Protein function predictions

Protein function predictions are bioinformatic methods (i.e. involving computation using software) that aim to predict the function of a protein. Protein function analyses use protein sequences and structures as inputs into software that generates experimentally testable predictions of function.

Latest Research and Reviews

News and Comment

  • News & Views |

    Constraining metabolic models by enzyme capacities greatly improves genotype–phenotype predictions. Now, a method for estimating enzyme turnovers based on deep learning has been developed and used to reconstruct enzyme-constrained genome-scale metabolic models for more than 300 yeast species.

    • Veda Sheersh Boorla
    • , Vikas Upadhyay
    •  & Costas D. Maranas
    Nature Catalysis 5, 655-657
  • News & Views |

    Determining the functional properties of a protein from its structure is challenging. This study presents an interpretable deep learning model that directly learns function-bearing structural motifs from raw data, allowing accurate mapping of protein binding sites and antibody epitopes onto a protein structure.

    Nature Methods 19, 660-661
  • Comments & Opinion |

    The splendid computational success of AlphaFold and RoseTTAFold in solving the 60-year-old problem of protein folding raises an obvious question: what new avenues should structural biology explore? We propose a strong pivot toward the goal of reading mechanism and function directly from the amino acid sequence. This ambitious goal will require new data analytical tools and an extensive database of the atomic-level structural trajectories traced out on energy landscapes as proteins perform their function.

    • Abbas Ourmazd
    • , Keith Moffat
    •  & Eaton Edward Lattman
    Nature Methods 19, 24-26
  • News & Views |

    Newly sequenced organisms present a challenge for protein function prediction, as they lack experimental characterisation. A network-propagation approach that integrates functional network relationships with protein annotations, transferred from well-studied organisms, produces a more complete picture of the possible protein functions.

    • Yingying Zhang
    • , Shayne D. Wierbowski
    •  & Haiyuan Yu