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Computational methods that operate on three-dimensional molecular structure have the potential to solve important questions in biology and chemistry. In particular, deep neural networks have gained significant attention, but their…
One-dimensional nuclear magnetic resonance (NMR) spectroscopy is essential for molecular structure elucidation in organic synthesis, drug discovery, natural product characterization, and metabolomics, yet its interpretation remains heavily…
The complexity of biological systems and processes, spanning molecular to macroscopic scales, necessitates the use of multiscale simulations to get a comprehensive understanding. Quantum mechanics/molecular mechanics (QM/MM) molecular…
The European Materials and Modelling Ontology (EMMO) is a top-level ontology designed by the European Materials Modelling Council to facilitate semantic interoperability between platforms, models, and tools in computational molecular…
Cryo-electron microscopy (cryo-EM) is a powerful technique in structural biology and drug discovery, enabling the study of biomolecules at high resolution. Significant advancements by structural biologists using cryo-EM have led to the…
Deep learning has become a powerful tool in computational biology, revolutionising the analysis and interpretation of biological data over time. In our article review, we delve into various aspects of deep learning in computational biology.…
Foundation models hold significant promise in healthcare, given their capacity to extract meaningful representations independent of downstream tasks. This property has enabled state-of-the-art performance across several clinical…
In recent years, an abundance of new molecular structures have been elucidated using cryo-electron microscopy (cryo-EM), largely due to advances in hardware technology and data processing techniques. Owing to these new exciting…
The rapid scaling of large computational models has led to a critical increase in energy and compute costs. Inspired by biological systems where structure and function emerge from low-energy configurations, we introduce StructuredDNA, a…
The rapid growth in biological sequence data is revolutionizing our understanding of genotypic diversity and challenging conventional approaches to informatics. With the increasing availability of genomic data, traditional bioinformatic…
Biological neural networks (BNNs) have been established as a powerful and adaptive substrate that offer the potential for incredibly energy and data efficient information processing with distinct learning mechanisms. Yet a core challenge to…
Microbial identification is a central issue in microbiology, in particular in the fields of infectious diseases diagnosis and industrial quality control. The concept of species is tightly linked to the concept of biological and clinical…
Protein complexes are macromolecules essential to the functioning and well-being of all living organisms. As the structure of a protein complex, in particular its region of interaction between multiple protein subunits (i.e., chains), has a…
This paper presents the principal challenges and opportunities associated with computational biomechanics research. The underlying cognitive control involved in the process of human motion is inherently complex, dynamic, multidimensional,…
Spectroscopic techniques are essential tools for determining the structure of molecules. Different spectroscopic techniques, such as Nuclear magnetic resonance (NMR), Infrared spectroscopy, and Mass Spectrometry, provide insight into the…
Applying machine learning to biological sequences - DNA, RNA and protein - has enormous potential to advance human health, environmental sustainability, and fundamental biological understanding. However, many existing machine learning…
Real-time monitoring of various structural behaviors, particularly displacement and acceleration, serves important and valuable information for people; for example, they can be used for active control or damage warning. With recent…
Disordered proteins and nucleic acids play key roles in cellular function and disease. Here we review recent advances in the computational exploration of the conformational dynamics of flexible biomolecules. We focus on hierarchical chain…
This review article provides an overview of structurally oriented experimental datasets that can be used to benchmark protein force fields, focusing on data generated by nuclear magnetic resonance (NMR) spectroscopy and room temperature…
Super-Resolution Microscopy (SRM) is emerging as a powerful and innovative tool for imaging, characterizing, and understanding the structure of Extracellular Vesicles (EVs). By addressing the need for single-particle analysis with the high…