables for ASAquick are available from Research and Information Systems at http://mamiris.com and from the Battelle Center for Mathematical Medicine at http://mathmed.org .
    Language English
    Publishing date 2017
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-6406-2_10
    Database MEDical Literature Analysis and Retrieval System OnLINE

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