Biomolecular modeling thrives in the age of technology
T Schlick, S Portillo-Ledesma - Nature computational science, 2021 - nature.com
The biomolecular modeling field has flourished since its early days in the 1970s due to the
rapid adaptation and tailoring of state-of-the-art technology. The resulting dramatic increase …
rapid adaptation and tailoring of state-of-the-art technology. The resulting dramatic increase …
[HTML][HTML] Scalable molecular dynamics on CPU and GPU architectures with NAMD
NAMD is a molecular dynamics program designed for high-performance simulations of very
large biological objects on CPU-and GPU-based architectures. NAMD offers scalable …
large biological objects on CPU-and GPU-based architectures. NAMD offers scalable …
[HTML][HTML] Heterogeneous parallelization and acceleration of molecular dynamics simulations in GROMACS
The introduction of accelerator devices such as graphics processing units (GPUs) has had
profound impact on molecular dynamics simulations and has enabled order-of-magnitude …
profound impact on molecular dynamics simulations and has enabled order-of-magnitude …
AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics
L Casalino, AC Dommer, Z Gaieb… - … Journal of High …, 2021 - journals.sagepub.com
We develop a generalizable AI-driven workflow that leverages heterogeneous HPC
resources to explore the time-dependent dynamics of molecular systems. We use this …
resources to explore the time-dependent dynamics of molecular systems. We use this …
Advancements in nanobody generation: Integrating conventional, in silico, and machine learning approaches
Nanobodies, derived from camelids and sharks, offer compact, single‐variable heavy‐chain
antibodies with diverse biomedical potential. This review explores their generation methods …
antibodies with diverse biomedical potential. This review explores their generation methods …
Biased cytochrome P450-mediated metabolism via small-molecule ligands binding P450 oxidoreductase
SB Jensen, S Thodberg, S Parween, ME Moses… - Nature …, 2021 - nature.com
Metabolic control is mediated by the dynamic assemblies and function of multiple redox
enzymes. A key element in these assemblies, the P450 oxidoreductase (POR), donates …
enzymes. A key element in these assemblies, the P450 oxidoreductase (POR), donates …
Modeling and scale-bridging using machine learning: Nanoconfinement effects in porous media
Fine-scale models that represent first-principles physics are challenging to represent at
larger scales of interest in many application areas. In nanoporous media such as tight-shale …
larger scales of interest in many application areas. In nanoporous media such as tight-shale …
Molecular simulations of hydrophobic gating of pentameric ligand gated ion channels: insights into water and ions
Ion channels are proteins which form gated nanopores in biological membranes. Many
channels exhibit hydrophobic gating, whereby functional closure of a pore occurs by local …
channels exhibit hydrophobic gating, whereby functional closure of a pore occurs by local …
Molecular basis for drug repurposing to study the interface of the S protein in SARS-CoV-2 and human ACE2 through docking, characterization, and molecular …
M Alazmi, O Motwalli - Journal of molecular modeling, 2020 - Springer
A novel coronavirus (SARS-CoV-2) identified in Wuhan state of China in 2019 is the
causative agent of deadly disease COVID-19. It has spread across the globe (more than 210 …
causative agent of deadly disease COVID-19. It has spread across the globe (more than 210 …
Combined 3D-QSAR, molecular docking and dynamics simulations studies to model and design TTK inhibitors
Tyrosine threonine kinase (TTK) is the key component of the spindle assembly checkpoint
(SAC) that ensures correct attachment of chromosomes to the mitotic spindle and thereby …
(SAC) that ensures correct attachment of chromosomes to the mitotic spindle and thereby …