Deepmind Technologies Limited

Gdm Holding LLC

John Jumper

Richard Andrew Evans

Andrew W Senior

Ruoxi Sun

Hugo Penedones

Karen Simonyan

James Kirkpatrick

Laurent Sifre

Chongli Qin

Alexander Pritzel

Stephan Gouws

Timothy Frederick Goldie Green

Mikhail Figurnov

Russell James Bates

Alexander Bridgland

Methods, systems, and apparatus, including computer programs encoded on a computer storage medium, for performing protein structure prediction. In one aspect, a method comprises, at each of one or more iterations: determining an alternative predicted structure of a given protein defined by alternative values of structure parameters; processing, using a geometry neural network, a network input comprising: (i) a representation of a sequence of amino acid residues in the given protein, and (ii) the alternative values of the structure parameters, to generate an output characterizing an alternative geometry score that is an estimate of a similarity measure between the alternative predicted structure and the actual structure of the given protein.

Predicting protein structures using geometry neural networks that estimate similarity between predicted protein structures and actual protein structures

Methods, systems, and apparatus, including computer programs encoded on a computer storage medium, for performing protein structure prediction. In one aspect, a method comprises generating a distance map for a given protein, wherein the given protein is defined by a sequence of amino acid residues arranged in a structure, wherein the distance map characterizes estimated distances between the amino acid residues in the structure, comprising: generating a plurality of distance map crops, wherein each distance map crop characterizes estimated distances between (i) amino acid residues in each of one or more respective first positions in the sequence and (ii) amino acid residues in each of one or more respective second positions in the sequence in the structure of the protein, wherein the first positions are a proper subset of the sequence; and generating the distance map for the given protein using the plurality of distance map crops.

Determining protein distance maps by combining distance maps crops

Methods, systems, and apparatus, including computer programs encoded on a computer storage medium, for determining a predicted structure of a protein that is specified by an amino acid sequence. In one aspect, a method comprises: obtaining an initial embedding and initial values of structure parameters for each amino acid in the amino acid sequence, wherein the structure parameters for each amino acid comprise location parameters that specify a predicted three-dimensional spatial location of the amino acid in the structure of the protein; and processing a network input comprising the initial embedding and the initial values of the structure parameters for each amino acid in the amino acid sequence using a folding neural network to generate a network output comprising final values of the structure parameters for each amino acid in the amino acid sequence.

Protein structure prediction using geometric attention neural networks

Methods, systems, and apparatus, including computer programs encoded on a computer storage medium, for determining a predicted structure of a protein that is specified by an amino acid sequence. In one aspect, a method comprises: obtaining a multiple sequence alignment for the protein; determining, from the multiple sequence alignment and for each pair of amino acids in the amino acid sequence of the protein, a respective initial embedding of the pair of amino acids; processing the initial embeddings of the pairs of amino acids using a pair embedding neural network comprising a plurality of self-attention neural network layers to generate a final embedding of each pair of amino acids; and determining the predicted structure of the protein based on the final embedding of each pair of amino acids.

Protein structure prediction from amino acid sequences using self-attention neural networks

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John Jumper