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CSAR Scoring Challenge Reveals the Need for New Concepts in Estimating Protein–Ligand Binding Affinity

https://doi.org/10.1021/ci200034y

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

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Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function

inferredcites →https://doi.org/10.1002/jcc.20634openalex-snapshot

A semiempirical free energy force field with charge‐based desolvation

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Assessment of programs for ligand binding affinity prediction

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Binding MOAD (Mother Of All Databases)

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TSAR, a new graph–theoretical approach to computational modeling of protein side‐chain flexibility: Modeling of ionization properties of proteins

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A Self-Consistent, Microenvironment Modulated Screened Coulomb Potential Approximation to Calculate pH-Dependent Electrostatic Effects in Proteins

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Lead Finder: An Approach To Improve Accuracy of Protein−Ligand Docking, Binding Energy Estimation, and Virtual Screening

inferredcites →https://doi.org/10.1021/jm030489hopenalex-snapshot

Assessing Scoring Functions for Protein−Ligand Interactions

inferredcites →https://doi.org/10.1021/jm030580lopenalex-snapshot

The PDBbind Database: Collection of Binding Affinities for Protein−Ligand Complexes with Known Three-Dimensional Structures

inferredcites →https://doi.org/10.1021/jm048957qopenalex-snapshot

The PDBbind Database: Methodologies and Updates

inferredcites →https://doi.org/10.1021/jm050038sopenalex-snapshot

PMF Scoring Revisited

inferredcites →https://doi.org/10.1021/jm050362nopenalex-snapshot

A Critical Assessment of Docking Programs and Scoring Functions

inferredcites →https://doi.org/10.1021/jm051256oopenalex-snapshot

Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein−Ligand Complexes

inferredcites →https://doi.org/10.1021/jm100112jopenalex-snapshot

A Medicinal Chemist’s Guide to Molecular Interactions

inferredcites →https://doi.org/10.1073/pnas.0407607101openalex-snapshot

Halogen bonds in biological molecules

inferredcites →https://doi.org/10.1093/nar/gkj039openalex-snapshot

AffinDB: a freely accessible database of affinities for protein-ligand complexes from the PDB

inferredcites →https://doi.org/10.1093/nar/gkl999openalex-snapshot

BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities

inferredcites →https://doi.org/10.1108/03684920410534506openalex-snapshot

Information Theory, Inference, and Learning Algorithms

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