Related papers: Modie Viewer: Protein Beasts and How to View Them
Interactive visualization tools are highly desirable to biologist and cancer researchers to explore the complex structures, detect patterns and find out the relationships among bio-molecules responsible for a cancer type. A pathway contains…
Multi-view transformers such as DUSt3R are revolutionizing 3D vision by solving 3D tasks in a feed-forward manner. However, contrary to previous optimization-based pipelines, the inner mechanisms of multi-view transformers are unclear.…
Intrinsically disordered proteins and regions are increasingly appreciated for their abundance in the proteome and the many functional roles they play in the cell. In this short review, we describe a variety of approaches used to obtain…
Training Artificial Intelligence (AI) models on 3D images presents unique challenges compared to the 2D case: Firstly, the demand for computational resources is significantly higher, and secondly, the availability of large datasets for…
Building a working mental model of a protein typically requires weeks of reading, cross-referencing crystal and predicted structures, and inspecting ligand complexes, an effort that is slow, unevenly accessible, and often requires…
Proteins perform a large variety of functions in living organisms, thus playing a key role in biology. As of now, available learning algorithms to process protein data do not consider several particularities of such data and/or do not scale…
Physical imaging is a foundational characterization method in areas from condensed matter physics and chemistry to astronomy and spans length scales from atomic to universe. Images encapsulate crucial data regarding atomic bonding,…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Synthetic biologists and molecular programmers design novel nucleic acid reactions, with many potential applications. Good visualization tools are needed to help domain experts make sense of the complex outputs of folding pathway…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Vector fields are one of the fundamental parts of mathematics which are key for modelling many physics phenomena such as electromagnetic fields or fluid and gas flows. Fields found in nature often exhibit complex structures which can be…
Modern particle physics experiments usually rely on highly complex and large-scale spectrometer devices. In high energy physics experiments, visualization helps detector design, data quality monitoring, offline data processing, and has…
In understanding and redesigning the function of proteins in modern biochemistry, protein engineers are increasingly focusing on exploring regions in proteins called loops. Analyzing various characteristics of these regions helps the…
With the advent of state-of-the-art machine learning and deep learning technologies, several industries are moving towards the field. Applications of such technologies are highly diverse ranging from natural language processing to computer…
Visual object tracking is a significant computer vision task which can be applied to many domains such as visual surveillance, human computer interaction, and video compression. In the literature, researchers have proposed a variety of 2D…
Virtual screening (VS) is an essential task in drug discovery, focusing on the identification of small-molecule ligands that bind to specific protein pockets. Existing deep learning methods, from early regression models to recent…
For over half a century, the computer mouse has been the primary tool for interacting with digital data, yet it remains a limiting factor in exploring complex, multi-scale scientific images. Traditional 2D visualization methods hinder…
In nature the three-dimensional structure of a protein is encoded in the corresponding gene. In this paper we describe a new method for encoding the three-dimensional structure of a protein into a binary sequence. The feature of the method…
The OpenMX Viewer (Open source package for Material eXplorer Viewer) is a web-based graphical user interface (GUI) program for visualization and analysis of crystalline and molecular structures and 3D grid data in the Gaussian cube format…
Computational methods for assessing the likely impacts of mutations, known as variant effect predictors (VEPs), are widely used in the assessment and interpretation of human genetic variation, as well as in other applications like protein…