Protein structures in the Protein Data Bank provide a wealth of data about the interactions
that determine the native states of proteins. Using the probability theory, we derive an atomic …

Here we report an orientation-dependent statistical all-atom potential derived from side-
chain packing, named OPUS-PSP. It features a basis set of 19 rigid-body blocks extracted …

Comparative structure models are available for two orders of magnitude more protein
sequences than are experimentally determined structures. These models, however, suffer …

Protein modeling has been a very challenging problem in drug discovery and computational
biology. The latest advances and progress in computational power have helped to solve this …

Background Protein dihedral angles provide a detailed description of protein local
conformation. Predicted dihedral angles can be used to narrow down the conformational …

Understanding protein structure is of crucial importance in science, medicine and
biotechnology. For about two decades, knowledge-based potentials based on pairwise …

Motivation Knowledge-based statistical potentials constitute a simpler and easier alternative
to physics-based potentials in many applications, including folding, docking and protein …

Aminopeptidases are part of the arsenal of virulence factors produced by bacterial
pathogens that inactivate host immune peptides. Mycoplasma hyopneumoniae is a genome …

Accurate ab initio simulation of protein folding is a critical step toward elucidation of protein-
folding mechanisms. Here, we demonstrate highly accurate folding of the 35 residue villin …

In this paper, we report a knowledge‐based potential function, named the OPUS‐Ca
potential, that requires only Cα positions as input. The contributions from other atomic …