Related papers: Interactive molecular dynamics in virtual reality …
All-atom molecular dynamics (MD) computer simulations are a valuable tool for characterizing the conformational ensembles of intrinsically disordered proteins (IDPs). IDP conformational ensembles are highly heterogeneous and contain…
Path integral molecular dynamics (PIMD), which maps a quantum particle onto a fictitious classical system of ring polymers and propagates the "beads" of this extended classical system using molecular dynamics, is widely used to capture…
Instruction following is crucial in contemporary LLM. However, when extended to multimodal setting, it often suffers from misalignment between specific textual instruction and targeted local region of an image. To achieve more accurate and…
Protein-ligand interactions are crucial for a wide range of physiological processes. Many cellular functions result in these non-covalent `bonds' being mechanically strained, and this can be integral to proper cellular function. Broadly,…
Stroke patients often experience upper limb impairments that restrict their mobility and daily activities. Physical therapy (PT) is the most effective method to improve impairments, but low patient adherence and participation in PT…
Docking is a crucial component in drug discovery aimed at predicting the binding conformation and affinity between small molecules and target proteins. ML-based docking has recently emerged as a prominent approach, outpacing traditional…
Many biologically important ligands of proteins are large, flexible, and often charged molecules that bind to extended regions on the protein surface. It is infeasible or expensive to locate such ligands on proteins with standard methods…
In this paper, we present the design of a multimodal interaction framework for intelligent virtual agents in wearable mixed reality environments, especially for interactive applications at museums, botanical gardens, and similar places.…
We present the Virtual Beamline (VBL) application, an interactive web-based platform for visualizing high-intensity laser-matter interactions using particle-in-cell (PIC) simulations, with future potential for experimental data…
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…
Transforming static images into interactive experiences remains a challenging task in computer vision. Tackling this challenge holds the potential to elevate mobile user experiences, notably through interactive and AR/VR applications.…
Due to the contribution of drug-target binding kinetics to drug efficacy, there is a high level of interest in developing methods to predict drug-target binding kinetic parameters. During the review period, a wide range of enhanced sampling…
The study of rigid protein-protein docking plays an essential role in a variety of tasks such as drug design and protein engineering. Recently, several learning-based methods have been proposed for the task, exhibiting much faster docking…
PLUMED-GUI is an interactive environment to develop and test complex PLUMED scripts within the Visual Molecular Dynamics (VMD) environment. Computational biophysicists can take advantage of both PLUMED's rich syntax to define collective…
Protein-ligand structure prediction is an essential task in drug discovery, predicting the binding interactions between small molecules (ligands) and target proteins (receptors). Recent advances have incorporated deep learning techniques to…
In this work, we propose a deep learning approach to improve docking-based virtual screening. The introduced deep neural network, DeepVS, uses the output of a docking program and learns how to extract relevant features from basic data such…
Light-activated drugs are a promising way to localize biological activity and minimize side effects. However, their development is complicated by the numerous photophysical and biological properties that must be simultaneously optimized. To…
Body actions and head gestures are natural interfaces for interaction in virtual environments. Existing methods for in-place body action recognition often require hardware more than a head-mounted display (HMD), making body action…
Molecular docking is a crucial step in the development of new drugs as it guides the positioning of a small molecule (ligand) within the pocket of a target protein. In the literature, a feasibility study explored the potential of D-Wave…
High-fidelity cinematic medical visualization on mobile virtual reality (VR) remains challenging. Although ClipGS enables cross-sectional exploration via 3D Gaussian Splatting, it lacks arbitrary-angle slicing on consumer-grade VR headsets.…