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  1. Article ; Online: Short Peptide Self-Assembly in the Martini Coarse-Grain Force Field Family.

    van Teijlingen, Alexander / Smith, Melissa C / Tuttle, Tell

    Accounts of chemical research

    2023  Volume 56, Issue 6, Page(s) 644–654

    Abstract: Pivotal to the success of any computational experiment is the ability to make reliable predictions about the system under study and the time required to yield these results. Biomolecular interactions is one area of research that sits in every camp of ... ...

    Abstract Pivotal to the success of any computational experiment is the ability to make reliable predictions about the system under study and the time required to yield these results. Biomolecular interactions is one area of research that sits in every camp of resolution vs the time required, from the quantum mechanical level to
    MeSH term(s) Peptides ; Molecular Dynamics Simulation ; Proteins/chemistry ; Solvents ; Water/chemistry ; Amino Acids ; Dipeptides
    Chemical Substances Peptides ; Proteins ; Solvents ; Water (059QF0KO0R) ; Amino Acids ; Dipeptides
    Language English
    Publishing date 2023-03-03
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1483291-4
    ISSN 1520-4898 ; 0001-4842
    ISSN (online) 1520-4898
    ISSN 0001-4842
    DOI 10.1021/acs.accounts.2c00810
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Beyond Tripeptides Two-Step Active Machine Learning for Very Large Data sets.

    van Teijlingen, Alexander / Tuttle, Tell

    Journal of chemical theory and computation

    2021  Volume 17, Issue 5, Page(s) 3221–3232

    Abstract: Self-assembling peptide nanostructures have been shown to be of great importance in nature and have presented many promising applications, for example, in medicine as drug-delivery vehicles, biosensors, and antivirals. Being very promising candidates for ...

    Abstract Self-assembling peptide nanostructures have been shown to be of great importance in nature and have presented many promising applications, for example, in medicine as drug-delivery vehicles, biosensors, and antivirals. Being very promising candidates for the growing field of bottom-up manufacture of functional nanomaterials, previous work (Frederix, et al. 2011 and 2015) has screened all possible amino acid combinations for di- and tripeptides in search of such materials. However, the enormous complexity and variety of linear combinations of the 20 amino acids make exhaustive simulation of all combinations of tetrapeptides and above infeasible. Therefore, we have developed an active machine-learning method (also known as "iterative learning" and "evolutionary search method") which leverages a lower-resolution data set encompassing the whole search space and a just-in-time high-resolution data set which further analyzes those target peptides selected by the lower-resolution model. This model uses newly generated data upon each iteration to improve both lower- and higher-resolution models in the search for ideal candidates. Curation of the lower-resolution data set is explored as a method to control the selected candidates, based on criteria such as log
    MeSH term(s) Algorithms ; Computational Chemistry ; Datasets as Topic ; Nanostructures/chemistry ; Oligopeptides/chemistry ; Programming Languages ; Protein Conformation ; Supervised Machine Learning
    Chemical Substances Oligopeptides
    Language English
    Publishing date 2021-04-27
    Publishing country United States
    Document type Journal Article
    ISSN 1549-9626
    ISSN (online) 1549-9626
    DOI 10.1021/acs.jctc.1c00159
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Martinoid: the peptoid martini force field.

    Swanson, Hamish W A / van Teijlingen, Alexander / Lau, King Hang Aaron / Tuttle, Tell

    Physical chemistry chemical physics : PCCP

    2024  Volume 26, Issue 6, Page(s) 4939–4953

    Abstract: Many exciting innovations have been made in the development of assembling peptoid materials. Typically, these have utilised large oligomeric sequences, though elsewhere the study of peptide self-assembly has yielded numerous examples of assemblers below ... ...

    Abstract Many exciting innovations have been made in the development of assembling peptoid materials. Typically, these have utilised large oligomeric sequences, though elsewhere the study of peptide self-assembly has yielded numerous examples of assemblers below 6-8 residues in length, evidencing that minimal peptoid assemblers are not only feasible but expected. A productive means of discovering such materials is through the application of
    Language English
    Publishing date 2024-02-07
    Publishing country England
    Document type Journal Article
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/d3cp05907c
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Integrating Computation, Experiment, and Machine Learning in the Design of Peptide-Based Supramolecular Materials and Systems.

    Ramakrishnan, Maithreyi / van Teijlingen, Alexander / Tuttle, Tell / Ulijn, R V

    Angewandte Chemie (International ed. in English)

    2023  Volume 62, Issue 18, Page(s) e202218067

    Abstract: Interest in peptide-based supramolecular materials has grown extensively since the 1980s and the application of computational methods has paralleled this. These methods contribute to the understanding of experimental observations based on interactions ... ...

    Abstract Interest in peptide-based supramolecular materials has grown extensively since the 1980s and the application of computational methods has paralleled this. These methods contribute to the understanding of experimental observations based on interactions and inform the design of new supramolecular systems. They are also used to virtually screen and navigate these very large design spaces. Increasingly, the use of artificial intelligence is employed to screen far more candidates than traditional methods. Based on a brief history of computational and experimentally integrated investigations of peptide structures, we explore recent impactful examples of computationally driven investigation into peptide self-assembly, focusing on recent advances in methodology development. It is clear that the integration between experiment and computation to understand and design new systems is becoming near seamless in this growing field.
    MeSH term(s) Artificial Intelligence ; Peptides/chemistry ; Machine Learning
    Chemical Substances Peptides
    Language English
    Publishing date 2023-02-14
    Publishing country Germany
    Document type Journal Article ; Review ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2011836-3
    ISSN 1521-3773 ; 1433-7851
    ISSN (online) 1521-3773
    ISSN 1433-7851
    DOI 10.1002/anie.202218067
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  5. Article ; Online: Integrating Computation, Experiment, and Machine Learning in the Design of Peptide‐Based Supramolecular Materials and Systems

    Ramakrishnan, Maithreyi / van Teijlingen, Alexander / Tuttle, Tell / Ulijn, R. V.

    Angewandte Chemie International Edition 2023 Apr. 24, v. 62, no. 18, p. e202218067

    2023  

    Abstract: Interest in peptide‐based supramolecular materials has grown extensively since the 1980s and the application of computational methods has paralleled this. These methods contribute to the understanding of experimental observations based on interactions ... ...

    Abstract Interest in peptide‐based supramolecular materials has grown extensively since the 1980s and the application of computational methods has paralleled this. These methods contribute to the understanding of experimental observations based on interactions and inform the design of new supramolecular systems. They are also used to virtually screen and navigate these very large design spaces. Increasingly, the use of artificial intelligence is employed to screen far more candidates than traditional methods. Based on a brief history of computational and experimentally integrated investigations of peptide structures, we explore recent impactful examples of computationally driven investigation into peptide self‐assembly, focusing on recent advances in methodology development. It is clear that the integration between experiment and computation to understand and design new systems is becoming near seamless in this growing field.
    Keywords application methods ; artificial intelligence ; computational methodology ; fields ; peptides ; screening ; systems engineering
    Language English
    Dates of publication 2023-0424
    Size p. e202218067
    Publishing place Wiley & Sons, Ltd.
    Document type Article ; Online
    Note REVIEW
    ZDB-ID 2011836-3
    ISSN 1521-3773 ; 1433-7851
    ISSN (online) 1521-3773
    ISSN 1433-7851
    DOI 10.1002/anie.202218067
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  6. Article ; Online: Size-dependent melting point depression of nickel nanoparticles.

    van Teijlingen, Alexander / Davis, Sean A / Hall, Simon R

    Nanoscale advances

    2020  Volume 2, Issue 6, Page(s) 2347–2351

    Abstract: We investigate the phase-transition behaviour of nickel nanoparticles (3-6 nm) ...

    Abstract We investigate the phase-transition behaviour of nickel nanoparticles (3-6 nm)
    Language English
    Publishing date 2020-04-21
    Publishing country England
    Document type Journal Article
    ISSN 2516-0230
    ISSN (online) 2516-0230
    DOI 10.1039/d0na00153h
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Constant pH Coarse-Grained Molecular Dynamics with Stochastic Charge Neutralization.

    van Teijlingen, Alexander / Swanson, Hamish W A / Lau, King Hang Aaron / Tuttle, Tell

    The journal of physical chemistry letters

    2022  Volume 13, Issue 18, Page(s) 4046–4051

    Abstract: pH dependence abounds in biochemical systems; however, many simulation methods used to investigate these systems do not consider this property. Using a modified version of the hybrid non-equilibrium molecular dynamics (MD)/Monte Carlo algorithm, we ... ...

    Abstract pH dependence abounds in biochemical systems; however, many simulation methods used to investigate these systems do not consider this property. Using a modified version of the hybrid non-equilibrium molecular dynamics (MD)/Monte Carlo algorithm, we include a stochastic charge neutralization method, which is particularly suited to the MARTINI force field and enables artifact-free Ewald summation methods in electrostatic calculations. We demonstrate the efficacy of this method by reproducing pH-dependent self-assembly and self-organization behavior previously reported in experimental literature. In addition, we have carried out experimental oleic acid titrations where we report the results in a more relevant way for the comparison with computational methods than has previously been done.
    MeSH term(s) Algorithms ; Hydrogen-Ion Concentration ; Molecular Dynamics Simulation ; Monte Carlo Method ; Static Electricity
    Language English
    Publishing date 2022-04-29
    Publishing country United States
    Document type Journal Article
    ISSN 1948-7185
    ISSN (online) 1948-7185
    DOI 10.1021/acs.jpclett.2c00544
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  8. Article ; Online: Alkali Metal Dihydropyridines in Transfer Hydrogenation Catalysis of Imines: Amide Basicity versus Hydride Surrogacy.

    Macdonald, Peter A / Banerjee, Sumanta / Kennedy, Alan R / van Teijlingen, Alexander / Robertson, Stuart D / Tuttle, Tell / Mulvey, Robert E

    Angewandte Chemie (International ed. in English)

    2023  Volume 62, Issue 27, Page(s) e202304966

    Abstract: Catalytic reduction of a representative set of imines, both aldimines and ketimines, to amines has been studied using transfer hydrogenation from 1,4-dicyclohexadiene. Unusually, this has been achieved using s-block pre-catalysts, namely 1-metallo-2-tert- ...

    Abstract Catalytic reduction of a representative set of imines, both aldimines and ketimines, to amines has been studied using transfer hydrogenation from 1,4-dicyclohexadiene. Unusually, this has been achieved using s-block pre-catalysts, namely 1-metallo-2-tert-butyl-1,2-dihydropyridines, 2-tBuC
    Language English
    Publishing date 2023-05-22
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2011836-3
    ISSN 1521-3773 ; 1433-7851
    ISSN (online) 1521-3773
    ISSN 1433-7851
    DOI 10.1002/anie.202304966
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  9. Article ; Online: Hydrocarbon Soluble Alkali-Metal-Aluminium Hydride Surrog[ATES].

    Banerjee, Sumanta / Macdonald, Peter A / Orr, Samantha A / Kennedy, Alan R / van Teijlingen, Alexander / Robertson, Stuart D / Tuttle, Tell / Mulvey, Robert E

    Chemistry (Weinheim an der Bergstrasse, Germany)

    2022  Volume 28, Issue 55, Page(s) e202201085

    Abstract: A series of group 1 hydrocarbon-soluble donor free aluminates [AM( ...

    Abstract A series of group 1 hydrocarbon-soluble donor free aluminates [AM(
    Language English
    Publishing date 2022-08-11
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 1478547-X
    ISSN 1521-3765 ; 0947-6539
    ISSN (online) 1521-3765
    ISSN 0947-6539
    DOI 10.1002/chem.202201085
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  10. Article: Artificial Intelligence and Health in Nepal.

    van Teijlingen, Alexander / Tuttle, Tell / Bouchachia, Hamid / Sathian, Brijesh / van Teijlingen, Edwin

    Nepal journal of epidemiology

    2020  Volume 10, Issue 3, Page(s) 915–918

    Abstract: The growth in information technology and computer capacity has opened up opportunities to deal with much and much larger data sets than even a decade ago. There has been a technological revolution of big data and Artificial Intelligence (AI). Perhaps ... ...

    Abstract The growth in information technology and computer capacity has opened up opportunities to deal with much and much larger data sets than even a decade ago. There has been a technological revolution of big data and Artificial Intelligence (AI). Perhaps many readers would immediately think about robotic surgery or self-driving cars, but there is much more to AI. This Short Communication starts with an overview of the key terms, including AI, machine learning, deep learning and Big Data. This Short Communication highlights so developments of AI in health that could benefit a low-income country like Nepal and stresses the need for Nepal's health and education systems to track such developments and apply them locally. Moreover, Nepal needs to start growing its own AI expertise to help develop national or South Asian solutions. This would require investing in local resources such as access to computer power/capacity as well as training young Nepali to work in AI.
    Keywords covid19
    Language English
    Publishing date 2020-09-30
    Publishing country Nepal
    Document type Journal Article
    ZDB-ID 2589539-4
    ISSN 2091-0800
    ISSN 2091-0800
    DOI 10.3126/nje.v10i3.31649
    Database MEDical Literature Analysis and Retrieval System OnLINE

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