Accuracy and interpretability: The devil and the holy grail. New routes across old boundaries in computational spectroscopy

C Puzzarini, J Bloino, N Tasinato, V Barone - Chemical reviews, 2019 - ACS Publications
The past decade has witnessed an increasing interaction between experiment and theory in
the field of molecular spectroscopy. On the computational side, ongoing developments of …

State of the art of molecular visualization in immersive virtual environments

D Kuťák, P Vázquez, T Isenberg… - Computer Graphics …, 2023 - Wiley Online Library
Visualization plays a crucial role in molecular and structural biology. It has been successfully
applied to a variety of tasks, including structural analysis and interactive drug design. While …

YASARA model–interactive molecular modeling from two dimensions to virtual realities

K Ozvoldik, T Stockner, E Krieger - Journal of Chemical …, 2023 - ACS Publications
The industry's transition from three-dimensional (3D) glasses to virtual reality (VR) headsets
has left modelers stranded without hardware supply, since walking around and waving arms …

Visualization of biomolecular structures: State of the art revisited

B Kozlíková, M Krone, M Falk, N Lindow… - Computer Graphics …, 2017 - Wiley Online Library
Structural properties of molecules are of primary concern in many fields. This report provides
a comprehensive overview on techniques that have been developed in the fields of …

Immersive virtual reality in computational chemistry: Applications to the analysis of QM and MM data

A Salvadori, G Del Frate, M Pagliai… - … journal of quantum …, 2016 - Wiley Online Library
Abstract The role of Virtual Reality (VR) tools in molecular sciences is analyzed in this
contribution through the presentation of the Caffeine software to the quantum chemistry …

Visualizing protein structures—tools and trends

X Martinez, M Chavent, M Baaden - Biochemical Society …, 2020 - portlandpress.com
Molecular visualization is fundamental in the current scientific literature, textbooks and
dissemination materials. It provides an essential support for presenting results, reasoning on …

Molecular dynamics visualization (mdv): stereoscopic 3d display of biomolecular structure and interactions using the unity game engine

M Wiebrands, CJ Malajczuk, AJ Woods… - Journal of integrative …, 2018 - degruyter.com
Molecular graphics systems are visualization tools which, upon integration into a 3D
immersive environment, provide a unique virtual reality experience for research and …

Evaluation of emerging energy-efficient heterogeneous computing platforms for biomolecular and cellular simulation workloads

JE Stone, MJ Hallock, JC Phillips… - 2016 IEEE …, 2016 - ieeexplore.ieee.org
Many of the continuing scientific advances achieved through computational biology are
predicated on the availability of ongoing increases in computational power required for …

Early experiences porting the NAMD and VMD molecular simulation and analysis software to GPU-accelerated OpenPOWER platforms

JE Stone, AP Hynninen, JC Phillips… - … Computing: ISC High …, 2016 - Springer
All-atom molecular dynamics simulations of biomolecules provide a powerful tool for
exploring the structure and dynamics of large protein complexes within realistic cellular …

Multiscale modeling and cinematic visualization of photosynthetic energy conversion processes from electronic to cell scales

M Sener, S Levy, JE Stone, AJ Christensen… - Parallel computing, 2021 - Elsevier
Conversion of sunlight into chemical energy, namely photosynthesis, is the primary energy
source of life on Earth. A visualization depicting this process, based on multiscale …