Related papers: Ten Simple Rules for Creating Biomolecular Graphic…
Image and shape editing are ubiquitous among digital artworks. Graphics algorithms facilitate artists and designers to achieve desired editing intents without going through manually tedious retouching. In the recent advance of machine…
This paper describes an ongoing multi-scale visual analytics approach for exploring and analyzing biomedical knowledge at scale.We utilize global and local views, hierarchical and flow-based graph layouts, multi-faceted search, neighborhood…
Recently, machine learning (ML) has established itself in various worldwide benchmarking competitions in computational biology, including Critical Assessment of Structure Prediction (CASP) and Drug Design Data Resource (D3R) Grand…
3D spatial graphs play a crucial role in biological and clinical research by modeling anatomical networks such as blood vessels,neurons, and airways. However, generating 3D biological graphs while maintaining anatomical validity remains…
Polymers are widely-studied materials with diverse properties and applications determined by different molecular structures. It is essential to represent these structures clearly and explore the full space of achievable chemical designs.…
Accurate physical modeling with 3D-printing techniques could lead to new approaches to study structure and dynamics of biological systems complementing computational methods. Computational biology has become an important part of research…
Mathematical methods provide useful framework for the analysis and design of complex systems. In newer contexts such as biology, however, there is a need to both adapt existing methods as well as to develop new ones. Using a combination of…
Searching new molecules in areas like drug discovery often starts from the core structures of candidate molecules to optimize the properties of interest. The way as such has called for a strategy of designing molecules retaining a…
The full understanding of cellular functions requires information about protein numbers for various biomolecular assemblies and their dynamics, which can be partly accessed by super-resolution fluorescence microscopy. Yet, many protein…
The distances over which biological molecules and their complexes can function range from a few nanometres, in the case of folded structures, to millimetres, for example during chromosome organization. Describing phenomena that cover such…
One approach to studying the system-wide organization of biochemistry is to use statistical graph theory. Even in such a heavily simplified method, which disregards most of the dynamic aspects of biochemistry, one is faced with fundamental…
Binding and unbinding of ligands to specific sites of a macromolecule are one of the most elementary molecular interactions inside the cell that embody the computational processes of biological regulations. The interaction between…
Despite their ability to understand chemical knowledge, large language models (LLMs) remain limited in their capacity to propose novel molecules with desired functions (e.g., drug-like properties). In addition, the molecules that LLMs…
We introduce RuleVis, a web-based application for defining and editing "correct-by-construction" executable rules that model biochemical functionality, which can be used to simulate the behavior of protein-protein interaction networks and…
Multiparticle systems on complicated metric graphs might have many applications in physics, biology and social life. But the corresponding science still does not exist. Here we start it with simplest examples where there is quadratic…
We present a method for producing documentary-style content using real-time scientific visualization. We produce molecumentaries, i.e., molecular documentaries featuring structural models from molecular biology. We employ scalable methods…
AI models for drug discovery and chemical literature mining must interpret molecular images and generate outputs consistent with 3D geometry and stereochemistry. Most molecular language models rely on strings or graphs, while…
The near-infinite chemical diversity of natural and artificial macromolecules arises from the vast range of possible component monomers, linkages, and polymers topologies. This enormous variety contributes to the ubiquity and…
With the technology development, the need of analyze and extraction of useful information is increasing. Bayesian networks contain knowledge from data and experts that could be used for decision making processes But they are not easily…
A biological circuit is a neural or biochemical cascade, taking inputs and producing outputs. How have biological circuits learned to solve environmental challenges over the history of life? The answer certainly follows Dobzhansky's famous…