Related papers: Bioblox 2.5D -- Developing an Educational Game Bas…
This work introduces GeoDirDock (GDD), a novel approach to molecular docking that enhances the accuracy and physical plausibility of ligand docking predictions. GDD guides the denoising process of a diffusion model along geodesic paths…
Get 'em Moles! is a single-player educational game inspired by the classic arcade game Whac-A-Mole. Primarily designed for touchscreen devices, Get 'em Moles! aims to teach English spelling and pronunciation through engaging game play. This…
This paper focuses on procedurally generating rules and communicating them to players to adjust the difficulty. This is part of a larger project to collect and adapt games in educational games for young children using a digital puzzle game…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
Most widely used ligand docking methods assume a rigid protein structure. This leads to problems when the structure of the target protein deforms upon ligand binding. In particular, the ligand's true binding pose is often scored very…
Games have always been a popular test bed for artificial intelligence techniques. Game developers are always in constant search for techniques that can automatically create computer games minimizing the developer's task. In this work we…
A long-standing goal of machine-learning-based protein engineering is to accelerate the discovery of novel mutations that improve the function of a known protein. We introduce a sampling framework for evolving proteins in silico that…
This paper presents a game based on storytelling, in which the players are faced with ethical dilemmas related to software engineering specific issues. The players' choices have consequences on how the story unfolds and could lead to…
Machine learning shows great potential in virtual screening for drug discovery. Current efforts on accelerating docking-based virtual screening do not consider using existing data of other previously developed targets. To make use of the…
Protein (receptor)--ligand interaction prediction is a critical component in computer-aided drug design, significantly influencing molecular docking and virtual screening processes. Despite the development of numerous scoring functions in…
Molecular docking is a core tool in drug discovery for predicting ligand-target interactions. Despite the availability of diverse search-based and machine learning approaches, no single docking algorithm consistently dominates, as…
The ultimate goal of drug design is to find novel compounds with desirable pharmacological properties. Designing molecules retaining particular scaffolds as the core structures of the molecules is one of the efficient ways to obtain…
Drug discovery projects entail cycles of design, synthesis, and testing that yield a series of chemically related small molecules whose properties, such as binding affinity to a given target protein, are progressively tailored to a…
We present initial research towards procedural generation of Simplified Boardgames and translating them into an efficient GDL code. This is a step towards establishing Simplified Boardgames as a comparison class for General Game Playing…
Introduction: This multi-disciplinary case study details how an interactive decision support tool leverages game design to inform an international plastic pollution treaty. Design: Seeking to make our scientific findings more usable within…
Protein-ligand scoring is a central component of structure-based drug design, underpinning molecular docking, virtual screening, and pose optimization. Conventional physics-based energy functions are often computationally expensive,…
Accurate blind docking has the potential to lead to new biological breakthroughs, but for this promise to be realized, docking methods must generalize well across the proteome. Existing benchmarks, however, fail to rigorously assess…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
Distillation attacks create a deployment trade-off for model providers: the same outputs that make a model more useful can also make it easier to imitate. We study this trade-off through a minimax game between a utility-constrained teacher…
Motivation: Ab initio protein docking represents a major challenge for optimizing a noisy and costly "black box"-like function in a high-dimensional space. Despite progress in this field, there is no docking method available for rigorous…