HADDOCK (High Ambiguity Driven protein-protein DOCKing) is an information-driven flexible docking approach for the modeling of biomolecular complexes. HADDOCK distinguishes itself from ab-initio docking methods in the fact that it encodes information from identified or predicted protein interfaces in ambiguous interaction restraints (AIRs) to ...

This tutorial will demonstrate the use of HADDOCK for modelling the 3D structure of a protein-protein complex from pairwise interfacial residue distances derived from multiple structural templates. The case we will be investigating is the complex between bonvine chymotrypsinogen*A and a recombinant variant of human pancreatic secretory trypsin ...

HADDOCK2.4 basic protein-protein docking tutorial: A tutorial demonstrating the use of the HADDOCK web server to model a protein-protein complex using interface information

This tutorial will demonstrate the use of HADDOCK for the modelling of protein-small molecule complexes. We will make use of a recently developed protocol whose key element is the use of template-derived shapes to drive the modelling process.

A protein-ligand docking example making use of the knowledge of a template ligand (a ligand similar to the ligand we want to dock and bind to the same receptor). The template ligand information is used in the form of shape consisting of dummy beads and positioned within the binding site to which distance restraints are defined.

2019年12月30日 · Our approach for these targets boils down to variations of our protein-peptide protocol 16 or threading on available templates and refining.

Protein-protein and protein-DNA/RNA docking based on a hybrid algorithm of template-based modeling and ab initio free docking. Specify the residues of the binding site. Yan Y, Tao H, He J, Huang...

2021年9月9日 · Here, we present a new protocol in HADDOCK (High Ambiguity Driven DOCKing), our integrative modeling platform, which incorporates homology information for both receptor and compounds. It makes use of HADDOCK’s unique ability to integrate information in the simulation to drive it toward conformations, which agree with the provided data.

2020年4月8日 · The HDOCK server (http://hdock.phys.hust.edu.cn/) is a highly integrated suite of homology search, template-based modeling, structure prediction, macromolecular docking, biological information...

2021年7月8日 · HADDOCK2.4 web server (https://bianca.science.uu.nl/haddock2.4/) [1] is used for protein-protein docking and their modeling. Not only proteins, but it can also process …