Using protein binding site prediction to improve protein docking

Gene ◽  
2008 ◽  
Vol 422 (1-2) ◽  
pp. 14-21 ◽  
Author(s):  
Bingding Huang ◽  
Michael Schroeder
Keyword(s):  
Protein Binding ◽  
Binding Site ◽  
Protein Docking ◽  
Protein Binding Site ◽  
Site Prediction ◽  
Binding Site Prediction

scholarly journals Regression applied to protein binding site prediction and comparison with classification

2009 ◽  
Vol 10 (1) ◽  
Author(s):  
Joachim Giard ◽  
Jérôme Ambroise ◽  
Jean-Luc Gala ◽  
Benoît Macq
Keyword(s):  
Protein Binding ◽  
Binding Site ◽  
Protein Binding Site ◽  
Site Prediction ◽  
Binding Site Prediction

scholarly journals Protein Binding Site Prediction by Combining Hidden Markov Support Vector Machine and Profile-Based Propensities

2014 ◽  
Vol 2014 ◽  
pp. 1-6 ◽  
Author(s):  
Bin Liu ◽  
Bingquan Liu ◽  
Fule Liu ◽  
Xiaolong Wang
Keyword(s):  
Support Vector Machine ◽  
Protein Binding ◽  
Binding Site ◽  
Hidden Markov ◽  
Accessible Surface Area ◽  
Protein Binding Site ◽  
Support Vector ◽  
Data Sets ◽  
Site Prediction ◽  
Binding Site Prediction

Identification of protein binding sites is critical for studying the function of the proteins. In this paper, we proposed a method for protein binding site prediction, which combined the order profile propensities and hidden Markov support vector machine (HM-SVM). This method employed the sequential labeling technique to the field of protein binding site prediction. The input features of HM-SVM include the profile-based propensities, the Position-Specific Score Matrix (PSSM), and Accessible Surface Area (ASA). When tested on different data sets, the proposed method showed promising results, and outperformed some closely relative methods by more than 10% in terms of AUC.

scholarly journals Division of Protein Surface Patches and Its Application in Protein Binding Site Prediction

2012 ◽  
Vol 28 (11) ◽  
pp. 2729-2734
Author(s):  
WANG Pan-Wen ◽  
◽  
GONG Xin-Qi ◽  
LI Chun-Hua ◽  
CHEN Wei-Zu ◽  
...  
Keyword(s):  
Protein Binding ◽  
Binding Site ◽  
Protein Binding Site ◽  
Protein Surface ◽  
Site Prediction ◽  
Binding Site Prediction ◽  
Surface Patches

Protein−Protein Binding Site Prediction by Local Structural Alignment

2010 ◽  
Vol 50 (10) ◽  
pp. 1906-1913 ◽  
Author(s):  
Nejc Carl ◽  
Janez Konc ◽  
Blaž Vehar ◽  
Dušanka Janežič
Keyword(s):  
Protein Binding ◽  
Binding Site ◽  
Structural Alignment ◽  
Protein Binding Site ◽  
Site Prediction ◽  
Binding Site Prediction
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