Protein Docking Analysis

PROTEIN DOCKING ANALYSIS

High-resolution protein-protein docking that explores flexibility during modeling.

NovaDock explores protein flexibility when docking, resulting in more accurate protein-protein interaction predictions.

Modeling a protein-protein docking interaction is generally more difficult than predicting the structure of an individual protein, and because of its complex nature, accuracy can be a concern. NovaDock offers the ability to predict protein-protein docking interactions for any two binding partners utilizing SwarmDock, one of the top algorithms validated in the CAPRI blind docking experiment. Utilizing the SwarmDock algorithm, NovaDock explores protein flexibility when docking, resulting in more accurate predictions. Simply provide your ligand and receptor PDB or structure files, proposing specific residue contacts between the binding partners if desired. NovaDock will then predict the three-dimensional structure of the macromolecular complex and provide energy score, cluster size, and number of ligand contacts for each model for analysis.

Protein docking in 4 simple steps

Step 1

Select receptor and ligand structures and specify prediction options

Step 2

Evaluate summary of ligand position and energy for each predicted model

Step 3

Analyze data for individual models and visualize residue contacts

Step 4

Open models to further explore structure and export images for publication

Learn more about Protein Docking

Resources | Tutorials | FAQs | User Guide

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Resources

Please see our resources below for more information on protein docking.

High-Resolution in silico Protein Structure Prediction and Docking

View Poster

High Resolution Protein and Antibody Modeling with NovaFold and NovaFold Antibody

Watch Webinar

How Can DNASTAR’s Protein Tools Help You?

Watch Webinar

Why Structure Prediction Matters

Read Blog Post

Nova Applications on Mac: Bringing the Power of Protein Modeling to the Desktop

Read Blog Post

Tutorials

Watch one of our videos or check out our user guide to learn more about using NovaDock for protein docking.

Lasergene Protein Overview

This video gives an overview of Lasergene Protein, consisting of Protean 3D, plus the optional services NovaFold, NovaFold Antibody and NovaDock.

FAQs

How can I predict protein-protein binding interactions?

By using NovaDock, a service that runs through the Protean 3D interface. NovaDock is used to predict atomic protein docking interactions between two binding partners, both of which must be proteins. One binding partner is the ligand (‘L’: usually the smaller partner or an antibody); the other is the receptor (‘R’: usually the larger partner or an antigen). Each binding partner can consist of one or multiple protein chains.

What file types are supported for importing proteins?

Protean 3D supports the following protein file formats: .aa, .fap, .fas, .fasta, .gp, .gbk, .sbd, .pro.

What is the protein-protein docking prediction method used?

NovaDock’s algorithm is based on SwarmDock, developed in Dr. Paul Bates’ laboratory at the Cancer Research UK’s London Research Institute, and ongoing at the Francis Crick Institute. NovaDock does not use a library of templates, but instead makes docking predictions based on a type of energy calculation known as “particle swarm optimization.”

How do I visualize the predicted docked structures?

Results of the completed NovaDock prediction are shown in a specialized Report view in Protean 3D. After running a prediction, the Report view opens automatically. The Report uses interactive images and tables to show which templates were used in the prediction and the models that were the best match to the query. Scroll to the prediction model of interest and click the link “Open model in new document” to open it as a new Protean 3D document for further analysis.

What details are available for each protein-protein interaction prediction?

Available statistics for each predicted model include the Energy, Cluster Size, Residue Contacts and Contacts Fulfilled. For each residue, you can also see its Intermolecular Contacts.

What analysis options are available after generating protein docking models?

The NovaDock Report view starts with information about the receptor and ligand structures that were used as inputs in the NovaDock prediction and continues with a table showing the top ten ligand-receptor docking models predicted by NovaDock. Below this are sections for each predicted model, including an image showing the predicted docking model with the receptor and ligand chain shown in contrasting colors; and interactive tables with information about the model.

Can I export a structure model for publication?

Yes. Protean 3D lets you export the secondary structure itself or an image of the structure. After running a NovaDock prediction, the Report view opens automatically. Scroll to the prediction model of interest and click the link “Open model in new document.” You can then export the predicted structure as a .pdb or .cif file using Export Data > Export Structure. You can also export an image of the predicted structure in .png, .jpg or .gif formats using File > Export Image > Structure.

How can I model antibody-antigen interactions?

You can use NovaDock to predict the structure of antibody-antigen complexes by inputting the antibody and antigen structures. If you don’t have an experimental antibody structure, first model the structure using NovaFold Antibody, which is specifically designed to generate models of antibodies and antibody fragments (Fv, Fab, VH, sdAb) starting from sequence data. The NovaFold Antibody algorithm utilizes a combination of homology modeling and ab initio loop prediction, resulting in highly accurate predictions which can then be used in NovaDock.

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