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  1. Article ; Online: AlphaFold2 reveals commonalities and novelties in protein structure space for 21 model organisms

    Nicola Bordin / Ian Sillitoe / Vamsi Nallapareddy / Clemens Rauer / Su Datt Lam / Vaishali P. Waman / Neeladri Sen / Michael Heinzinger / Maria Littmann / Stephanie Kim / Sameer Velankar / Martin Steinegger / Burkhard Rost / Christine Orengo

    Communications Biology, Vol 6, Iss 1, Pp 1-

    2023  Volume 12

    Abstract: A new protein domain classification protocol incorporating deep learning strategies for detecting sequence and structure similarities between domain is used to systematically study and analyse the predicted AlphaFold2 structural models for proteins of 21 ...

    Abstract A new protein domain classification protocol incorporating deep learning strategies for detecting sequence and structure similarities between domain is used to systematically study and analyse the predicted AlphaFold2 structural models for proteins of 21 organisms.
    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2023-02-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article: In silico methods for design of biological therapeutics

    Roy, Ankit / M.S. Madhusudhan / Neeladri Sen / Neelesh Soni / Sanjana Nair

    Methods. 2017 Dec. 01, v. 131

    2017  

    Abstract: It has been twenty years since the first rationally designed small molecule drug was introduced into the market. Since then, we have progressed from designing small molecules to designing biotherapeutics. This class of therapeutics includes designed ... ...

    Abstract It has been twenty years since the first rationally designed small molecule drug was introduced into the market. Since then, we have progressed from designing small molecules to designing biotherapeutics. This class of therapeutics includes designed proteins, peptides and nucleic acids that could more effectively combat drug resistance and even act in cases where the disease is caused because of a molecular deficiency. Computational methods are crucial in this design exercise and this review discusses the various elements of designing biotherapeutic proteins and peptides. Many of the techniques discussed here, such as the deterministic and stochastic design methods, are generally used in protein design. We have devoted special attention to the design of antibodies and vaccines. In addition to the methods for designing these molecules, we have included a comprehensive list of all biotherapeutics approved for clinical use. Also included is an overview of methods that predict the binding affinity, cell penetration ability, half-life, solubility, immunogenicity and toxicity of the designed therapeutics. Biotherapeutics are only going to grow in clinical importance and are set to herald a new generation of disease management and cure.
    Keywords antibodies ; binding capacity ; disease control ; drug resistance ; half life ; immune response ; nucleic acids ; peptides ; proteins ; solubility ; therapeutics ; toxicity ; vaccines
    Language English
    Dates of publication 2017-1201
    Size p. 33-65.
    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.2017.09.008
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: Predicting and designing therapeutics against the Nipah virus.

    Neeladri Sen / Tejashree Rajaram Kanitkar / Ankit Animesh Roy / Neelesh Soni / Kaustubh Amritkar / Shreyas Supekar / Sanjana Nair / Gulzar Singh / M S Madhusudhan

    PLoS Neglected Tropical Diseases, Vol 13, Iss 12, p e

    2019  Volume 0007419

    Abstract: Despite Nipah virus outbreaks having high mortality rates (>70% in Southeast Asia), there are no licensed drugs against it. In this study, we have considered all 9 Nipah proteins as potential therapeutic targets and computationally identified 4 putative ... ...

    Abstract Despite Nipah virus outbreaks having high mortality rates (>70% in Southeast Asia), there are no licensed drugs against it. In this study, we have considered all 9 Nipah proteins as potential therapeutic targets and computationally identified 4 putative peptide inhibitors (against G, F and M proteins) and 146 small molecule inhibitors (against F, G, M, N, and P proteins). The computations include extensive homology/ab initio modeling, peptide design and small molecule docking. An important contribution of this study is the increased structural characterization of Nipah proteins by approximately 90% of what is deposited in the PDB. In addition, we have carried out molecular dynamics simulations on all the designed protein-peptide complexes and on 13 of the top shortlisted small molecule ligands to check for stability and to estimate binding strengths. Details, including atomic coordinates of all the proteins and their ligand bound complexes, can be accessed at http://cospi.iiserpune.ac.in/Nipah. Our strategy was to tackle the development of therapeutics on a proteome wide scale and the lead compounds identified could be attractive starting points for drug development. To counter the threat of drug resistance, we have analysed the sequences of the viral strains from different outbreaks, to check whether they would be sensitive to the binding of the proposed inhibitors.
    Keywords Arctic medicine. Tropical medicine ; RC955-962 ; Public aspects of medicine ; RA1-1270
    Subject code 540
    Language English
    Publishing date 2019-12-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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