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Assessing the Geometric Diversity of Cytochrome P450 Ligand Conformers by Hierarchical Clustering with a Stop Criterion

https://doi.org/10.1021/ci800275k
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/cmdc.200500024openalex-snapshot
Prediction of Small‐Molecule Binding to Cytochrome P450 3A4: Flexible Docking Combined with Multidimensional QSAR
inferredcites →https://doi.org/10.1002/jcc.540140907openalex-snapshot
Conformational searching methods for small molecules. I. Study of the sybyl search method
inferredcites →https://doi.org/10.1002/jcc.540150811openalex-snapshot
Cluster analysis of molecular conformations
inferredcites →https://doi.org/10.1002/pro.5560041025openalex-snapshot
Modeling conformational changes in cyclosporin A
inferredcites →https://doi.org/10.1007/bf02294245openalex-snapshot
An Examination of Procedures for Determining the Number of Clusters in a Data Set
inferredcites →https://doi.org/10.1007/bf02294393openalex-snapshot
Comparative Evaluation of Two Superior Stopping Rules for Hierarchical Cluster Analysis
inferredcites →https://doi.org/10.1016/0031-3203(87)90034-3openalex-snapshot
How many clusters are best? - An experiment
inferredcites →https://doi.org/10.1016/0378-3758(89)90033-5openalex-snapshot
Algorithms for clustering data
inferredcites →https://doi.org/10.1016/0891-5849(96)83807-xopenalex-snapshot
Cytochrome P450: Structure, mechanism, and biochemistry
inferredcites →https://doi.org/10.1016/s0097-8485(98)00017-5openalex-snapshot
Interactive maximal common 3D substructure searching with the combined SDM/RMS algorithm
inferredcites →https://doi.org/10.1016/s0165-1684(02)00475-9openalex-snapshot
Cluster validation techniques for genome expression data
inferredcites →https://doi.org/10.1016/s0166-1280(96)04649-0openalex-snapshot
Conformer clustering algorithm and its application for crown-type macrocycles
inferredcites →https://doi.org/10.1016/s0167-8655(02)00257-xopenalex-snapshot
Validation indices for graph clustering
inferredcites →https://doi.org/10.1016/s1093-3263(03)00123-2openalex-snapshot
Analysis and optimization of structure-based virtual screening protocols (1): exploration of ligand conformational sampling techniques
inferredcites →https://doi.org/10.1021/bi700876aopenalex-snapshot
Unusual Regioselectivity and Active Site Topology of Human Cytochrome P450 2J2
inferredcites →https://doi.org/10.1021/ci700010topenalex-snapshot
Ligand-Based Models for the Isoform Specificity of Cytochrome P450 3A4, 2D6, and 2C9 Substrates
inferredcites →https://doi.org/10.1021/ci7000956openalex-snapshot
Assessment of Conformational Ensemble Sizes Necessary for Specific Resolutions of Coverage of Conformational Space
inferredcites →https://doi.org/10.1021/ci700313eopenalex-snapshot
Receptor-Based Virtual Ligand Screening for the Identification of Novel CDC25 Phosphatase Inhibitors
inferredcites →https://doi.org/10.1021/ci9603700openalex-snapshot
Three-Dimensional Pattern Recognition from Molecular Distance Minimization
inferredcites →https://doi.org/10.1021/ja00299a024openalex-snapshot
Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model
inferredcites →https://doi.org/10.1023/a:1015930826903openalex-snapshot
Reproducing the conformations of protein-bound ligands: A critical evaluation of several popular conformational searching tools
inferredcites →https://doi.org/10.1023/a:1021394316112openalex-snapshot
A Decision Criterion for the Optimal Number of Clusters in Hierarchical Clustering
inferredcites →https://doi.org/10.1046/j.1365-2125.1999.00073.xopenalex-snapshot
CYP3A4 drug interactions: correlation of 10 in vitro probe substrates
inferredcites →https://doi.org/10.1063/1.1484559openalex-snapshot
Chiral mixtures
inferredcites →https://doi.org/10.1063/1.532988openalex-snapshot
On the root mean square quantitative chirality and quantitative symmetry measures
inferredcites →https://doi.org/10.1093/comjnl/20.4.359openalex-snapshot
Hierarchical grouping methods and stopping rules: an evaluation
inferredcites →https://doi.org/10.1093/nar/gkm289openalex-snapshot
Frog: a FRee Online druG 3D conformation generator
inferredcites →https://doi.org/10.1109/3477.678624openalex-snapshot
Some new indexes of cluster validity
inferredcites →https://doi.org/10.1111/j.1399-3011.1994.tb01021.xopenalex-snapshot
Conformational study of cyclosporin A in acetone at low temperature
inferredcites →https://doi.org/10.1124/mol.107.042861openalex-snapshot
Improvement of Cyclophosphamide Activation by CYP2B6 Mutants: From in Silico to ex Vivo
inferredcites →https://doi.org/10.1201/9781420034912openalex-snapshot
Clustering for Data Mining

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Spheres Unions and Intersections and Some of their Applications in Molecular Modeling
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Molecular dynamics simulations reveal the inhibition mechanism of Cdc42 by RhoGDI1
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The molecular determinants of neurosteroid binding in the GABA(A) receptor
inferred← citeshttps://doi.org/10.1021/acs.jcim.6c00490openalex-snapshot
Exploring Conformer Search Workflows Using OpenBabel, Hierarchical Clustering, and Quantum Chemical Optimizations: A Workflow Study Including Oligothiophenes and Y6
inferred← citeshttps://doi.org/10.1021/acs.jpcb.8b06523openalex-snapshot
Evaluation of Ca2+ Binding Sites in Tacrolimus by Infrared Multiple Photon Dissociation Spectroscopy
inferred← citeshttps://doi.org/10.1021/acs.jpcb.8b10767openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/jm4000566openalex-snapshot
Structural Basis and SAR for G007-LK, a Lead Stage 1,2,4-Triazole Based Specific Tankyrase 1/2 Inhibitor
inferred← citeshttps://doi.org/10.1093/bioinformatics/btt644openalex-snapshot
Computing cavities, channels, pores and pockets in proteins from non-spherical ligands models
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Multiple functional neurosteroid binding sites on GABAA receptors
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Three-dimensional structure generators of drug-like compounds: DG-AMMOS, an open-source package
inferred← citeshttps://doi.org/10.3390/ijms20040987openalex-snapshot
Four Major Channels Detected in the Cytochrome P450 3A4: A Step toward Understanding Its Multispecificity
inferred← citeshttps://doi.org/10.3390/molecules29163902openalex-snapshot
Clustering Molecules at a Large Scale: Integrating Spectral Geometry with Deep Learning
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The Symmetric Difference Distance: A New Way to Evaluate the Evolution of Interfaces along Molecular Dynamics Trajectories; Application to Influenza Hemagglutinin
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Site-specific effects of neurosteroids on GABAA receptor activation and desensitization
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