PMID- 28059133
OWN - NLM
STAT- PubMed-not-MEDLINE
DCOM- 20180621
LR  - 20181113
IS  - 2045-2322 (Electronic)
IS  - 2045-2322 (Linking)
VI  - 7
DP  - 2017 Jan 6
TI  - Prediction of N-Methyl-D-Aspartate Receptor GluN1-Ligand Binding Affinity by a 
      Novel SVM-Pose/SVM-Score Combinatorial Ensemble Docking Scheme.
PG  - 40053
LID - 10.1038/srep40053 [doi]
LID - 40053
AB  - The glycine-binding site of the N-methyl-D-aspartate receptor (NMDAR) subunit 
      GluN1 is a potential pharmacological target for neurodegenerative disorders. A 
      novel combinatorial ensemble docking scheme using ligand and protein conformation 
      ensembles and customized support vector machine (SVM)-based models to select the 
      docked pose and to predict the docking score was generated for predicting the 
      NMDAR GluN1-ligand binding affinity. The predicted root mean square deviation 
      (RMSD) values in pose by SVM-Pose models were found to be in good agreement with 
      the observed values (n = 30, r(2) = 0.928-0.988,  = 0.894-0.954, 
      RMSE = 0.002-0.412, s = 0.001-0.214), and the predicted pK(i) values by SVM-Score 
      were found to be in good agreement with the observed values for the training 
      samples (n = 24, r(2) = 0.967,  = 0.899, RMSE = 0.295, s = 0.170) and test 
      samples (n = 13, q(2) = 0.894, RMSE = 0.437, s = 0.202). When subjected to 
      various statistical validations, the developed SVM-Pose and SVM-Score models 
      consistently met the most stringent criteria. A mock test asserted the 
      predictivity of this novel docking scheme. Collectively, this accurate novel 
      combinatorial ensemble docking scheme can be used to predict the NMDAR 
      GluN1-ligand binding affinity for facilitating drug discovery.
FAU - Leong, Max K
AU  - Leong MK
AD  - Department of Chemistry, National Dong Hwa University, Shoufeng, Hualien 97401, 
      Taiwan.
AD  - Department of Life Science and Institute of Biotechnology, National Dong Hwa 
      University, Shoufeng, Hualien 97401, Taiwan.
FAU - Syu, Ren-Guei
AU  - Syu RG
AD  - Department of Chemistry, National Dong Hwa University, Shoufeng, Hualien 97401, 
      Taiwan.
FAU - Ding, Yi-Lung
AU  - Ding YL
AD  - Department of Chemistry, National Dong Hwa University, Shoufeng, Hualien 97401, 
      Taiwan.
FAU - Weng, Ching-Feng
AU  - Weng CF
AD  - Department of Life Science and Institute of Biotechnology, National Dong Hwa 
      University, Shoufeng, Hualien 97401, Taiwan.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20170106
PL  - England
TA  - Sci Rep
JT  - Scientific reports
JID - 101563288
PMC - PMC5216401
EDAT- 2017/01/07 06:00
MHDA- 2017/01/07 06:01
PMCR- 2017/01/06
CRDT- 2017/01/07 06:00
PHST- 2016/08/19 00:00 [received]
PHST- 2016/11/30 00:00 [accepted]
PHST- 2017/01/07 06:00 [entrez]
PHST- 2017/01/07 06:00 [pubmed]
PHST- 2017/01/07 06:01 [medline]
PHST- 2017/01/06 00:00 [pmc-release]
AID - srep40053 [pii]
AID - 10.1038/srep40053 [doi]
PST - epublish
SO  - Sci Rep. 2017 Jan 6;7:40053. doi: 10.1038/srep40053.