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Global Free Energy Scoring Functions Based on Distance-Dependent Atom-Type Pair Descriptors

https://doi.org/10.1021/ci100473d
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What this work says

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

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SFCscore: Scoring functions for affinity prediction of protein–ligand complexes
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Docking and scoring with alternative side‐chain conformations
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Knowledge-based scoring function to predict protein-ligand interactions
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Customizing scoring functions for docking
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A geometric approach to macromolecule-ligand interactions
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Target-biased scoring approaches and expert systems in structure-based virtual screening
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The role of quantum mechanics in structure-based drug design
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Order Changes within Receptor Systems upon Ligand Binding: Receptor Tightening/Oligomerisation and the Interpretation of Binding Parameters
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Cooperative biotin binding by streptavidin. Electrophoretic behavior and subunit association of streptavidin in the presence of 6 M urea.
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Progress in Medicinal Chemistry
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Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings 1PII of original article: S0169-409X(96)00423-1. The article was originally published in Advanced Drug Delivery Reviews 23 (1997) 3–25. 1
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Efficient Drug Lead Discovery and Optimization
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Predicting Protein−Ligand Binding Affinities Using Novel Geometrical Descriptors and Machine-Learning Methods
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QSAR − How Good Is It in Practice? Comparison of Descriptor Sets on an Unbiased Cross Section of Corporate Data Sets
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Test MM-PB/SA on True Conformational Ensembles of Protein−Ligand Complexes
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Leave-Cluster-Out Cross-Validation Is Appropriate for Scoring Functions Derived from Diverse Protein Data Sets
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Binding Affinity Prediction with Property-Encoded Shape Distribution Signatures
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Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
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Molecular Dynamics Studies of the Hydration of α,α-Trehalose
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Simple, Intuitive Calculations of Free Energy of Binding for Protein−Ligand Complexes. 1. Models without Explicit Constrained Water
inferredcites →https://doi.org/10.1021/jm030489hopenalex-snapshot
Assessing Scoring Functions for Protein−Ligand Interactions
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The PDBbind Database: Collection of Binding Affinities for Protein−Ligand Complexes with Known Three-Dimensional Structures
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The PDBbind Database: Methodologies and Updates
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Large-Scale Validation of a Quantum Mechanics Based Scoring Function: Predicting the Binding Affinity and the Binding Mode of a Diverse Set of Protein−Ligand Complexes
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inferredcites →https://doi.org/10.1023/a:1016357811882openalex-snapshot
Further development and validation of empirical scoring functions for structure-based binding affinity prediction
inferredcites →https://doi.org/10.1023/a:1020155510718openalex-snapshot
A review of protein-small molecule docking methods
inferredcites →https://doi.org/10.1063/1.2378907openalex-snapshot
Comparison of free energy methods for molecular systems
inferredcites →https://doi.org/10.1093/bioinformatics/btq112openalex-snapshot
A machine learning approach to predicting protein–ligand binding affinity with applications to molecular docking
inferredcites →https://doi.org/10.1110/ps.051970306openalex-snapshot
Cooperative hydrogen bond interactions in the streptavidin–biotin system
inferredcites →https://doi.org/10.1146/annurev.biophys.36.040306.132550openalex-snapshot
Calculation of Protein-Ligand Binding Affinities
inferredcites →https://doi.org/10.1146/annurev.pharmtox.37.1.71openalex-snapshot
STRUCTURE-BASED DRUG DESIGN:Computational Advances
inferredcites →https://doi.org/10.2174/092986706778521797openalex-snapshot
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inferredcites →https://doi.org/10.2174/138920306778559395openalex-snapshot
Scoring Functions for Protein-Ligand Docking
inferredcites →https://doi.org/10.2174/138920306778559412openalex-snapshot
eHiTS: An Innovative Approach to the Docking and Scoring Function Problems
inferredcites →https://doi.org/10.2174/138920307781369382openalex-snapshot
Structure-Based Drug Design: Docking and Scoring
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Docking Screens: Right for the Right Reasons?
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What points at this work

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

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Scoring Functions for Protein–Ligand Interactions
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