NPDock

NPDock predicts structures of protein–nucleic acid complexes from separate protein and nucleic acid (DNA or RNA) structures to model protein–DNA and protein–RNA interactions.

Key Features:

• Input structures: Starts from separate protein and nucleic acid (DNA or RNA) coordinates and accepts structures in PDB format.
• Docking: Performs docking to generate potential protein–nucleic acid binding poses.
• Scoring: Scores docking poses to evaluate potential interactions between proteins and nucleic acids.
• Clustering: Clusters best-scored models to identify consensus and representative solutions.
• Refinement: Refines selected models to improve the accuracy and reliability of predicted complexes.
• Macromolecule scope: Applicable to both RNA–protein and DNA–protein complex modeling.

Scientific Applications:

• Structural prediction: Prediction of protein–DNA and protein–RNA complex structures from separate component structures.
• Interaction analysis: Investigation of protein–nucleic acid interfaces and potential interaction mechanisms.
• Experimental alternative: Computational modeling of complexes when experimental structure determination is time-consuming or infeasible.

Methodology:

Beginning from separate protein and nucleic acid structures, NPDock performs docking to generate poses, scores those poses, clusters the best-scored models, and refines the most promising solutions.