AI Networking Cookbook: Practical recipes for AI-assisted network automation and development
TL;DR
This study extends HADDOCK to deal with DNA flexibility and is able to successfully predict protein (cid:1) DNA complexes from unbound constituents using non-structural experimental data to drive the docking.
The interface prediction program WHISCY is presented, which combines surface conservation and structural information to predict protein–protein interfaces and demonstrates the potential of using interface predictions to drive protein–protein docking.
Histidine-rich peptides are widely used in affinity-based purification because imidazole donors can coordinate transition-metal ions. To examine how fixed metal-coordination models may alter the predicted DNA-contacting behavior of a histidine hexamer, a fully in silico comparison was performed using metal-free His6 an...
Double‐stranded DNA molecules are sharply bent into arcs with radii on the order of 10 nanometers in the formation of nucleosomes in biology and when they are looped into minicircles for nanoscale applications. In this Personal Account, we describe our computational efforts over the past several years to understand t...
GHBfix-18Ab, an 18-component hydrogen-bond correction that distinguishes NH and NH□ donors, is developed, demonstrating that targeted refinement of hydrogen-bond interactions provides a practical strategy for systematic improvement of RNA force fields toward more accurate modeling of noncanonical RNA motifs.
Evaluating modern AMBER-based parametrizations across diverse structural motifs, including aptamers, duplexes, and quadruplex-duplex hybrids, provides critical insights for developing next-generation DNA force fields capable of accurately modeling non-native structures and enabling balanced sampling essential for predi...
Interactions between the components of the complex determine the molecular field that ensures complementarity between the contacting structures. In this article, we propose to use AlteQ approach to study DNA polymerase complementarity. The AlteQ approach with good quality describes the experimental electron density whi...
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