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This study employed an artificial intelligence-enhanced molecular simulation framework to enable efficient Path Integral Molecular Dynamics (PIMD) simulations. Owing to its modular architecture and high-throughput capabilities, the…

The advent of highly accurate protein structure prediction methods has fueled an exponential expansion of the protein structure database. Consequently, there is a rising demand for rapid and precise structural homolog search. Traditional…

Molecular dynamics simulations provide detailed trajectories at the atomic level, but extracting interpretable and robust insights from these high-dimensional data remains challenging. In practice, analyses typically rely on a single…

The high arithmetic performance and intrinsic parallelism of recent graphical processing units (GPUs) can offer a technological edge for molecular dynamics simulations. ACEMD is a production-class bio-molecular dynamics (MD) simulation…

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…

A generalized computational method for folding proteins with a fully transferable potential and geometrically realistic all-atom model is presented and tested on seven different helix bundle proteins. The protocol, which includes…

The biological functions of proteins often depend on dynamic structural ensembles. In this work, we develop a flow-based generative modeling approach for learning and sampling the conformational landscapes of proteins. We repurpose highly…

Visual Molecular Dynamics (VMD) is one of the most widely used molecular graphics software in the community of theoretical simulations. So far, however, it still lacks a graphical user interface (GUI) for molecular manipulations when doing…

AlphaFold has transformed protein structure prediction, but emerging applications such as virtual ligand screening, proteome-wide folding, and de novo binder design demand predictions at a massive scale, where runtime and memory costs…

Virtual reality is a powerful tool with the ability to immerse a user within a completely external environment. This immersion is particularly useful when visualizing and analyzing interactions between small organic molecules, molecular…

Many diseases cause significant changes to the concentrations of small molecules (aka metabolites) that appear in a person's biofluids, which means such diseases can often be readily detected from a person's "metabolic profile". This…

We present a fast learning-based algorithm for deformable, pairwise 3D medical image registration. Current registration methods optimize an objective function independently for each pair of images, which can be time-consuming for large…

In this work, we propose a simple transformer-based baseline for multimodal molecular representation learning, integrating three distinct modalities: SMILES strings, 2D graph representations, and 3D conformers of molecules. A key aspect of…

Alterations in nuclear morphology are useful adjuncts and even diagnostic tools used by pathologists in the diagnosis and grading of many tumors, particularly malignant tumors. Large datasets such as TCGA and the Human Protein Atlas, in…

Obtaining a rigorous and reliable method for linking computer simulations of polymer blends and composites at different length scales of interest is a highly desirable goal in soft matter physics. In this paper a multiscale modeling…

Comprehending the long-timescale dynamics of protein-ligand complexes is very important for drug discovery and structural biology, but it continues to be computationally challenging for large biomolecular systems. We introduce…

Storyboarding is a core skill in visual storytelling for film, animation, and games. However, automating this process requires a system to achieve two properties that current approaches rarely satisfy simultaneously: inter-shot consistency…

Artificial Intelligence models encoding biology and chemistry are opening new routes to high-throughput and high-quality in-silico drug development. However, their training increasingly relies on computational scale, with recent protein…

Force field-based molecular dynamics (MD) simulations are indispensable for probing the structure, dynamics, and functions of biomolecular systems, including proteins and protein-ligand complexes. Despite their broad utility in drug…

With the rapid advancement of computational techniques, Molecular Dynamics (MD) simulations have emerged as powerful tools in biomedical research, enabling in-depth investigations of biological systems at the atomic level. Among the diverse…