The traditional computational modeling of protein structure, dynamics, and interactions
remains difficult for many protein systems. It is mostly due to the size of protein …

Highlights•General improvement of protein FFs leads to more accurate representation of
IDPs.•Increasing protein–water interaction allows sampling of more extended states of …

Predicting protein–ligand binding affinities and the associated thermodynamics of
biomolecular recognition is a primary objective of structure-based drug design. Alchemical …

Predicting a protein's structure from its amino acid sequence remains an unsolved problem
after several decades of efforts. If the query protein has a homolog of known structure, the …

Refinement is the last step in protein structure prediction pipelines to convert approximate
homology models to experimental accuracy. Protocols based on molecular dynamics (MD) …

Protein structure prediction has long been available as an alternative to experimental
structure determination, especially via homology modeling based on templates from related …

Protein structures are essential in modern biology yet experimental methods are far from
being able to catch up with the rapid increase in available genomic data. Computational …

The refinement of predicted 3D protein models is crucial in bringing them closer towards
experimental accuracy for further computational studies. Refinement approaches can be …

Enhanced sampling methods such as metadynamics and umbrella sampling have become
essential tools for exploring the configuration space of molecules and materials. At the same …

Plant cytochrome P450s play key roles in the diversification and functional modification of
plant natural products. Although over 200,000 plant P450 gene sequences have been …