Molecular dynamics simulations: advances and applications
Molecular dynamics simulations have evolved into a mature technique that can be used
effectively to understand macromolecular structure-to-function relationships. Present …
effectively to understand macromolecular structure-to-function relationships. Present …
Enhancing important fluctuations: Rare events and metadynamics from a conceptual viewpoint
Atomistic simulations play a central role in many fields of science. However, their usefulness
is often limited by the fact that many systems are characterized by several metastable states …
is often limited by the fact that many systems are characterized by several metastable states …
[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 …
Molecular dynamics simulation of protein and protein–ligand complexes
R Shukla, T Tripathi - Computer-aided drug design, 2020 - Springer
Biomacromolecules, including proteins and their complexes, adopt multiple conformations
that are linked to their biological functions. Though some of the structural heterogeneity can …
that are linked to their biological functions. Though some of the structural heterogeneity can …
Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application
L Boldon, F Laliberte, L Liu - Nano reviews, 2015 - Taylor & Francis
In this paper, the fundamental concepts and equations necessary for performing small angle
X-ray scattering (SAXS) experiments, molecular dynamics (MD) simulations, and MD-SAXS …
X-ray scattering (SAXS) experiments, molecular dynamics (MD) simulations, and MD-SAXS …
[HTML][HTML] Membrane proteins structures: A review on computational modeling tools
Abstract Background Membrane proteins (MPs) play diverse and important functions in
living organisms. They constitute 20% to 30% of the known bacterial, archaean and …
living organisms. They constitute 20% to 30% of the known bacterial, archaean and …
Current tools and methods in molecular dynamics (MD) simulations for drug design
M Hernández-Rodríguez… - Current medicinal …, 2016 - benthamdirect.com
Molecular Dynamics (MD) simulations is a computational method that employs Newton's
laws to evaluate the motions of water, ions, small molecules, and macromolecules or more …
laws to evaluate the motions of water, ions, small molecules, and macromolecules or more …
Ligand access channels in cytochrome P450 enzymes: A review
Quantitative structure-activity relationships may bring invaluable information on structural
elements of both enzymes and substrates that, together, govern substrate specificity. Buried …
elements of both enzymes and substrates that, together, govern substrate specificity. Buried …
Pathways to structure–property relationships of peptide–materials interfaces: Challenges in predicting molecular structures
TR Walsh - Accounts of Chemical Research, 2017 - ACS Publications
Conspectus An in-depth appreciation of how to manipulate the molecular-level recognition
between peptides and aqueous materials interfaces, including nanoparticles, will advance …
between peptides and aqueous materials interfaces, including nanoparticles, will advance …
Flexible receptor docking for drug discovery
CF Wong - Expert opinion on drug discovery, 2015 - Taylor & Francis
Introduction: Molecular docking has become a popular method for virtual screening. Docking
small molecules to a rigid biological receptor is fast but could produce many false negatives …
small molecules to a rigid biological receptor is fast but could produce many false negatives …