AI Article Synopsis
- ClusPro is an automated web tool for docking protein structures, allowing users to upload protein files or enter PDB codes for analysis.
- It uses techniques like rigid body docking, energy screening, and clustering to generate ranked models of possible protein complexes.
- A newer version integrates the PIPER docking program, enhancing its capabilities to produce more accurate near-native docked structures.
Article Abstract
ClusPro is the first fully automated, web-based program for docking protein structures. Users may upload the coordinate files of two protein structures through ClusPro's web interface, or enter the PDB codes of the respective structures. The server performs rigid body docking, energy screening, and clustering to produce models. The program output is a short list of putative complexes ranked according to their clustering properties. ClusPro has been participating in CAPRI since January 2003, submitting predictions within 24 h after a target becomes available. In Rounds 6-11, ClusPro generated acceptable submissions for Targets 22, 25, and 27. In general, acceptable models were obtained for the relatively easy targets without substantial conformational changes upon binding. We also describe the new version of ClusPro that incorporates our recently developed docking program PIPER. PIPER is based on the fast Fourier transform correlation approach, but the method is extended to use pairwise interaction potentials, thereby increasing the number of near-native docked structures.
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| http://dx.doi.org/10.1002/prot.21795 | DOI Listing |
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