相关论文: Modie Viewer: Protein Beasts and How to View Them

Protein representation learning plays a crucial role in understanding the structure and function of proteins, which are essential biomolecules involved in various biological processes. In recent years, deep learning has emerged as a…

The formation of biomolecular condensates inside cells often involve intrinsically disordered proteins (IDPs), and several of these IDPs are also capable of forming droplet-like dense assemblies on their own, through liquid-liquid phase…

The Vision Transformer (ViT) has demonstrated remarkable performance in Self-Supervised Learning (SSL) for 3D medical image analysis. Masked AutoEncoder (MAE) for feature pre-training can further unleash the potential of ViT on various…

Scientists often explore and analyze large-scale scientific simulation data by leveraging two- and three-dimensional visualizations. The data and tasks can be complex and therefore best supported using myriad display technologies, from…

The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over…

One of the challenges of the proteomic analysis by 2D-gel is to visualize the low abundance proteins, particularly those localized in organelles. An additional problem with nuclear proteins lies in their strong interaction with nuclear…

We examine several currently used techniques for visualizing complex-valued functions applied to modular forms. We plot several examples and study the benefits and limitations of each technique. We then introduce a method of visualization…

This paper presents details of our winning solutions to the task IV of NIPS 2017 Competition Track entitled Classifying Clinically Actionable Genetic Mutations. The machine learning task aims to classify genetic mutations based on text…

We present VISTA (Visualization of Internal States and Their Associations), a novel pipeline for visually exploring and interpreting neural network representations. VISTA addresses the challenge of analyzing vast multidimensional spaces in…

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…

Proteins are miniature machines whose function depends on their three-dimensional (3D) structure. Determining this structure computationally remains an unsolved grand challenge. A major bottleneck involves selecting the most accurate…

Understanding the mechanisms underlying deep neural networks remains a fundamental challenge in machine learning and computer vision. One promising, yet only preliminarily explored approach, is feature inversion, which attempts to…

Molecular visualization software has long supported research and education in chemical and structural sciences, but consumer devices constrained to 2D inputs and outputs pose two major challenges: they poorly convey 3D nature, and 3D…

Protein-ligand interactions are one of the fundamental types of molecular interactions in living systems. Ligands are small molecules that interact with protein molecules at specific regions on their surfaces called binding sites. Tasks…

Colorization involves the synthesis of colors on a target image while preserving structural content as well as the semantics of the target image. This is a well-explored problem in 2D with many state-of-the-art solutions. We propose a novel…

Structural flexibility and/or dynamic interactions with other molecules is a critical aspect of protein function. CryoEM provides direct visualization of individual macromolecules sampling different conformational and compositional states.…

Transformers have shown great potential in various computer vision tasks owing to their strong capability in modeling long-range dependency using the self-attention mechanism. Nevertheless, vision transformers treat an image as 1D sequence…

Significant advances in biotechnology have allowed for simultaneous measurement of molecular data points across multiple genomic and transcriptomic levels from a single tumor/cancer sample. This has motivated systematic approaches to…

Advances in sequencing have revealed that each individual carries about 10,000 missense variants. For the vast majority, we do not know what the functional consequences - if any - will be. Further, mechanistic insight, such as structural…

Proteins play crucial roles in every cellular process by interacting with each other, with nucleic acids, metabolites, and other molecules. The resulting assemblies can be very large and intricate and pose challenges to experimental…