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Title: ClusPro in rounds 38 to 45 of CAPRI: Toward combining template‐based methods with free docking
Abstract

Targets in the protein docking experiment CAPRI (Critical Assessment of Predicted Interactions) generally present new challenges and contribute to new developments in methodology. In rounds 38 to 45 of CAPRI, most targets could be effectively predicted using template‐based methods. However, the server ClusPro required structures rather than sequences as input, and hence we had to generate and dock homology models. The available templates also provided distance restraints that were directly used as input to the server. We show here that such an approach has some advantages. Free docking with template‐based restraints using ClusPro reproduced some interfaces suggested by weak or ambiguous templates while not reproducing others, resulting in correct server predicted models. More recently we developed the fully automated ClusPro TBM server that performs template‐based modeling and thus can use sequences rather than structures of component proteins as input. The performance of the server, freely available for noncommercial use athttps://tbm.cluspro.org, is demonstrated by predicting the protein‐protein targets of rounds 38 to 45 of CAPRI.

 
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Award ID(s):
1816314 1759277 1759472
NSF-PAR ID:
10456279
Author(s) / Creator(s):
 ;  ;  ;  ;  ;  ;  ;  ;  ;  ;  ;  ;  ;  ;  
Publisher / Repository:
Wiley Blackwell (John Wiley & Sons)
Date Published:
Journal Name:
Proteins: Structure, Function, and Bioinformatics
Volume:
88
Issue:
8
ISSN:
0887-3585
Page Range / eLocation ID:
p. 1082-1090
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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