What is Rosetta docking?

What is Rosetta docking?

RosettaDock is a Monte Carlo (MC) based multi-scale docking algorithm that incorporates both a low-resolution, centroid-mode, coarse-grain stage and a high-resolution, all-atom refinement stage that optimizes both rigid-body orientation and side-chain conformation.

What does a docking protein do?

Docking proteins comprise a distinct category of intracellular, noncatalytic signalling protein, that function downstream of a variety of receptor and receptor-associated tyrosine kinases and regulate diverse physiological and pathological processes.

What method is used for protein protein docking?

SwarmDock [14,15] is a flexible docking method which uses a population-based memetic algorithm to optimize parameters characterizing the orientation, position, and conformations of protein subunits.

What is global docking?

Global docking assumes a spherical general structure of the proteins and rotates the smaller protein (ligand) around the larger protein (receptor). Due to the large space sampled, global docking requires a large number of runs to converge on a structure, typically 10,000-100,000.

Why is molecular docking important?

Molecular docking is a key tool in structural molecular biology and computer-assisted drug design. The goal of ligand-protein docking is to predict the predominant binding mode(s) of a ligand with a protein of known three-dimensional structure.

How is molecular docking done?

Molecular docking is a kind of bioinformatic modelling which involves the interaction of two or more molecules to give the stable adduct. Depending upon binding properties of ligand and target, it predicts the three-dimensional structure of any complex.

What is peptide docking?

In recent years, a variety of approaches have been developed for ‘protein–peptide docking’, that is, predicting the structure of the protein–peptide complex, starting from the protein structure and the peptide sequence, including variable degrees of information about the peptide binding site and/or conformation.

Which software is best for protein-protein docking?

Among these programs, AutoDock Vina, GOLD, and MOE-Dock predicted top ranking poses with best scores. GOLD and LeDock were able to identify the correct ligand binding poses. Both Glide (XP) and GOLD predict the poses consistently with a 90.0% accuracy (Wang et al. 2016).

Which software is best for protein protein docking?

What is a pose in molecular docking?

Most docking programs in use account for the whole conformational space of the ligand (flexible ligand), and several attempt to model a flexible protein receptor. Each “snapshot” of the pair is referred to as a pose. A variety of conformational search strategies have been applied to the ligand and to the receptor.

How do you dock a flexible protein in Rosetta?

Docking Flexible Proteins As mentioned in the introduction, the docking protocol in Rosetta assumes a fixed backbone. If the backbone changes a lot between the unbound and the bound conformations, we dock conformational ensembles of the proteins.

What is Rosetta used for?

Overview. The Rosetta software suite includes algorithms for computational modeling and analysis of protein structures. It has enabled notable scientific advances in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes. Rosetta…

How does Rosetta dock conformational ensembles?

As mentioned in the introduction, the docking protocol in Rosetta assumes a fixed backbone. If the backbone changes a lot between the unbound and the bound conformations, we dock conformational ensembles of the proteins.

What is RosettaDock?

The following description has been adapted from Chaudhury, et al., 2011, PLoS One: RosettaDock is a Monte Carlo (MC) based multi-scale docking algorithm that incorporates both a low-resolution, centroid-mode, coarse-grain stage and a high-resolution, all-atom refinement stage that optimizes both rigid-body orientation and side-chain conformation.