Molecular graphics: bridging structural biologists and computer scientists

X Martinez, M Krone, N Alharbi, AS Rose, RS Laramee… - Structure, 2019 - cell.com
Visualization of molecular structures is one of the most common tasks carried out by
structural biologists, typically using software, such as Chimera, COOT, PyMOL, or VMD. In …

Multiscale visualization: A structured literature analysis

E Cakmak, D Jäckle, T Schreck… - IEEE Transactions on …, 2021 - ieeexplore.ieee.org
Multiscale visualizations are typically used to analyze multiscale processes and data in
various application domains, such as the visual exploration of hierarchical genome …

Predicting drug–target interactions with deep-embedding learning of graphs and sequences

W Chen, G Chen, L Zhao… - The Journal of Physical …, 2021 - ACS Publications
Computational approaches for predicting drug–target interactions (DTIs) play an important
role in drug discovery since conventional screening experiments are time-consuming and …

Vivern–a virtual environment for multiscale visualization and modeling of DNA nanostructures

D Kuťák, MN Selzer, J Byška… - … on Visualization and …, 2021 - ieeexplore.ieee.org
DNA nanostructures offer promising applications, particularly in the biomedical domain, as
they can be used for targeted drug delivery, construction of nanorobots, or as a basis for …

The Simularium Viewer: an interactive online tool for sharing spatiotemporal biological models

B Lyons, E Isaac, NH Choi, TP Do, J Domingus… - Nature …, 2022 - nature.com
To the Editor—We present the Simularium Viewer, a user-friendly, open-source application
that makes it easy to share and interrogate interactive three-dimensional (3D) visualizations …

Analysis of long molecular dynamics simulations using interactive focus+ context visualization

J Byška, T Trautner, SM Marques… - Computer Graphics …, 2019 - Wiley Online Library
Analyzing molecular dynamics (MD) simulations is a key aspect to understand protein
dynamics and function. With increasing computational power, it is now possible to generate …

Creative molecular model design for chemistry edutainment

W Li - Proceedings of the 14th International Conference on …, 2022 - dl.acm.org
Since 3D molecular structure visualization is important for chemistry education, lots of
successful works have been focused on molecular visualization. However, most of the …

LifeBrush: Painting, simulating, and visualizing dense biomolecular environments

T Davison, F Samavati, C Jacob - Computers & Graphics, 2019 - Elsevier
LifeBrush is a Cyberworld for painting dynamic molecular illustrations in virtual reality (VR)
that then come to life as interactive simulations. We designed our system for the biological …

Scale Trotter: Illustrative visual travels across negative scales

S Halladjian, H Miao, D Kouřil… - … on Visualization and …, 2019 - ieeexplore.ieee.org
We present ScaleTrotter, a conceptual framework for an interactive, multi-scale visualization
of biological mesoscale data and, specifically, genome data. ScaleTrotter allows viewers to …

Nanoscape, a data-driven 3D real-time interactive virtual cell environment

SR Kadir, A Lilja, N Gunn, C Strong, RT Hughes… - Elife, 2021 - elifesciences.org
Our understanding of cellular and structural biology has reached unprecedented levels of
detail, and computer visualisation techniques can be used to create three-dimensional (3D) …