Applications of rDock Software

rDock is an open-source molecular docking software designed primarily for high-throughput virtual screening and prediction of binding modes. rDock was developed by Vernalis for high-throughput VS (HTVS) applications. Evolving from RiboDock, this program can be used for proteins and nucleic acids, and is designed to be very computationally efficient and allow users to incorporate additional constraints and information as biases to guide docking. If you compare rDock with two reference programs AutoDock Vina and Schrodinger's Glide. In terms of computational speed for virtual screening, rDock is faster than Vina and on par with Glide. For binding mode prediction, rDock and Vina outperform Glide. rDock is primarily written in C++, with accompanying scripts and programs written in C++, perl, or python. The full rDock package requires less than 50 MB of hard disk space and can be compiled on all Linux computers (currently only). Due to its design and implementation, it can be installed on a computing cluster and deployed on an unlimited number of CPUs, enabling HTVS activities to be performed within days.

Our Services Based on rDock Software

rDock software is designed for high-throughput virtual screening (HTVS) and binding mode prediction studies. On the rDock software platform, CD ComputaBio can provide docking of small molecules to proteins and nucleic acids.

• RNA-ligand Binding Mode Predictions
  CD ComputaBio predicts how a ligand will bind to a given molecule. rDock calculations converge after 20-50 GA runs. For rDock, the predicted binding mode is correct about 80% of the time, while Glide's performance is close to 70%.
• Efficient Virtual Screening
  CD ComputaBio harnesses the power of computer computing farms to run millions of compounds in a short period of time. rDock's VS performance is significantly better than Vina, but not as good as Glide in most systems unless pharmacophore constraints are used. The program is released under the less permissive General Public License and can be downloaded for free, along with a manual, example files, and a complete set of tests
• Small Molecules and Nucleic Acids Docking
  Nucleic acids have become increasingly important drug targets, where the structural determination of nucleic acid-ligand complexes is critical for understanding their function and thus developing therapeutic interventions. Prediction of nucleic acid binding to small molecules by applying our intrinsic scoring function for nucleic acid-ligand interactions.
• Results Analysis
  The methods of CD ComputaBio analysis results include RMSD analysis, RMSF analysis, energy analysis, principal component analysis, combining mode analysis and secondary structure content analysis, etc.

The Features of rDock Software

• Simple Way to Solve Difficult Problems
  rDock is a software application that can be used to dock multiple protein structures in a common coordinate frame. This application is based on the Rosetta software package and has been shown to be more accurate than other methods of determining structure. rDock can be used to improve the accuracy of 3D reconstructions and correct errors in protein-protein docking simulations.
• Sampling
  rDock uses a combination of stochastic and deterministic search techniques to generate low-energy ligand poses. The standard docking protocol to generate a single ligand pose uses 3 stages of a genetic algorithm search (GA1, GA2, GA3). rDock's scoring function parameters vary between stages to facilitate efficient sampling of starting poses while maximizing significantly reducing the likelihood of poses being trapped early in the search.

Project Sample

Our computational biology team has extensive experience in the research of docking on our rDock software platform. The following is a small snapshot of our research process for reference only. For details, please feel free to consult our professional team.

Related Links

rDOCK Tutorial