Deepmind Technologies Limited

Gdm Holding LLC

Hugo Penedones

Karen Simonyan

James Kirkpatrick

Richard Andrew Evans

Andrew W Senior

Laurent Sifre

Chongli Qin

John Jumper

Ruoxi Sun

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

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Zurich, Switzerland

Hugo Penedones