Highlights•Binding free energy calculations are increasing used in drug design and
biotechnology.•We distinguish end-state methods, alchemical methods and pathway …

Physics and physical chemistry are an important thread in computational protein design,
complementary to knowledge-based tools. They provide molecular mechanics scoring …

We describe methods for physics-based protein design and some recent applications from
our work. We present the physical interpretation of a MC simulation in sequence space and …

Computational protein design, ab initio protein/RNA folding, and protein–ligand screening
can be too computationally demanding for explicit treatment of solvent. For these …

Computational protein design relies on simulations of a protein structure, where selected
amino acids can mutate randomly, and mutations are selected to enhance a target property …

Computational protein design (CPD) aims to predict amino acid sequences that fold to
specific structures and perform desired functions. CPD depends on a rotamer library, an …

Computational protein design (CPD) is a powerful technique for engineering new proteins,
with both great fundamental implications and diverse practical interests. However, the …

The coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is
responsible for the coronavirus disease 2019 pandemic, and the closely related SARS-CoV …

Designed enzymes are of fundamental and technological interest. Experimental directed
evolution still has significant limitations, and computational approaches are a …

Amino acids (AAs) with a noncanonical backbone would be a valuable tool for protein
engineering, enabling new structural motifs and building blocks. To incorporate them into an …