Related papers: Visualizing biomolecular electrostatics in virtual…
The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and…
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…
The ability to precisely visualize the atomic geometry of the interactions between a drug and its protein target in structural models is critical in predicting the correct modifications in previously identified inhibitors to create more…
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…
PACKMOL is a widely utilized molecular modeling tool within the computational chemistry community. However, its perceivable advantages have been impeded by the long-standing lack of a robust open-source graphical user interface (GUI) that…
The potential of virtual reality (VR) to contribute to drug design and development has been recognised for many years. Hardware and software developments now mean that this potential is beginning to be realised, and VR methods are being…
This article reports prototype web apps that use commodity, open-source technologies for augmented and virtual reality to provide immersive, interactive human-computer interfaces for chemistry, structural biology and related disciplines.…
Plasma physics simulations create complex datasets for which researchers need state-of-the-art visualization tools to gain insights. These datasets are 3D in nature but are commonly depicted and analyzed using 2D idioms displayed on 2D…
Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In…
In this and the associated article 'BioBlender: Fast and Efficient All Atom Morphing of Proteins Using Blender Game Engine', by Zini et al., we present BioBlender, a complete instrument for the elaboration of motion (Zini et al.) and the…
VTX is an open-source molecular visualization software designed to overcome the scaling limitations of existing real-time molecular visualization software when handling massive molecular datasets. VTX employs a meshless molecular graphics…
Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off…
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…
Recent advances in distance-based protein folding have led to a paradigm shift in protein structure prediction. Through sufficiently precise estimation of the inter-residue distance matrix for a protein sequence, it is now feasible to…
In recent years, machine learning (ML) has gained significant popularity in the field of chemical informatics and electronic structure theory. These techniques often require researchers to engineer abstract "features" that encode chemical…
Ultrasound-matter interactions underpin numerous biomedical and soft-matter applications, yet simulating these phenomena is challenging due to the large separation of viscous and sonic time scales. Continuum methods capture large-scale wave…
This preprint presents a web app (essentially a web page-based program) with which two or more users (peers) can view and handle 3D molecular structures in a concurrent, interactive way through their web browsers. This means they can share…
Molecular dynamics (MD) simulations provide crucial insight into molecular interactions and biomolecular function. With interactive MD simulations in VR (iMD-VR), chemists can now interact with these molecular simulations in real-time. Our…
Virtual reality (VR) enables data visualization in an immersive and engaging manner, and it can be used for creating ways to explore scientific data. Here, we use VR for visualization of 3D histology data, creating a novel interface for…
Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules. Specialized software packages are required to…