Efficient GPU computation of large protein Solvent-Excluded Surface.

The Solvent-Excluded Surface (SES) is an essential representation of molecules which is massively used in molecular modeling and drug discovery since it represents the interacting surface between molecules. Based on its properties, it supports the visualization of both large scale shapes and details of molecules. While several methods targeted its computation, the ability to process large molecular structures to address the introduction of big complex analysis while leveraging the massively parallel architecture of GPUs has remained a challenge. This is mostly caused by the need for consequent memory allocation or by the complexity of the parallelization of its processing. In this paper, we leverage the last theoretical advances made for the depiction of the SES to provide fast analytical computation with low impact on memory. We show that our method is able to compute the complete surface while handling large molecular complexes with competitive computation time costs compared to previous works.

UDock2: interactive real-time multi-body protein-protein docking software.

MOTIVATION: Protein-protein docking aims at predicting the geometry of protein interactions to gain insights into the mechanisms underlying these processes and develop new strategies for drug discovery. Interactive and user-oriented manipulation tools can support this task complementary to automated software. RESULTS: This article presents an interactive multi-body protein-protein docking software, UDock2, designed for research but also usable for teaching and popularization of science purposes due to its high usability. In UDock2, the users tackle the conformational space of protein interfaces using an intuitive real-time docking procedure with on-the-fly scoring. UDock2 integrates traditional computer graphics methods to facilitate the visualization and to provide better insight into protein surfaces, interfaces, and properties. AVAILABILITY AND IMPLEMENTATION: UDock2 is open-source, cross-platform (Windows and Linux), and available at http://udock.fr. The code can be accessed at https://gitlab.com/Udock/Udock2.

CovCopCan: An efficient tool to detect Copy Number Variation from amplicon sequencing data in inherited diseases and cancer.

Molecular diagnosis is an essential step of patient care. An increasing number of Copy Number Variations (CNVs) have been identified that are involved in inherited and somatic diseases. However, there are few existing tools to identify them among amplicon sequencing data generated by Next Generation Sequencing (NGS). We present here a new tool, CovCopCan, that allows the rapid and easy detection of CNVs in inherited diseases, as well as somatic data of patients with cancer, even with a low ratio of cancer cells to healthy cells. This tool could be very useful for molecular geneticists to rapidly identify CNVs in an interactive and user-friendly way.

Urban Weathering: Interactive Rendering of Polluted Cities.

Weathering effects are ubiquitous phenomena in cities. Buildings age and deteriorate over time as they interact with the environment. Pollution accumulating on facades is a particularly visible consequence of this. Even though relevant work has been done to produce impressive images of virtual urban environments including weathering effects, so far, no technique using a global approach has been proposed to deal with weathering effects. Here, we propose a technique based on a fast physically-inspired approach, that focuses on modeling the changes in appearance due to pollution soiling on an urban scale. We consider pollution effects to depend on three main factors: wind, rain and sun exposure, and we take into account three intervening steps: deposition, reaction and washing. Using a low-cost pre-computation, we evaluate the pollution distribution throughout the city. Based on this and the use of screen-space operators, our method results in an efficient approach able to generate realistic images of urban scenes by combining the intervening factors at interactive rates. In addition, the pre-computation demands a reduced amount of memory to store the resulting pollution map and, as it is independent from scene complexity, it can suit large and complex models by adapting the map resolution.

Simulating how salt decay ages buildings.

Salt-based aging plays an important part in the realism of scenes featuring stone structures and monuments. A proposed model, based on physical behaviors and principles, replaces the simulation of complex physical formulations with ad hoc algorithms. It leads to plausible results, ultimately helping designers create aging patterns on affected objects.