Prediction of N-Methyl-D-Aspartate Receptor GluN1-Ligand Binding Affinity by a Novel SVM-Pose/SVM-Score Combinatorial Ensemble Docking Scheme

scientific article published on 06 January 2017

Prediction of N-Methyl-D-Aspartate Receptor GluN1-Ligand Binding Affinity by a Novel SVM-Pose/SVM-Score Combinatorial Ensemble Docking Scheme is …
instance of (P31):
scholarly articleQ13442814

External links are
P356DOI10.1038/SREP40053
P932PMC publication ID5216401
P698PubMed publication ID28059133

P50authorChing-Feng WengQ43275475
P2093author name stringMax K Leong
Yi-Lung Ding
Ren-Guei Syu
P2860cites workGene Selection for Cancer Classification using Support Vector MachinesQ56535529
Virtual screening of organic molecule databases. Design of focused libraries of potential ligands of NMDA and AMPA receptorsQ56983093
Synthesis and excitatory amino acid pharmacology of a series of heterocyclic-fused quinoxalinones and quinazolinonesQ67542644
Scoring noncovalent protein-ligand interactions: a continuous differentiable function tuned to compute binding affinitiesQ71851460
LigScore: a novel scoring function for predicting binding affinitiesQ81552453
Comparative studies on some metrics for external validation of QSPR modelsQ83142287
Subunit-specific roles of glycine-binding domains in activation of NR1/NR3 N-methyl-D-aspartate receptorsQ24307479
A nomenclature for ligand-gated ion channelsQ24609005
Flexible ligand docking using conformational ensemblesQ24673137
Novel NMDA receptor modulators: an updateQ26849614
Virtual screening using protein-ligand docking: avoiding artificial enrichmentQ53639582
Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexesQ53678858
Neural network studies. 1. Comparison of overfitting and overtrainingQ55968238
Averaged shifted histogramQ56049050
NMDA receptor modulators: an updated patent review (2013-2014)Q26997407
Mechanisms of activation, inhibition and specificity: crystal structures of the NMDA receptor NR1 ligand-binding coreQ27641433
Ligand-specific deactivation time course of GluN1/GluN2D NMDA receptorsQ27667580
Subunit arrangement and phenylethanolamine binding in GluN1/GluN2B NMDA receptorsQ27670455
Conformational Analysis of NMDA Receptor GluN1, GluN2, and GluN3 Ligand-Binding Domains Reveals Subtype-Specific CharacteristicsQ27679791
Crystal Structure and Pharmacological Characterization of a Novel N-Methyl-D-aspartate (NMDA) Receptor Antagonist at the GluN1 Glycine Binding SiteQ27680080
Structural Insights into Competitive Antagonism in NMDA ReceptorsQ27681450
Crystal structure of a heterotetrameric NMDA receptor ion channelQ27684006
NMDA receptor structures reveal subunit arrangement and pore architectureQ27684638
Positive Allosteric Modulators of GluN2A-Containing NMDARs with Distinct Modes of Action and Impacts on Circuit FunctionQ27704016
LIGPLOT: a program to generate schematic diagrams of protein-ligand interactionsQ27861128
QSAR modeling: where have you been? Where are you going to?Q28222668
PMF scoring revisitedQ28265646
Comparison of consensus scoring strategies for evaluating computational models of protein-ligand complexesQ28292827
A machine learning-based method to improve docking scoring functions and its application to drug repurposingQ28304560
L-701,324, a selective antagonist at the glycine site of the NMDA receptor, counteracts haloperidol-induced muscle rigidity in ratsQ28377268
Application of Consensus Scoring and Principal Component Analysis for Virtual Screening against β-Secretase (BACE-1)Q28484175
Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94Q28842789
Development and testing of a general amber force fieldQ29547642
A critical assessment of docking programs and scoring functionsQ29616761
CSAR Benchmark Exercise 2011–2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric SeriesQ30543685
Evaluation of docking performance: comparative data on docking algorithmsQ30889483
How does consensus scoring work for virtual library screening? An idealized computer experimentQ31017163
Tandem 3D-QSARs approach as a valuable tool to predict binding affinity data: design of new Gly/NMDA receptor antagonists as a key study.Q31122723
Rational selection of training and test sets for the development of validated QSAR modelsQ31165909
GFscore: a general nonlinear consensus scoring function for high-throughput dockingQ33251333
SeleX-CS: a new consensus scoring algorithm for hit discovery and lead optimizationQ33410990
Target-specific support vector machine scoring in structure-based virtual screening: computational validation, in vitro testing in kinases, and effects on lung cancer cell proliferationQ33856208
NMDA receptor subunits: diversity, development and diseaseQ33950711
Mechanism of partial agonist action at the NR1 subunit of NMDA receptorsQ33988352
Mechanistic insights into xenon inhibition of NMDA receptors from MD simulationsQ33990281
Real External Predictivity of QSAR Models. Part 2. New Intercomparable Thresholds for Different Validation Criteria and the Need for Scatter Plot InspectionQ34283181
Docking and scoring in virtual screening for drug discovery: methods and applicationsQ34364227
Comparative assessment of scoring functions on an updated benchmark: 1. Compilation of the test set.Q34414478
1-Substituted pyrazolo[1,5-c]quinazolines as novel Gly/NMDA receptor antagonists: synthesis, biological evaluation, and molecular modeling studyQ46640611
Molecular docking to ensembles of protein structuresQ46668232
ID-Score: A New Empirical Scoring Function Based on a Comprehensive Set of Descriptors Related to Protein–Ligand InteractionsQ46690363
3-Hydroxy-1H-quinazoline-2,4-dione derivatives as new antagonists at ionotropic glutamate receptors: molecular modeling and pharmacological studiesQ46885828
The N-terminal domain of the GluN3A subunit determines the efficacy of glycine-activated NMDA receptorsQ48559577
Numerical Errors and Chaotic Behavior in Docking SimulationsQ48562868
Substituted indole-2-carboxylates as in vivo potent antagonists acting as the strychnine-insensitive glycine binding siteQ48765974
Ifenprodil discriminates subtypes of the N-methyl-D-aspartate receptor: selectivity and mechanisms at recombinant heteromeric receptorsQ49132765
Application of Genetic Function Approximation to Quantitative Structure-Activity Relationships and Quantitative Structure-Property RelationshipsQ51614833
Supervised consensus scoring for docking and virtual screeningQ51994661
Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinationsQ52069951
Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteinsQ52132563
A general and fast scoring function for protein-ligand interactions: a simplified potential approachQ52222006
Giant nonlinear response from plasmonic metasurfaces coupled to intersubband transitions.Q53510846
Characterization of protein conformational states by normal-mode frequenciesQ53564115
Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programmingQ34447822
Optimization of molecular docking scores with support vector rank regressionQ34625066
NMDA receptor subunit diversity: impact on receptor properties, synaptic plasticity and diseaseQ34651972
Structure-based discovery of antagonists for GluN3-containing N-methyl-D-aspartate receptorsQ34968786
Predicting protein functions using incomplete hierarchical labelsQ35543419
Machine-learning scoring functions for identifying native poses of ligands docked to known and novel proteinsQ35558950
Docking and Scoring with Target-Specific Pose Classifier Succeeds in Native-Like Pose Identification But Not Binding Affinity Prediction in the CSAR 2014 Benchmark ExerciseQ35981309
Describing the validity of carcinogen screening testsQ36042747
Agonist binding to the NMDA receptor drives movement of its cytoplasmic domain without ion flow.Q36332086
Consensus scoring for protein-ligand interactionsQ36458866
What is a support vector machine?Q36679246
Protons Potentiate GluN1/GluN3A Currents by Attenuating Their Desensitisation.Q36713681
Stereoselectivity in drug metabolismQ36788391
[3H]MDL 105,519, a high-affinity radioligand for the N-methyl-D-aspartate receptor-associated glycine recognition site.Q36825802
Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection--what can we learn from earlier mistakes?Q37057393
Rescoring ligand docking poses.Q37742544
Structural ensemble in computational drug screeningQ37750881
GluN3 subunit-containing NMDA receptors: not just one-trick poniesQ37975344
Latest developments in molecular docking: 2010–2011 in reviewQ38092807
Targeting of NMDA receptors in new treatments for schizophreniaQ38223276
NMDARs in neurological diseases: a potential therapeutic targetQ38232734
In silico Prediction of Aqueous Solubility: a Comparative Study of Local and Global Predictive ModelsQ39525606
Prediction of Protein-Ligand Binding Poses via a Combination of Induced Fit Docking and Metadynamics SimulationsQ39795344
Synthesis, structural activity-relationships, and biological evaluation of novel amide-based allosteric binding site antagonists in NR1A/NR2B N-methyl-D-aspartate receptorsQ39818021
Glycine/NMDA receptor antagonists as potential CNS therapeutic agents: ACEA-1021 and related compoundsQ40322844
Structural Basis for Negative Allosteric Modulation of GluN2A-Containing NMDA ReceptorsQ41159277
Consensus scoring for ligand/protein interactionsQ42670601
QSAR modeling and prediction of the endocrine-disrupting potencies of brominated flame retardantsQ43090710
Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichmentsQ44012277
CoMFA and homology-based models of the glycine binding site of N-methyl-d-aspartate receptorQ44406084
Comparative evaluation of 11 scoring functions for molecular dockingQ44457437
The ensemble performance index: an improved measure for assessing ensemble pose prediction performance.Q44636889
Model structures of the N-methyl-D-aspartate receptor subunit NR1 explain the molecular recognition of agonist and antagonist ligandsQ44762506
SFCscoreRF: A Random Forest-Based Scoring Function for Improved Affinity Prediction of Protein–Ligand ComplexesQ45805013
In Silico Predictions of Human Skin Permeability using Nonlinear Quantitative Structure-Property Relationship Models.Q45955189
Predicting mutagenicity of aromatic amines by various machine learning approaches.Q45962910
Protein docking using surface matching and supervised machine learning.Q45965397
Combination of a naive Bayes classifier with consensus scoring improves enrichment of high-throughput docking results.Q45966697
P275copyright licenseCreative Commons Attribution 4.0 InternationalQ20007257
P6216copyright statuscopyrightedQ50423863
P407language of work or nameEnglishQ1860
P921main subjectligand bindingQ61659151
P304page(s)40053
P577publication date2017-01-06
P1433published inScientific ReportsQ2261792
P1476titlePrediction of N-Methyl-D-Aspartate Receptor GluN1-Ligand Binding Affinity by a Novel SVM-Pose/SVM-Score Combinatorial Ensemble Docking Scheme
P478volume7

Reverse relations

cites work (P2860)
Q64121450Exponential consensus ranking improves the outcome in docking and receptor ensemble docking
Q93126855Molecular Docking: Shifting Paradigms in Drug Discovery
Q91012235Natural phenolic compounds potentiate hypoglycemia via inhibition of Dipeptidyl peptidase IV
Q47355897Potential natural mTOR inhibitors screened by in silico approach and suppress hepatic stellate cells activation.
Q90291678The perceptions of natural compounds against dipeptidyl peptidase 4 in diabetes: from in silico to in vivo
Q90420762Theoretical Prediction of the Complex P-Glycoprotein Substrate Efflux Based on the Novel Hierarchical Support Vector Regression Scheme

Search more.