Molecular modelling articles within Nature

Featured

  • Article |

    A computational model generates conformational ensembles of 28,058 intrinsically disordered proteins and regions (IDRs) in the human proteome and sheds light on the relationship between sequence, conformational properties and functions of IDRs.

    • Giulio Tesei
    • , Anna Ida Trolle
    •  & Kresten Lindorff-Larsen

  • Article
    | Open Access

    A protein interaction network constructed with data from high-throughput affinity enrichment coupled to mass spectrometry provides a highly saturated yeast interactome with 31,004 interactions, including low-abundance complexes, membrane protein complexes and non-taggable protein complexes.

    • André C. Michaelis
    • , Andreas-David Brunner
    •  & Matthias Mann

  • Article
    | Open Access

    The extent to which the AlphaFold database has structurally illuminated proteins that are challenging to annotate for function or putative biological role using standard homology-based approaches at high predicted accuracy is investigated.

    • Janani Durairaj
    • , Andrew M. Waterhouse
    •  & Joana Pereira

  • Article |

    Integrative structural biology combining quantitative live imaging, cryo-correlative microscopy, subtomogram averaging and molecular modelling enables in situ determination of the structure of the endoplasmic reticulum–mitochondria encounter complex in yeast.

    • Michael R. Wozny
    • , Andrea Di Luca
    •  & Wanda Kukulski

  • Article
    | Open Access

    Single-molecule calibrated live microscopy and computational modelling have revealed that human nuclear pore complex assembly takes different pathways during the exit from mitosis and during nuclear growth in interphase.

    • Shotaro Otsuka
    • , Jeremy O. B. Tempkin
    •  & Jan Ellenberg

  • Article |

    V-SYNTHES, a scalable and computationally cost-effective synthon-based approach to compound screening, identified compounds with a high affinity for CB2 and CB1 in a hierarchical structure-based screen of more than 11 billion compounds.

    • Arman A. Sadybekov
    • , Anastasiia V. Sadybekov
    •  & Vsevolod Katritch

  • Letter |

    Proteins designed de novo by players of the online protein-folding game Foldit can be expressed in Escherichia coli and adopt the designed structure in solution.

    • Brian Koepnick
    • , Jeff Flatten
    •  & David Baker

  • Article |

    The structure of a complex containing calcitonin gene-related peptide, the human calcitonin gene-related peptide receptor and the Gs heterotrimer, determined using Volta phase-plate cryo-electron microscopy, provides structural insight into the regulation of G-protein-coupled receptors by receptor activity modifying protein 1.

    • Yi-Lynn Liang
    • , Maryam Khoshouei
    •  & Patrick M. Sexton

  • Article |

    The structure of the yeast nuclear pore complex, determined at sub-nanometre precision using an integrative approach that combines a wide range of data, reveals details of its architecture, transport mechanism and evolutionary origins.

    • Seung Joong Kim
    • , Javier Fernandez-Martinez
    •  & Michael P. Rout

  • Letter |

    Some peptoids—synthetic structural relatives of polypeptides—can assemble into two-dimensional nanometre-scale sheets; simulations and experimental measurements show that these nanosheets contain a motif unique to peptoids, namely zigzag Σ-strands, which interlock and enable the nanosheets to extend in two dimensions only.

    • Ranjan V. Mannige
    • , Thomas K. Haxton
    •  & Stephen Whitelam

  • Article |

    The cryo-electron microscopy structure of the eukaryotic initiation factor 3 (eIF3) within the larger 43S complex is determined; the improved resolution enables visualization of the secondary structures of the subunits, as well as the contacts between eIF3 and both eIF2 and DHX29.

    • Amedee des Georges
    • , Vidya Dhote
    •  & Yaser Hashem

  • Letter |

    A method, termed hiCLIP, has been developed to determine the RNA duplexes bound by RNA-binding proteins, revealing an unforeseen prevalence of long-range duplexes in 3′ untranslated regions (UTRs), and a decreased incidence of SNPs in duplex-forming regions; the results also show that RNA structure is able to regulate gene expression.

    • Yoichiro Sugimoto
    • , Alessandra Vigilante
    •  & Jernej Ule

  • Letter |

    A set of parameters based on the response of a molecule’s properties to infrared vibrations can be used to model and predict selectivity trends for molecular reactions with interlinked steric and electronic effects at positions of interest

    • Anat Milo
    • , Elizabeth N. Bess
    •  & Matthew S. Sigman

  • Letter |

    The HIV virion has a cone-shaped core composed of capsid proteins, which take either pentameric or hexameric form. The crystal structure of the capsid hexamer had been solved previously. Now the structure of the pentamer is provided, which allows the proposal of the first atomic-level model of the mature HIV capsid.

    • Owen Pornillos
    • , Barbie K. Ganser-Pornillos
    •  & Mark Yeager

  • Column |

    Is Bill Gates's decision to invest in software company Schrödinger an early sign of a new computer-aided era for drug design, asks Derek Lowe. Or is it just another small step on what's been a rather lengthy journey?

    • Derek Lowe

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