Related Experiment Video
Updated: May 2, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
DOCK/PIERR: web server for structure prediction of protein-protein complexes
Shruthi Viswanath1, D V S Ravikant, Ron Elber
1Department of Computer Science, University of Texas at Austin, Austin, TX, USA.
Abstract:
In protein docking we aim to find the structure of the complex formed when two proteins interact. Protein-protein interactions are crucial for cell function. Here we discuss the usage of DOCK/PIERR. In DOCK/PIERR, a uniformly discrete sampling of orientations of one protein with respect to the other, are scored, followed by clustering, refinement, and reranking of structures. The novelty of this method lies in the scoring functions used. These are obtained by examining hundreds of millions of correctly and incorrectly docked structures, using an algorithm based on mathematical programming, with provable convergence properties.
Related Concept Videos
Protein-protein Interfaces
Protein-Protein Interfaces
Protein Organization
The primary structure of a protein is its amino acid sequence....
Protein Complexes with Interchangeable Parts
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...
Protein Complexes with Interchangeable Parts
Protein Networks
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

