What method to use for protein–protein docking?
Highlights•The best servers based on “free” docking methods find acceptable models
among the top 10 predictions for around 40% of the targets.•Re-ranking the predictions by a …
among the top 10 predictions for around 40% of the targets.•Re-ranking the predictions by a …
Search strategies and evaluation in protein–protein docking: principles, advances and challenges
SY Huang - Drug discovery today, 2014 - Elsevier
Highlights•Search strategies of current protein–protein docking algorithms were
reviewed.•Challenges and future directions of established approaches were discussed.•Post …
reviewed.•Challenges and future directions of established approaches were discussed.•Post …
The ClusPro web server for protein–protein docking
Abstract The ClusPro server (https://cluspro. org) is a widely used tool for protein–protein
docking. The server provides a simple home page for basic use, requiring only two files in …
docking. The server provides a simple home page for basic use, requiring only two files in …
New additions to the C lus P ro server motivated by CAPRI
The heavily used protein–protein docking server ClusPro performs three computational
steps as follows:(1) rigid body docking,(2) RMSD based clustering of the 1000 lowest energy …
steps as follows:(1) rigid body docking,(2) RMSD based clustering of the 1000 lowest energy …
Updates to the integrated protein–protein interaction benchmarks: docking benchmark version 5 and affinity benchmark version 2
We present an updated and integrated version of our widely used protein–protein docking
and binding affinity benchmarks. The benchmarks consist of non-redundant, high-quality …
and binding affinity benchmarks. The benchmarks consist of non-redundant, high-quality …
How good is automated protein docking?
The protein docking server ClusPro has been participating in critical assessment of
prediction of interactions (CAPRI) since its introduction in 2004. This article evaluates the …
prediction of interactions (CAPRI) since its introduction in 2004. This article evaluates the …
PatchDock and SymmDock: servers for rigid and symmetric docking
D Schneidman-Duhovny, Y Inbar… - Nucleic acids …, 2005 - academic.oup.com
Here, we describe two freely available web servers for molecular docking. The PatchDock
method performs structure prediction of protein–protein and protein–small molecule …
method performs structure prediction of protein–protein and protein–small molecule …
ZDOCK: an initial‐stage protein‐docking algorithm
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 …
present a new scoring function for the initial stage of unbound docking. It combines our …
Protein–protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
Protein–protein docking algorithms provide a means to elucidate structural details for
presently unknown complexes. Here, we present and evaluate a new method to predict …
presently unknown complexes. Here, we present and evaluate a new method to predict …
PIPER: an FFT‐based protein docking program with pairwise potentials
Abstract The Fast Fourier Transform (FFT) correlation approach to protein–protein docking
can evaluate the energies of billions of docked conformations on a grid if the energy is …
can evaluate the energies of billions of docked conformations on a grid if the energy is …