相关论文: Bioblox 2.5D -- Developing an Educational Game Bas…
Learning to program has become common in schools, higher education and individual learning. Although testing is an important aspect of programming, it is often neglected in education due to a perceived lack of time and knowledge, or simply…
Despite the large corpus of biology training text, the impact of reasoning models on biological research generally lags behind math and coding. In this work, we show that biology questions from current large-scale reasoning datasets do not…
This paper describes the development needed to support the functional and teaching requirements of iRead, a 4-year EU-funded project which produced an award-winning serious game utilising lexical and syntactical game content. The main…
Numerous cellular functions rely on protein$\unicode{x2013}$protein interactions. Efforts to comprehensively characterize them remain challenged however by the diversity of molecular recognition mechanisms employed within the proteome. Deep…
The process of screening molecules for desirable properties is a key step in several applications, ranging from drug discovery to material design. During the process of drug discovery specifically, protein-ligand docking, or chemical…
Computational methods for predicting and designing biomolecular structures are increasingly powerful. While previous approaches relied on physics-based modeling, modern tools, such as AlphaFold2 in CASP14, leverage artificial intelligence…
Can outreach inspire and lead to research and vice versa? In this work, we introduce our approach to the gamification of research in mathematics and computer science through three illustrative examples. We discuss our primary motivations…
Structure-based drug design (SBDD) aims to generate 3D ligand molecules that bind to specific protein targets. Existing 3D deep generative models including diffusion models have shown great promise for SBDD. However, it is complex to…
MiBoard (Multiplayer Interactive Board Game) is an online, turnbased board game that was developed to assess the integration of game characteristics (point rewards, game-like interaction, and peer feedback) and how that might affect student…
The cornerstone of computational drug design is the calculation of binding affinity between two biological counterparts, especially a chemical compound, i.e., a ligand, and a protein. Predicting the strength of protein-ligand binding with…
Players of coevolutionary games may update not only their strategies but also their networks of interaction. Based on interpreting the payoff of players as fitness, dynamic landscape models are proposed. The modeling procedure is carried…
Phishing continues to be a difficult problem for individuals and organisations. Educational games and simulations have been increasingly acknowledged as enormous and powerful teaching tools, yet little work has examined how to engage users…
Deep generative models are rapidly advancing structure-based drug design, offering substantial promise for generating small molecule ligands that bind to specific protein targets. However, most current approaches assume a rigid protein…
Molecular docking is a central method in the computer-based screening of compound libraries as a part of the rational approach to drug design. Although the method has proved its competence in predicting binding modes correctly, its inherent…
Search and recommendation ecosystems exhibit competition among content creators. This competition has been tackled in a variety of game-theoretic frameworks. Content creators generate documents with the aim of being recommended by a content…
Accurately predicting the binding conformation of small-molecule ligands to protein targets is a critical step in rational drug design. Although recent deep learning-based docking surpasses traditional methods in speed and accuracy, many…
Deep Learning (DL) algorithms hold great promise for applications in the field of computational biophysics. In fact, the vast amount of available molecular structures, as well as their notable complexity, constitutes an ideal context in…
Developing complex biomolecular workflows is not always straightforward. It requires tedious developments to enable the interoperability between the different biomolecular simulation and analysis tools. Moreover, the need to execute the…
Evolutionary game dynamics are often studied in the context of different population structures. Here we propose a new population structure that is inspired by simple multicellular life forms. In our model, cells reproduce but can stay…
This document describes the development of a video game prototype designed to encourage physical activity among children and older adults. The prototype consists of a laptop, a camera with 3D sensors, and optionally requires an LCD screen…