Volume 17 Issue 2, February 2020

Volume 17 Issue 2

Protein interaction fingerprinting using deep learning

An artistic representation of molecular surface interaction fingerprinting (MaSIF). Information flows in living systems, such as when proteins interact with each other. The watercolor medium expresses that flow, which is further highlighted by the neural network, identifying their connection.

See Gainza et al.

Image: Laura Persat, Lausanne, Switzerland. Cover design: Erin Dewalt

Editorial

  • Editorial |

    This month, we take a look back on the first year of the online Springer Nature Protocols and Methods Community.

This Month

  • This Month |

    A love of math and biology comes together with a SPARK.

    • Vivien Marx

Correspondence

Research Highlights

Technology Feature

Perspectives

  • Perspective |

    This Perspective highlights open-source software for single-cell analysis released as part of the Bioconductor project, providing an overview for users and developers.

    • Robert A. Amezquita
    • , Aaron T. L. Lun
    • , Etienne Becht
    • , Vince J. Carey
    • , Lindsay N. Carpp
    • , Ludwig Geistlinger
    • , Federico Marini
    • , Kevin Rue-Albrecht
    • , Davide Risso
    • , Charlotte Soneson
    • , Levi Waldron
    • , Hervé Pagès
    • , Mike L. Smith
    • , Wolfgang Huber
    • , Martin Morgan
    • , Raphael Gottardo
    •  & Stephanie C. Hicks

Analysis

Brief Communications

  • Brief Communication |

    Wtdbg2 assembles genomes with comparable contiguity and accuracy to existing tools using long-read sequencing data, and is several times faster, especially for large genomes.

    • Jue Ruan
    •  & Heng Li
  • Brief Communication |

    An adaptive excitation source enables two- and three-photon imaging of the awake mouse brain with high spatial and temporal resolution at 30-fold-reduced laser power relative to conventional approaches.

    • Bo Li
    • , Chunyan Wu
    • , Mengran Wang
    • , Kriti Charan
    •  & Chris Xu

Articles

  • Article |

    An optogenetic strategy enables selection of proteases with improved catalytic rates. The developed TEV protease variants are well suited for biotechnology applications, including FLARE assays with substantially improved temporal resolution.

    • Mateo I. Sanchez
    •  & Alice Y. Ting
  • Article |

    The unique advantages of single-particle cryo-electron microscopy and cryo-electron tomography are combined in a method called TYGRESS, here applied to determine the structure of the intact ciliary axoneme at a resolution of 12 Å.

    • Kangkang Song
    • , Zhiguo Shang
    • , Xiaofeng Fu
    • , Xiaochu Lou
    • , Nikolaus Grigorieff
    •  & Daniela Nicastro
  • Article |

    Advances in MINFLUX nanoscopy enable multicolor imaging over large fields of view, bringing true nanometer-scale fluorescence imaging to labeled structures in fixed and living cells.

    • Klaus C. Gwosch
    • , Jasmin K. Pape
    • , Francisco Balzarotti
    • , Philipp Hoess
    • , Jan Ellenberg
    • , Jonas Ries
    •  & Stefan W. Hell
  • Article |

    4Pi single-molecule switching microscopy combined with ‘salvaged fluorescence’ enables improved ratiometric imaging that bypasses chromatic aberrations and allows for multicolor whole-cell imaging with sub-10-nm localization precision.

    • Yongdeng Zhang
    • , Lena K. Schroeder
    • , Mark D. Lessard
    • , Phylicia Kidd
    • , Jeeyun Chung
    • , Yuanbin Song
    • , Lorena Benedetti
    • , Yiming Li
    • , Jonas Ries
    • , Jonathan B. Grimm
    • , Luke D. Lavis
    • , Pietro De Camilli
    • , James E. Rothman
    • , David Baddeley
    •  & Joerg Bewersdorf
  • Article |

    A new method of autophagy measurement is based on the detection of phospho-ATG16L1, a conserved early marker of autophagy. Sensitive detection can be achieved in multiple biological systems and assays with advantages over standard methods.

    • Wensheng Tian
    • , Reham Alsaadi
    • , Zhihao Guo
    • , Alena Kalinina
    • , Micaël Carrier
    • , Marie-Eve Tremblay
    • , Baptiste Lacoste
    • , Diane Lagace
    •  & Ryan C. Russell

Amendments & Corrections