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Use of Experimental Design To Optimize Docking Performance: The Case of LiGenDock, the Docking Module of Ligen, a New De Novo Design Program

https://doi.org/10.1021/ci400079k
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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
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Gaussian docking functions
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Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database
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ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
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Principles of docking: An overview of search algorithms and a guide to scoring functions
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A new test set for validating predictions of protein–ligand interaction
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A Fast Flexible Docking Method using an Incremental Construction Algorithm
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LigBuilder: A Multi-Purpose Program for Structure-Based Drug Design
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Recommendations for evaluation of computational methods
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Evaluation of DOCK 6 as a pose generation and database enrichment tool
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Docking performance of the glide program as evaluated on the Astex and DUD datasets: a complete set of glide SP results and selected results for a new scoring function integrating WaterMap and glide
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Response surface methodology (RSM) as a tool for optimization in analytical chemistry
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Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings
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Experimental design and optimization
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POEM: Parameter Optimization Using Ensemble Methods: Application to Target Specific Scoring Functions
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Recognizing Pitfalls in Virtual Screening: A Critical Review
inferredcites →https://doi.org/10.1021/ci400078gopenalex-snapshot
LiGen: A High Performance Workflow for Chemistry Driven de Novo Design
inferredcites →https://doi.org/10.1021/ci600426eopenalex-snapshot
Evaluating Virtual Screening Methods: Good and Bad Metrics for the “Early Recognition” Problem
inferredcites →https://doi.org/10.1021/ci6005596openalex-snapshot
A Multivariate Approach to Investigate Docking Parameters' Effects on Docking Performance
inferredcites →https://doi.org/10.1021/ci7000378openalex-snapshot
Evaluations of Molecular Docking Programs for Virtual Screening
inferredcites →https://doi.org/10.1021/ci900056copenalex-snapshot
Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy
inferredcites →https://doi.org/10.1021/jm020406hopenalex-snapshot
Surflex: Fully Automatic Flexible Molecular Docking Using a Molecular Similarity-Based Search Engine
inferredcites →https://doi.org/10.1021/jm0302997openalex-snapshot
Evaluation of Docking Performance: Comparative Data on Docking Algorithms
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/jm0306430openalex-snapshot
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
inferredcites →https://doi.org/10.1021/jm048957qopenalex-snapshot
The PDBbind Database: Methodologies and Updates
inferredcites →https://doi.org/10.1021/jm0608356openalex-snapshot
Benchmarking Sets for Molecular Docking
inferredcites →https://doi.org/10.1023/a:1007907728892openalex-snapshot
QXP: Powerful, rapid computer algorithms for structure-based drug design
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Further development and validation of empirical scoring functions for structure-based binding affinity prediction
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Comparative study of several algorithms for flexible ligand docking
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Docking and scoring in virtual screening for drug discovery: methods and applications
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The Kolmogorov-Smirnov Test for Goodness of Fit
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Matching chemistry and shape in molecular docking
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On the Experimental Attainment of Optimum Conditions
inferredcites →https://doi.org/10.1146/annurev.biophys.32.110601.142532openalex-snapshot
Molecular Recognition and Docking Algorithms
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Statistics for Experimenters: Design, Innovation and Discovery
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Inhibitors of Helicobacter pylori Protease HtrA Found by ‘Virtual Ligand’ Screening Combat Bacterial Invasion of Epithelia
inferredcites →https://doi.org/10.2174/138920306778559412openalex-snapshot
eHiTS: An Innovative Approach to the Docking and Scoring Function Problems
inferredcites →https://doi.org/10.2174/138945008786949432openalex-snapshot
Molecular Docking Algorithms

What points at this work

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

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Improvements, trends, and new ideas in molecular docking: 2012–2013 in review
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Exploiting OpenMP and OpenACC to accelerate a geometric approach to molecular docking in heterogeneous HPC nodes
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ANTAREX -- AutoTuning and Adaptivity appRoach for Energy Efficient eXascale HPC Systems
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Understanding the I/O Impact on the Performance of High-Throughput Molecular Docking
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mARGOt: A Dynamic Autotuning Framework for Self-Aware Approximate Computing
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Autotuning and adaptivity in energy efficient HPC systems
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Accelerating a Geometric Approach to Molecular Docking with OpenACC
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Binding Mode Exploration of B1 Receptor Antagonists’ by the Use of Molecular Dynamics and Docking Simulation—How Different Target Engagement Can Determine Different Biological Effects
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