The development of scoring functions is of great importance to protein docking. Here we
present a new scoring function for the initial stage of unbound docking. It combines our …

We present a simple and effective algorithm RDOCK for refining unbound predictions
generated by a rigid‐body docking algorithm ZDOCK, which has been developed earlier by …

The CAPRI Challenge is a blind test of protein–protein‐docking algorithms that predict the
complex structure from the crystal structures of the interacting proteins. We participated in …

Most state‐of‐the‐art protein–protein docking algorithms use the Fast Fourier Transform
(FFT) technique to sample the six‐dimensional translational and rotational space. Scoring …

Protein–protein docking requires fast and effective methods to quickly discriminate correct
from incorrect predictions generated by initial‐stage docking. We have developed and …

The accurate scoring of rigid‐body docking orientations represents one of the major
difficulties in protein–protein docking prediction. Other challenges are the development of …

Here, we present FireDock, an efficient method for the refinement and rescoring of rigid‐
body docking solutions. The refinement process consists of two main steps:(1) …

Most scoring functions for protein–protein docking algorithms are either atom‐based or
residue‐based, with the former being able to produce higher quality structures and latter …

To determine the structures of protein–protein interactions, protein docking is a valuable tool
that complements experimental methods to characterize protein complexes. Although …

We present version 3.0 of our publicly available protein–protein docking benchmark. This
update includes 40 new test cases, representing a 48% increase from Benchmark 2.0. For …