LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 7 of total 7

Search options

  1. Article ; Online: Memdock: An α-Helical Membrane Protein Docking Algorithm.

    Hurwitz, Naama / Wolfson, Haim J

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

    2021  Volume 2315, Page(s) 111–117

    Abstract: Memdock is a tool for docking α-helical membrane proteins which takes into consideration the lipid bilayer environment. Given two α-helical membrane located protein molecules, the method outputs a list of potential complexes sorted by energy criteria. ... ...

    Abstract Memdock is a tool for docking α-helical membrane proteins which takes into consideration the lipid bilayer environment. Given two α-helical membrane located protein molecules, the method outputs a list of potential complexes sorted by energy criteria. The program includes three steps: docking, refinement, and re-ranking of the results. All three docking steps have been customized to the membrane environment in order to improve performance and reduce program run-time. In this chapter, we describe the application of our web server, referred to as Memdock, for prediction of the docking complex for a pair of input membrane protein structures. Memdock is freely available for academic users without registration at http://bioinfo3d.cs.tau.ac.il/Memdock/index.html .
    MeSH term(s) Algorithms ; Computational Biology/methods ; Internet ; Membrane Proteins/chemistry ; Models, Molecular ; Molecular Docking Simulation/methods ; Protein Conformation, alpha-Helical/physiology ; Software ; User-Computer Interface
    Chemical Substances Membrane Proteins
    Language English
    Publishing date 2021-07-23
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-1468-6_7
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

    More links

    Kategorien

    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.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  2. Article ; Online: Pep-Whisperer: Inhibitory peptide design.

    Hurwitz, Naama / Zaidman, Daniel / Wolfson, Haim J

    Proteins

    2022  Volume 90, Issue 11, Page(s) 1886–1895

    Abstract: Designing peptides for protein-protein interaction inhibition is of significant interest in computer-aided drug design. Such inhibitory peptides could mimic and compete with the binding of the partner protein to the inhibition target. Experimental ... ...

    Abstract Designing peptides for protein-protein interaction inhibition is of significant interest in computer-aided drug design. Such inhibitory peptides could mimic and compete with the binding of the partner protein to the inhibition target. Experimental peptide design is a laborious, time consuming, and expensive multi-step process. Therefore, in silico peptide design can be beneficial for achieving this task. We present a novel algorithm, Pep-Whisperer, which aims to design inhibitory peptides for protein-protein interaction. The desirable peptides would have a relatively high predicted binding affinity to the target protein in a given protein-protein complex. The algorithm outputs linear peptides which are based on an initial template. The template could either be a peptide which is retrieved from the interaction site, or a patch of nonconsecutive amino acids from the protein-protein interface which is completed to a linear peptide by short polyalanine linkers. In addition, the algorithm takes into consideration the conservation of the amino acids in the ligand-protein binding site by using evolutionary information for choosing the preferred amino acids in each position of the designed peptide. Our algorithm was able to design peptides with high predicted binding affinity to the target protein. The method is fully automated and available as a web server at http://bioinfo3d.cs.tau.ac.il/PepWhisperer/.
    MeSH term(s) Amino Acids/metabolism ; Drug Design ; Ligands ; Peptides/chemistry ; Protein Binding ; Proteins/chemistry
    Chemical Substances Amino Acids ; Ligands ; Peptides ; Proteins
    Language English
    Publishing date 2022-06-11
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 806683-8
    ISSN 1097-0134 ; 0887-3585
    ISSN (online) 1097-0134
    ISSN 0887-3585
    DOI 10.1002/prot.26384
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 2291: 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.

  3. Article ; Online: Memdock: an α-helical membrane protein docking algorithm.

    Hurwitz, Naama / Schneidman-Duhovny, Dina / Wolfson, Haim J

    Bioinformatics (Oxford, England)

    2016  Volume 32, Issue 16, Page(s) 2444–2450

    Abstract: Motivation: A wide range of fundamental biological processes are mediated by membrane proteins. Despite their large number and importance, less than 1% of all 3D protein structures deposited in the Protein Data Bank are of membrane proteins. This is ... ...

    Abstract Motivation: A wide range of fundamental biological processes are mediated by membrane proteins. Despite their large number and importance, less than 1% of all 3D protein structures deposited in the Protein Data Bank are of membrane proteins. This is mainly due to the challenges of crystallizing such proteins or performing NMR spectroscopy analyses. All the more so, there is only a small number of membrane protein-protein complexes with known structure. Therefore, developing computational tools for docking membrane proteins is crucial. Numerous methods for docking globular proteins exist, however few have been developed especially for membrane proteins and designed to address docking within the lipid bilayer environment.
    Results: We present a novel algorithm, Memdock, for docking α-helical membrane proteins which takes into consideration the lipid bilayer environment for docking as well as for refining and ranking the docking candidates. We show that our algorithm improves both the docking accuracy and the candidates ranking compared to a standard protein-protein docking algorithm.
    Availability and implementation: http://bioinfo3d.cs.tau.ac.il/Memdock/
    Contacts: namih@tau.ac.il or wolfson@tau.ac.il
    Supplementary information: Supplementary data are available at Bioinformatics online.
    MeSH term(s) Algorithms ; Databases, Protein ; Membrane Proteins ; Models, Molecular
    Chemical Substances Membrane Proteins
    Language English
    Publishing date 2016-08-15
    Publishing country England
    Document type Journal Article
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btw184
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 2374: 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.

  4. Article: Memdock: an α-helical membrane protein docking algorithm

    Hurwitz, Naama / Schneidman-Duhovny, Dina / Wolfson, Haim J

    Bioinformatics. 2016 Aug. 15, v. 32, no. 16

    2016  

    Abstract: Motivation: A wide range of fundamental biological processes are mediated by membrane proteins. Despite their large number and importance, less than 1% of all 3D protein structures deposited in the Protein Data Bank are of membrane proteins. This is ... ...

    Abstract Motivation: A wide range of fundamental biological processes are mediated by membrane proteins. Despite their large number and importance, less than 1% of all 3D protein structures deposited in the Protein Data Bank are of membrane proteins. This is mainly due to the challenges of crystallizing such proteins or performing NMR spectroscopy analyses. All the more so, there is only a small number of membrane protein–protein complexes with known structure. Therefore, developing computational tools for docking membrane proteins is crucial. Numerous methods for docking globular proteins exist, however few have been developed especially for membrane proteins and designed to address docking within the lipid bilayer environment. Results: We present a novel algorithm, Memdock, for docking α-helical membrane proteins which takes into consideration the lipid bilayer environment for docking as well as for refining and ranking the docking candidates. We show that our algorithm improves both the docking accuracy and the candidates ranking compared to a standard protein–protein docking algorithm. Availability and Implementation: http://bioinfo3d.cs.tau.ac.il/Memdock/ Contacts: namih@tau.ac.il or wolfson@tau.ac.il Supplementary information: Supplementary data are available at Bioinformatics online.
    Keywords algorithms ; bioinformatics ; crystallization ; databases ; lipid bilayers ; membrane proteins ; nuclear magnetic resonance spectroscopy ; protein structure
    Language English
    Dates of publication 2016-0815
    Size p. 2444-2450.
    Publishing place Oxford University Press
    Document type Article
    ZDB-ID 1468345-3
    ISSN 1460-2059 ; 1367-4803
    ISSN (online) 1460-2059
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btw184
    Database NAL-Catalogue (AGRICOLA)

    More links

    Kategorien

    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.

  5. Article ; Online: Design of Disruptors of the Hsp90-Cdc37 Interface.

    D'Annessa, Ilda / Hurwitz, Naama / Pirota, Valentina / Beretta, Giovanni Luca / Tinelli, Stella / Woodford, Mark / Freccero, Mauro / Mollapour, Mehdi / Zaffaroni, Nadia / Wolfson, Haim / Colombo, Giorgio

    Molecules (Basel, Switzerland)

    2020  Volume 25, Issue 2

    Abstract: The molecular chaperone Hsp90 is a ubiquitous ATPase-directed protein responsible for the activation and structural stabilization of a large clientele of proteins. As such, Hsp90 has emerged as a suitable candidate for the treatment of a diverse set of ... ...

    Abstract The molecular chaperone Hsp90 is a ubiquitous ATPase-directed protein responsible for the activation and structural stabilization of a large clientele of proteins. As such, Hsp90 has emerged as a suitable candidate for the treatment of a diverse set of diseases, such as cancer and neurodegeneration. The inhibition of the chaperone through ATP-competitive inhibitors, however, was shown to lead to undesirable side effects. One strategy to alleviate this problem is the development of molecules that are able to disrupt specific protein-protein interactions, thus modulating the activity of Hsp90 only in the particular cellular pathway that needs to be targeted. Here, we exploit novel computational and theoretical approaches to design a set of peptides that are able to bind Hsp90 and compete for its interaction with the co-chaperone Cdc37, which is found to be responsible for the promotion of cancer cell proliferation. In spite of their capability to disrupt the Hsp90-Cdc37 interaction, no important cytotoxicity was observed in human cancer cells exposed to designed compounds. These findings imply the need for further optimization of the compounds, which may lead to new ways of interfering with the Hsp90 mechanisms that are important for tumour growth.
    MeSH term(s) Antineoplastic Agents/pharmacology ; Cell Cycle Proteins/antagonists & inhibitors ; Cell Cycle Proteins/metabolism ; Chaperonins/antagonists & inhibitors ; Chaperonins/metabolism ; Drug Design ; HSP90 Heat-Shock Proteins/antagonists & inhibitors ; HSP90 Heat-Shock Proteins/metabolism ; Humans ; Neoplasms/drug therapy ; Neoplasms/metabolism ; Neoplasms/pathology ; Peptide Fragments/pharmacology ; Protein Binding ; Protein Conformation ; Protein Interaction Domains and Motifs/drug effects
    Chemical Substances Antineoplastic Agents ; CDC37 protein, human ; Cell Cycle Proteins ; HSP90 Heat-Shock Proteins ; Peptide Fragments ; Chaperonins (EC 3.6.1.-)
    Language English
    Publishing date 2020-01-15
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 1413402-0
    ISSN 1420-3049 ; 1431-5165 ; 1420-3049
    ISSN (online) 1420-3049
    ISSN 1431-5165 ; 1420-3049
    DOI 10.3390/molecules25020360
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.MO 81: Show issues

    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.

  6. Article ; Online: Design of Disruptors of the Hsp90–Cdc37 Interface

    Ilda D’Annessa / Naama Hurwitz / Valentina Pirota / Giovanni Luca Beretta / Stella Tinelli / Mark Woodford / Mauro Freccero / Mehdi Mollapour / Nadia Zaffaroni / Haim Wolfson / Giorgio Colombo

    Molecules, Vol 25, Iss 2, p

    2020  Volume 360

    Abstract: The molecular chaperone Hsp90 is a ubiquitous ATPase-directed protein responsible for the activation and structural stabilization of a large clientele of proteins. As such, Hsp90 has emerged as a suitable candidate for the treatment of a diverse set of ... ...

    Abstract The molecular chaperone Hsp90 is a ubiquitous ATPase-directed protein responsible for the activation and structural stabilization of a large clientele of proteins. As such, Hsp90 has emerged as a suitable candidate for the treatment of a diverse set of diseases, such as cancer and neurodegeneration. The inhibition of the chaperone through ATP-competitive inhibitors, however, was shown to lead to undesirable side effects. One strategy to alleviate this problem is the development of molecules that are able to disrupt specific protein−protein interactions, thus modulating the activity of Hsp90 only in the particular cellular pathway that needs to be targeted. Here, we exploit novel computational and theoretical approaches to design a set of peptides that are able to bind Hsp90 and compete for its interaction with the co-chaperone Cdc37, which is found to be responsible for the promotion of cancer cell proliferation. In spite of their capability to disrupt the Hsp90−Cdc37 interaction, no important cytotoxicity was observed in human cancer cells exposed to designed compounds. These findings imply the need for further optimization of the compounds, which may lead to new ways of interfering with the Hsp90 mechanisms that are important for tumour growth.
    Keywords hsp90 ; cdc37 ; protein–protein interaction ; peptide design ; Organic chemistry ; QD241-441
    Subject code 570
    Language English
    Publishing date 2020-01-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  7. Article: Towards genome-scale structure prediction for transmembrane proteins.

    Hurwitz, Naama / Pellegrini-Calace, Marialuisa / Jones, David T

    Philosophical transactions of the Royal Society of London. Series B, Biological sciences

    2006  Volume 361, Issue 1467, Page(s) 465–475

    Abstract: In this paper we briefly review some of the recent progress made by ourselves and others in developing methods for predicting the structures of transmembrane proteins from amino acid sequence. Transmembrane proteins are an important class of proteins ... ...

    Abstract In this paper we briefly review some of the recent progress made by ourselves and others in developing methods for predicting the structures of transmembrane proteins from amino acid sequence. Transmembrane proteins are an important class of proteins involved in many diverse biological functions, many of which have great impact in terms of disease mechanism and drug discovery. Despite their biological importance, it has proven very difficult to solve the structures of these proteins by experimental techniques, and so there is a great deal of pressure to develop effective methods for predicting their structure. The methods we discuss range from methods for transmembrane topology prediction to new methods for low resolution folding simulations in a knowledge-based force field. This potential is designed to reproduce the properties of the lipid bilayer. Our eventual aim is to apply these methods in tandem so that useful three-dimensional models can be built for a large fraction of the transmembrane protein domains in whole proteomes.
    MeSH term(s) Cell Membrane/chemistry ; Cell Membrane/metabolism ; Computational Biology ; Genome ; Membrane Proteins/chemistry ; Membrane Proteins/classification ; Membrane Proteins/genetics ; Membrane Proteins/metabolism ; Models, Molecular ; Protein Folding
    Chemical Substances Membrane Proteins
    Language English
    Publishing date 2006-03-08
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 208382-6
    ISSN 1471-2970 ; 0962-8436 ; 0080-4622 ; 0264-3839
    ISSN (online) 1471-2970
    ISSN 0962-8436 ; 0080-4622 ; 0264-3839
    DOI 10.1098/rstb.2005.1804
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Einzelsignatur: Show issues

    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.

To top