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 …

By focusing on essential features, while averaging over less important details, coarse-
grained (CG) models provide significant computational and conceptual advantages with …

Computational methods for protein structure modelling are routinely used to complement
experimental structure determination, thus they help to address a broad spectrum of …

Determination of side-chain conformations is an important step in protein structure prediction
and protein design. Many such methods have been presented, although only a small …

Motivation Protein structure and function are essentially determined by how the side-chain
atoms interact with each other. Thus, accurate protein side-chain packing (PSCP) is a critical …

Accurate protein side-chain modeling is crucial for protein folding and protein design. In the
past decades, many successful methods have been proposed to address this issue …

Site-directed spin-labeling electron paramagnetic resonance spectroscopy is a powerful
technique for the investigation of protein structure and dynamics. Accurate spin-label …

Three-dimensional protein structures, whether determined experimentally or theoretically,
are often too low resolution. In this mini-review, we outline the computational methods for …

Motivation: Modeling of side chain conformations constitutes an indispensable effort in
protein structure modeling, protein–protein docking and protein design. Thanks to an …

We developed a fast and accurate side-chain modeling program [Optimized Side Chain
Atomic eneRgy (OSCAR)-star] based on orientation-dependent energy functions and a rigid …