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Cheminformatics Meets Molecular Mechanics: A Combined Application of Knowledge-Based Pose Scoring and Physical Force Field-Based Hit Scoring Functions Improves the Accuracy of Structure-Based Virtual Screening

https://doi.org/10.1021/ci2002507

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What this work says

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

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Gaussian docking functions

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An iterative knowledge‐based scoring function to predict protein–ligand interactions: II. Validation of the scoring function

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Best Practices for QSAR Model Development, Validation, and Exploitation

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Minimizing false positives in kinase virtual screens

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Knowledge-based scoring function to predict protein-ligand interactions

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How to do an evaluation: pitfalls and traps

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Optimization of CAMD techniques 3. Virtual screening enrichment studies: a help or hindrance in tool selection?

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What do we know and when do we know it?

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Managing bias in ROC curves

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Recommendations for evaluation of computational methods

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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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Is it possible to increase hit rates in structure-based virtual screening by pharmacophore filtering? An investigation of the advantages and pitfalls of post-filtering

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Beware of q2!

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Virtual screening and fast automated docking methods

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Knowledge-Based Interaction Fingerprint Scoring: A Simple Method for Improving the Effectiveness of Fast Scoring Functions

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Rapid Flexible Docking Using a Stochastic Rotamer Library of Ligands

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FLAP: GRID Molecular Interaction Fields in Virtual Screening. Validation using the DUD Data Set

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Supervised Consensus Scoring for Docking and Virtual Screening

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Consensus Scoring with Feature Selection for Structure-Based Virtual Screening

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Structure-Based Virtual Screening with Supervised Consensus Scoring: Evaluation of Pose Prediction and Enrichment Factors

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FieldScreen: Virtual Screening Using Molecular Fields. Application to the DUD Data Set

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MedusaScore: An Accurate Force Field-Based Scoring Function for Virtual Drug Screening

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Docking Ligands into Flexible and Solvated Macromolecules. 4. Are Popular Scoring Functions Accurate for this Class of Proteins?

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Position Specific Interaction Dependent Scoring Technique for Virtual Screening Based on Weighted Protein−Ligand Interaction Fingerprint Profiles

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Comparative Assessment of Scoring Functions on a Diverse Test Set

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APIF: A New Interaction Fingerprint Based on Atom Pairs and Its Application to Virtual Screening

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Docking Ligands into Flexible and Solvated Macromolecules. 5. Force-Field-Based Prediction of Binding Affinities of Ligands to Proteins

inferredcites →https://doi.org/10.1021/ci900382eopenalex-snapshot

Combining Machine Learning and Pharmacophore-Based Interaction Fingerprint for in Silico Screening

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Conceptual Density Functional Theory

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Electrophilicity Index

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Comparative Evaluation of 11 Scoring Functions for Molecular Docking

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Decoys for Docking

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Interaction Profiles of Protein Kinase−Inhibitor Complexes and Their Application to Virtual Screening

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Development of Quantitative Structure−Binding Affinity Relationship Models Based on Novel Geometrical Chemical Descriptors of the Protein−Ligand Interfaces

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A Critical Assessment of Docking Programs and Scoring Functions

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Benchmarking Sets for Molecular Docking

inferredcites →https://doi.org/10.1021/jm980536jopenalex-snapshot

A General and Fast Scoring Function for Protein−Ligand Interactions: A Simplified Potential Approach

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Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes

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Deciphering common failures in molecular docking of ligand-protein complexes

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/10.1038/nchembio799openalex-snapshot

Rational design of inhibitors that bind to inactive kinase conformations

inferredcites →https://doi.org/10.1038/nrd1549openalex-snapshot

Docking and scoring in virtual screening for drug discovery: methods and applications

inferredcites →https://doi.org/10.1107/s0907444909042073openalex-snapshot

MolProbity : all-atom structure validation for macromolecular crystallography

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LIBSVM

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Density-Functional Theory of the Electronic Structure of Molecules

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Optimal assignment methods for ligand-based virtual screening

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Emergence of Protein Fold Families through Rational Design

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Predictive QSAR Modeling Workflow, Model Applicability Domains, and Virtual Screening

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eHiTS: An Innovative Approach to the Docking and Scoring Function Problems

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Conceptual Density Functional Theory and Some Recent Developments

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Docking and Scoring with Target-Specific Pose Classifier Succeeds in Native-Like Pose Identification But Not Binding Affinity Prediction in the CSAR 2014 Benchmark Exercise

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