PDBench: evaluating computational methods for protein-sequence design.

SUMMARY: Ever increasing amounts of protein structure data, combined with advances in machine learning, have led to the rapid proliferation of methods available for protein-sequence design. In order to utilize a design method effectively, it is important to understand the nuances of its performance and how it varies by design target. Here, we present PDBench, a set of proteins and a number of standard tests for assessing the performance of sequence-design methods. PDBench aims to maximize the structural diversity of the benchmark, compared with previous benchmarking sets, in order to provide useful biological insight into the behaviour of sequence-design methods, which is essential for evaluating their performance and practical utility. We believe that these tools are useful for guiding the development of novel sequence design algorithms and will enable users to choose a method that best suits their design target. AVAILABILITY AND IMPLEMENTATION: https://github.com/wells-wood-research/PDBench. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

TIMED-Design: flexible and accessible protein sequence design with convolutional neural networks.

Sequence design is a crucial step in the process of designing or engineering proteins. Traditionally, physics-based methods have been used to solve for optimal sequences, with the main disadvantages being that they are computationally intensive for the end user. Deep learning-based methods offer an attractive alternative, outperforming physics-based methods at a significantly lower computational cost. In this paper, we explore the application of Convolutional Neural Networks (CNNs) for sequence design. We describe the development and benchmarking of a range of networks, as well as reimplementations of previously described CNNs. We demonstrate the flexibility of representing proteins in a three-dimensional voxel grid by encoding additional design constraints into the input data. Finally, we describe TIMED-Design, a web application and command line tool for exploring and applying the models described in this paper. The user interface will be available at the URL: https://pragmaticproteindesign.bio.ed.ac.uk/timed. The source code for TIMED-Design is available at https://github.com/wells-wood-research/timed-design.

Widening Viewing Angles of Automultiscopic Displays Using Refractive Inserts.

Displays that can portray environments that are perceivable from multiple views are known as multiscopic displays. Some multiscopic displays enable realistic perception of 3D environments without the need for cumbersome mounts or fragile head-tracking algorithms. These automultiscopic displays carefully control the distribution of emitted light over space, direction (angle) and time so that even a static image displayed can encode parallax across viewing directions (Iightfield). This allows simultaneous observation by multiple viewers, each perceiving 3D from their own (correct) perspective. Currently, the illusion can only be effectively maintained over a narrow range of viewing angles. In this paper, we propose and analyze a simple solution to widen the range of viewing angles for automultiscopic displays that use parallax barriers. We propose the use of a refractive medium, with a high refractive index, between the display and parallax barriers. The inserted medium warps the exitant lightfield in a way that increases the potential viewing angle. We analyze the consequences of this warp and build a prototype with a 93% increase in the effective viewing angle.

Interactive rendering of acquired materials on dynamic geometry using frequency analysis.

Shading acquired materials with high-frequency illumination is computationally expensive. Estimating the shading integral requires multiple samples of the incident illumination. The number of samples required may vary across the image, and the image itself may have high- and low-frequency variations, depending on a combination of several factors. Adaptively distributing computational budget across the pixels for shading is a challenging problem. In this paper, we depict complex materials such as acquired reflectances, interactively, without any precomputation based on geometry. In each frame, we first estimate the frequencies in the local light field arriving at each pixel, as well as the variance of the shading integrand. Our frequency analysis accounts for combinations of a variety of factors: the reflectance of the object projecting to the pixel, the nature of the illumination, the local geometry and the camera position relative to the geometry and lighting. We then exploit this frequency information (bandwidth and variance) to adaptively sample for reconstruction and integration. For example, fewer pixels per unit area are shaded for pixels projecting onto diffuse objects, and fewer samples are used for integrating illumination incident on specular objects.

Real-time rendering of rough refraction.

We present an algorithm to render objects made of transparent materials with rough surfaces in real-time, under all-frequency distant illumination. Rough surfaces cause wide scattering as light enters and exits objects, which significantly complicates the rendering of such materials. We present two contributions to approximate the successive scattering events at interfaces, due to rough refraction: First, an approximation of the Bidirectional Transmittance Distribution Function (BTDF), using spherical Gaussians, suitable for real-time estimation of environment lighting using preconvolution; second, a combination of cone tracing and macrogeometry filtering to efficiently integrate the scattered rays at the exiting interface of the object. We demonstrate the quality of our approximation by comparison against stochastic ray tracing. Furthermore we propose two extensions to our method for supporting spatially varying roughness on object surfaces and local lighting for thin objects.