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The AlphaFold Protein Structure Database (AlphaFold DB, https://alphafold.ebi.ac.uk) is an openly accessible, extensive database of high-accuracy protein-structure predictions. Powered by AlphaFold v2.0 of DeepMind, it has enabled an unprecedented expansion of the structural coverage of the known protein-sequence space. AlphaFold DB provides programmatic access to and interactive visualization of predicted atomic coordinates, per-residue and pairwise model-confidence estimates and predicted aligned errors. The initial release of AlphaFold DB contains over 360,000 predicted structures across 21 model-organism proteomes, which will soon be expanded to cover most of the (over 100 million) representative sequences from the UniRef90 data set.

Abstract. We present an approach to interpret the major surfaces, objects, and support relations of an indoor scene from an RGBD image. Most existing work ignores physical interactions or is applied only to tidy rooms and hallways. Our goal is to parse typical, often messy, indoor scenes into floor, walls, supporting surfaces, and object regions, and to recover support relationships. One of our main interests is to better understand how 3D cues can best inform a structured 3D interpretation. We also contribute a novel integer programming formulation to infer physical support relations. We offer a new dataset of 1449 RGBD images, capturing 464 diverse indoor scenes, with detailed annotations. Our experiments demonstrate our ability to infer support relations in complex scenes and verify that our 3D scene cues and inferred support lead to better object segmentation.

While the vast majority of well-structured single protein chains can now be predicted to high accuracy due to the recent AlphaFold [1] model, the prediction of multi-chain protein complexes remains a challenge in many cases. In this work, we demonstrate that an AlphaFold model trained specifically for multimeric inputs of known stoichiometry, which we call AlphaFold-Multimer, significantly increases accuracy of predicted multimeric interfaces over input-adapted single-chain AlphaFold while maintaining high intra-chain accuracy. On a benchmark dataset of 17 heterodimer proteins without templates (introduced in [2]) we achieve at least medium accuracy (DockQ [3]≥0.49) on 14 targets and high accuracy (DockQ≥0.8) on 6 targets, compared to 9 targets of at least medium accuracy and 4 of high accuracy for the previous state of the art system (an AlphaFold-based system from [2]). We also predict structures for a large dataset of 4,433 recent protein complexes, from which we score all non-redundant interfaces with low template identity. For heteromeric interfaces we successfully predict the interface (DockQ≥0.23) in 67% of cases, and produce high accuracy predictions (DockQ≥0.8) in 23% of cases, an improvement of +25 and +11 percentage points over the flexible linker modification of AlphaFold [4] respectively. For homomeric interfaces we successfully predict the interface in 69% of cases, and produce high accuracy predictions in 34% of cases, an improvement of +5 percentage points in both instances.

Protein structure prediction aims to determine the three-dimensional shape of a protein from its amino acid sequence 1. This problem is of fundamental importance to biology as the structure of a protein largely determines its function 2 but can be hard to determine experimentally. In recent years, considerable progress has been made by leveraging genetic information: analysing the co-variation of homologous sequences can allow one to infer which amino acid residues are in contact, which in turn can aid structure prediction 3. In this work, we show that we can train a neural network to accurately predict the distances between pairs of residues in a protein which convey more about structure than contact predictions. With this information we construct a potential of mean force 4 that can accurately describe the shape of a protein. We find that the resulting potential can be optimised by a simple gradient descent algorithm, to realise structures without the need for complex sampling procedures. The resulting system, named AlphaFold, has been shown to achieve high accuracy, even for sequences with relatively few homologous sequences. In the most recent Critical Assessment of Protein Structure Prediction 5 (CASP13), a blind assessment of the state of the field of protein structure prediction, AlphaFold created high-accuracy structures (with TM-scores † of 0.7 or higher) for 24 out of 43 free modelling domains whereas the next best method, using sampling and contact information, achieved such accuracy for only 14 out of 43 domains. AlphaFold represents a significant advance in protein structure prediction. We expect the increased accuracy of structure predictions for proteins to enable insights in understanding the function and malfunction of these proteins, especially in cases where no homologous proteins have been experimentally determined 7. Proteins are at the core of most biological processes. Since the function of a protein is dependent on its structure, understanding protein structure has been a grand challenge in biology for decades. While several experimental structure determination techniques have been developed † Template Modelling score 6 , between 0 and 1, measures the degree of match of the overall (backbone) shape of a proposed structure to a native structure.

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Figure 1: Example output from our system, generated in real-time with a handheld Kinect depth camera and no other sensing infrastructure. Normal maps (colour) and Phong-shaded renderings (greyscale) from our dense reconstruction system are shown. On the left for comparison is an example of the live, incomplete, and noisy data from the Kinect sensor (used as input to our system). ABSTRACTWe present a system for accurate real-time mapping of complex and arbitrary indoor scenes in variable lighting conditions, using only a moving low-cost depth camera and commodity graphics hardware. We fuse all of the depth data streamed from a Kinect sensor into a single global implicit surface model of the observed scene in real-time. The current sensor pose is simultaneously obtained by tracking the live depth frame relative to the global model using a coarse-to-fine iterative closest point (ICP) algorithm, which uses all of the observed depth data available. We demonstrate the advantages of tracking against the growing full surface model compared with frame-to-frame tracking, obtaining tracking and mapping results in constant time within room sized scenes with limited drift and high accuracy. We also show both qualitative and quantitative results relating to various aspects of our tracking and mapping system. Modelling of natural scenes, in real-time with only commodity sensor and GPU hardware, promises an exciting step forward in augmented reality (AR), in particular, it allows dense surfaces to be reconstructed in real-time, with a level of detail and robustness beyond any solution yet presented using passive computer vision.

How noncoding DNA determines gene expression in different cell types is a major unsolved problem, and critical downstream applications in human genetics depend on improved solutions. Here, we report substantially improved gene expression prediction accuracy from DNA sequences through the use of a deep learning architecture, called Enformer, that is able to integrate information from long-range interactions (up to 100 kb away) in the genome. This improvement yielded more accurate variant effect predictions on gene expression for both natural genetic variants and saturation mutagenesis measured by massively parallel reporter assays. Furthermore, Enformer learned to predict enhancer–promoter interactions directly from the DNA sequence competitively with methods that take direct experimental data as input. We expect that these advances will enable more effective fine-mapping of human disease associations and provide a framework to interpret cis-regulatory evolution.