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

An accurate scoring function is a key component for successful protein structure prediction.
To address this important unsolved problem, we develop a generalized orientation and …

Given the importance of protein–protein interactions for nearly all biological processes, the
design of protein affinity reagents for use in research, diagnosis or therapy is an important …

Motivation: Structural prediction of protein interactions currently remains a challenging but
fundamental goal. In particular, progress in scoring functions is critical for the efficient …

Classical cadherin cell–cell adhesion proteins are essential for the formation and
maintenance of tissue structures; their primary function is to physically couple neighboring …

In this study, we have developed a statistical mechanics‐based iterative method to extract
statistical atomic interaction potentials from known, nonredundant protein structures. Our …

Protein sequence matching presently fails to identify many structures that are highly similar,
even when they are known to have the same function. The high packing densities in …

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 …

Understanding the key factors that influence the interaction preferences of amino acids in
the folding of proteins have remained a challenge. Here we present a knowledge‐based …

The prediction of protein-protein kinetic rate constants provides a fundamental test of our
understanding of molecular recognition, and will play an important role in the modeling of …