Docking Protocol RosettaDock Rosetta Commons

GPCR Model Dock Protocol Capture Rosetta Commons

Tutorials intended as a gentle introduction to Rosetta concepts and using common functionality of Rosetta These demos are designed to guide users through sample procedures in computational modeling from the point of view of solving a specific problem

PDF File S1 ResearchGate

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

Sivasubramanian A Chao G Pressler H M Witrup K D and Gray J J Structural model of the mAb 806 EGFR complex using computational docking followed by computational and experimental mutagenesis

Ligand Docking Rosetta Commons

Supplementary Material Protocol capture for GPCR comparative modeling and ligand docking computational methods This protocol capture contains the steps necessary to obtain the results presented in the manuscript

Gpcr Model Dock Protocol Capture Rosetta Commons

Rosetta Tutorials Demos and Protocol Captures Rosetta Commons

Model database and methods for generating models of GPCRs using Rosetta Resources

Ligand Docking with Orphan GPCR RosettaCommons

Protein Protein Docking Rosetta Commons

This particular D3 eticlopride protein ligand complex was used as a target in the GPCR Dock 2010 assessment the results of which are discussed here Kufareva I et al Status of GPCR modeling and docking as reflected by community wide GPCR Dock 2010 assessment Structure 19 1108 1126 2011

ROSIE Docking Protocol Rosetta Commons

Does comparative modeling works for membrane proteins

Demos and Protocol Captures by topic Rosetta Commons

Assessment and Challenges of Ligand Docking into Comparative

Rosetta Commons

The Topology Broker application in Rosetta can be used to build loops and flexible regions in membrane proteins The protocol allows for the inclusion of membrane span and lipophilicity information as well as membrane weight set for the scoring function

The scripts and input files that accompany this demo can be found in the demos protocol captures directory of the Rosetta weekly releases This is a protocol capture and represents the protocol at a fixed point in time

clustering Clustering Group similar decoys with the Rosetta cluster application cryo em tutorial Modeling using low to medium resolution cryoEM data patched residue types in centroid fullatom protocols Tutorial for using modified residue types in centroid level applications

We have proposed and evaluated a novel three stage protocol for prediction of GPCR peptide complexes The method employs CABS dock docking simulations for generation of a large number of coarse grained receptor peptide complexes followed by PD2 model reconstruction to all atom representation

GitHub benderb1 rosettagpcr Model database and methods for

To predict their binding modes ligand conformers of the 14 ligands co crystalized with the GPCRs were docked against the top ranked comparative models In contrast to the comparative models themselves however it remains difficult to unambiguously identify correct binding modes by score alone

GPCR Model Dock Protocol Capture docs rosettacommons org

Demos are designed to guide users through sample procedures in computational modeling from the point of view of solving a specific problem Full input files for the demos are located in the demos public directory of the Rosetta distribution

Protocol Name Loop Building for Membrane Proteins with

Docking of peptides to GPCRs using a combination of CABS dock

This protocol capture contains the steps necessary to obtain the results presented in the manuscript Assessment and challenges of ligand docking into comparative models of G protein

Gpcr Model Dock Protocol Capture Rosetta Commons

Videos for Gpcr Model Dock Protocol Capture Rosetta Commons

When you run the protocol the StartFromMover will pick a random starting position move the ligand to that position and then run the docking You need to have the ligand present in the input file but it doesn 39 t need to be in a particular location

LowModeMD with the MMFFx94 force field and Generalized Born solvation model was used to generate conformations within the specified energy cutoff The ligand conformations were then saved as an sdf file for conversion to pdb and params files for Rosetta

Demos Grouped by Keyword docs rosettacommons org

According to the abstract this protocol has been used for modeling of metabotropic glutamate receptor subtype 5 protein using GPRC crystal structures But the flags is only for rebuilding loops of a membrane protein whose crystal structure is known

How to analyse the best docked model Docking in Rosetta Docking in Rosetta in a two stage protocol the first stage where aggresive sampling is done is done in the centroid mode and the second stage where smaller movements take place is done in the full atom mode