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Assessment of Conformational Ensemble Sizes Necessary for Specific Resolutions of Coverage of Conformational Space

https://doi.org/10.1021/ci7000956
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What this work says

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

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Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94
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MMFF VI. MMFF94s option for energy minimization studies
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Handbook of Chemoinformatics
inferredcites →https://doi.org/10.1002/9783527618279.ch9bopenalex-snapshot
Conformational Analysis and Searching
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Comparative Performance Assessment of the Conformational Model Generators Omega and Catalyst: A Large‐Scale Survey on the Retrieval of Protein‐Bound Ligand Conformations.
inferredcites →https://doi.org/10.1007/978-3-642-78027-1_26openalex-snapshot
Conformational Freedom in 3-D Databases
inferredcites →https://doi.org/10.1007/bf00123667openalex-snapshot
A fast and efficient method to generate biologically relevant conformations
inferredcites →https://doi.org/10.1016/0968-0896(95)00031-bopenalex-snapshot
Conformational changes of small molecules binding to proteins
inferredcites →https://doi.org/10.1016/s0166-1280(96)04565-4openalex-snapshot
Systematic search in conformational analysis
inferredcites →https://doi.org/10.1016/s1093-3263(02)00204-8openalex-snapshot
Assessing the performance of OMEGA with respect to retrieving bioactive conformations
inferredcites →https://doi.org/10.1016/s1093-3263(97)00014-4openalex-snapshot
Conformational analysis using distance geometry methods
inferredcites →https://doi.org/10.1021/ci00017a025openalex-snapshot
Flexible 3D searching: The directed tweak technique
inferredcites →https://doi.org/10.1021/ci00022a012openalex-snapshot
Chemical Function Queries for 3D Database Search
inferredcites →https://doi.org/10.1021/ci00024a018openalex-snapshot
Analysis of Conformational Coverage. 1. Validation and Estimation of Coverage
inferredcites →https://doi.org/10.1021/ci00024a019openalex-snapshot
Analysis of Conformational Coverage. 2. Applications of Conformational Models
inferredcites →https://doi.org/10.1021/ci00067a017openalex-snapshot
Automated conformational analysis and structure generation: algorithms for molecular perception
inferredcites →https://doi.org/10.1021/ci049731zopenalex-snapshot
Comparison of Conformational Analysis Techniques To Generate Pharmacophore Hypotheses Using Catalyst
inferredcites →https://doi.org/10.1021/ci049753lopenalex-snapshot
Comparative Analysis of Protein-Bound Ligand Conformations with Respect to Catalyst's Conformational Space Subsampling Algorithms
inferredcites →https://doi.org/10.1021/ci050075sopenalex-snapshot
Impact of Conformational Flexibility on Three-Dimensional Similarity Searching Using Correlation Vectors
inferredcites →https://doi.org/10.1021/ci060084gopenalex-snapshot
Comparative Performance Assessment of the Conformational Model Generators Omega and Catalyst: A Large-Scale Survey on the Retrieval of Protein-Bound Ligand Conformations
inferredcites →https://doi.org/10.1021/j100389a010openalex-snapshot
DREIDING: a generic force field for molecular simulations
inferredcites →https://doi.org/10.1021/ja952478mopenalex-snapshot
Low Mode Search. An Efficient, Automated Computational Method for Conformational Analysis: Application to Cyclic and Acyclic Alkanes and Cyclic Peptides
inferredcites →https://doi.org/10.1021/jm030563wopenalex-snapshot
Conformational Analysis of Drug-Like Molecules Bound to Proteins: An Extensive Study of Ligand Reorganization upon Binding
inferredcites →https://doi.org/10.1023/a:1008007507641openalex-snapshot
Conformational energy penalties of protein-bound ligands
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:1016320106741openalex-snapshot
Can we separate active from inactive conformations?
inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot
The Protein Data Bank
inferredcites →https://doi.org/10.1093/nar/30.1.249openalex-snapshot
MMDB: Entrez's 3D-structure database
inferredcites →https://doi.org/10.1093/nar/gkg086openalex-snapshot
MMDB: Entrez's 3D-structure database

What points at this work

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

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Consensus Models of Activity Landscapes
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Challenges in Mechanistic Investigation of a Flexible Aminocatalyst as Demonstrated through Enamine Formation
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Finding Potential Multitarget Ligands Using PubChem
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Dynamic clustering threshold reduces conformer ensemble size while maintaining a biologically relevant ensemble
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Conformational analysis of macrocycles: comparing general and specialized methods
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Tackling the conformational sampling of larger flexible compounds and macrocycles in pharmacology and drug discovery
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Conformational study of melamine crosslinkers and spectroscopical comparison of HMMM molecules by practical measurements and quantum chemical calculations
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Toward Focusing Conformational Ensembles on Bioactive Conformations: A Molecular Mechanics/Quantum Mechanics Study
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Conformation Generation: The State of the Art
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ConfGen: A Conformational Search Method for Efficient Generation of Bioactive Conformers
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Drug-like Bioactive Structures and Conformational Coverage with the LigPrep/ConfGen Suite: Comparison to Programs MOE and Catalyst
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Consensus Models of Activity Landscapes with Multiple Chemical, Conformer, and Property Representations
inferred← citeshttps://doi.org/10.1021/ci200442hopenalex-snapshot
Modeling Flexible Pharmacophores with Distance Geometry, Scoring, and Bound Stretching
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Macrocycle Conformational Sampling with MacroModel
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Fast and Efficient in Silico 3D Screening: Toward Maximum Computational Efficiency of Pharmacophore-Based and Shape-Based Approaches
inferred← citeshttps://doi.org/10.1021/ci800130kopenalex-snapshot
Conformational Sampling of Druglike Molecules with MOE and Catalyst: Implications for Pharmacophore Modeling and Virtual Screening
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Assessing the Geometric Diversity of Cytochrome P450 Ligand Conformers by Hierarchical Clustering with a Stop Criterion
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Novel Method for the Evaluation of 3D Conformation Generators
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Bioactive Conformational Biasing: A New Method for Focusing Conformational Ensembles on Bioactive-Like Conformers
inferred← citeshttps://doi.org/10.1039/d5cp01263eopenalex-snapshot
Combining simulations and experiments – a perspective on maximum entropy methods
inferred← citeshttps://doi.org/10.1186/1758-2946-3-4openalex-snapshot
PubChem3D: Conformer generation
inferred← citeshttps://doi.org/10.1186/1758-2946-3-8openalex-snapshot
Confab - Systematic generation of diverse low-energy conformers
inferred← citeshttps://doi.org/10.1186/1758-2946-4-28openalex-snapshot
Effects of multiple conformers per compound upon 3-D similarity search and bioassay data analysis
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PubChem3D: conformer ensemble accuracy
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PubChem structure–activity relationship (SAR) clusters
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Biasing conformational ensembles towards bioactive-like conformers for ligand-based drug design
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Exploiting PubChem for virtual screening
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Energy Windows for Computed Compound Conformers: Covering Artefacts Or Truly Large Reorganization Energies?
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