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Evaluation and Optimization of Virtual Screening Workflows with DEKOIS 2.0 – A Public Library of Challenging Docking Benchmark Sets

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What this work says

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

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AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

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CovalentDock: Automated covalent docking with parameterized covalent linkage energy estimation and molecular geometry constraints

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Challenges and advances in computational docking: 2009 in review

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Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen

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Ligand-Guided Receptor Optimization

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Molecular Graphics - Trends and Perspectives

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Epik: a software program for pK a prediction and protonation state generation for drug-like molecules

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Bias, reporting, and sharing: computational evaluations of docking methods

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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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Customizing scoring functions for docking

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Managing bias in ROC curves

inferredcites →https://doi.org/10.1007/s10822-008-9189-4openalex-snapshot

Community benchmarks for virtual screening

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Recommendations for evaluation of computational methods

inferredcites →https://doi.org/10.1007/s10822-010-9385-xopenalex-snapshot

pKa based protonation states and microspecies for protein–ligand docking

inferredcites →https://doi.org/10.1007/s10822-011-9533-yopenalex-snapshot

Surflex-Dock: Docking benchmarks and real-world application

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Are predefined decoy sets of ligand poses able to quantify scoring function accuracy?

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Docking and scoring with ICM: the benchmarking results and strategies for improvement

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Using halogen bonds to address the protein backbone: a systematic evaluation

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Virtual screening strategies in drug discovery

inferredcites →https://doi.org/10.1016/j.tibs.2010.04.009openalex-snapshot

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events

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Structural biology and drug discovery for protein–protein interactions

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Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation

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Human liver glycogen phosphorylase inhibitors bind at a new allosteric site

inferredcites →https://doi.org/10.1021/ci034289qopenalex-snapshot

Virtual Screening Using Protein−Ligand Docking: Avoiding Artificial Enrichment

inferredcites →https://doi.org/10.1021/ci100374fopenalex-snapshot

Virtual Decoy Sets for Molecular Docking Benchmarks

inferredcites →https://doi.org/10.1021/ci2001549openalex-snapshot

DEKOIS: Demanding Evaluation Kits for Objective in Silico Screening — A Versatile Tool for Benchmarking Docking Programs and Scoring Functions

inferredcites →https://doi.org/10.1021/ci200319eopenalex-snapshot

Rationalizing Tight Ligand Binding through Cooperative Interaction Networks

inferredcites →https://doi.org/10.1021/ci200412popenalex-snapshot

Ligand and Decoy Sets for Docking to G Protein-Coupled Receptors

inferredcites →https://doi.org/10.1021/ci200528dopenalex-snapshot

Recognizing Pitfalls in Virtual Screening: A Critical Review

inferredcites →https://doi.org/10.1021/ci700052xopenalex-snapshot

Comparison of Topological, Shape, and Docking Methods in Virtual Screening

inferredcites →https://doi.org/10.1021/ci700099uopenalex-snapshot

Impact of Benchmark Data Set Topology on the Validation of Virtual Screening Methods: Exploration and Quantification by Spatial Statistics

inferredcites →https://doi.org/10.1021/ci8002649openalex-snapshot

Maximum Unbiased Validation (MUV) Data Sets for Virtual Screening Based on PubChem Bioactivity Data

inferredcites →https://doi.org/10.1021/ci800298zopenalex-snapshot

Empirical Scoring Functions for Advanced Protein−Ligand Docking with PLANTS

inferredcites →https://doi.org/10.1021/ci8003978openalex-snapshot

Better than Random? The Chemotype Enrichment Problem

inferredcites →https://doi.org/10.1021/ci800420zopenalex-snapshot

Influence of Protonation, Tautomeric, and Stereoisomeric States on Protein−Ligand Docking Results

inferredcites →https://doi.org/10.1021/cr010182vopenalex-snapshot

Irreversible Inhibitors of Serine, Cysteine, and Threonine Proteases

inferredcites →https://doi.org/10.1021/ja301056aopenalex-snapshot

Halogen-Enriched Fragment Libraries as Leads for Drug Rescue of Mutant p53

inferredcites →https://doi.org/10.1021/jm001044lopenalex-snapshot

Protein-Based Virtual Screening of Chemical Databases. 1. Evaluation of Different Docking/Scoring Combinations

inferredcites →https://doi.org/10.1021/jm0300330openalex-snapshot

Information Decay in Molecular Docking Screens against Holo, Apo, and Modeled Conformations of Enzymes

inferredcites →https://doi.org/10.1021/jm030209yopenalex-snapshot

Lessons in Molecular Recognition: The Effects of Ligand and Protein Flexibility on Molecular Docking Accuracy

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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/jm030644sopenalex-snapshot

Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening

inferredcites →https://doi.org/10.1021/jm050040jopenalex-snapshot

Parameter Estimation for Scoring Protein−Ligand Interactions Using Negative Training Data

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The First Potent Inhibitors for Human Glutaminyl Cyclase: Synthesis and Structure−Activity Relationship

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/jm0608356openalex-snapshot

Benchmarking Sets for Molecular Docking

inferredcites →https://doi.org/10.1021/jm061277yopenalex-snapshot

Diverse, High-Quality Test Set for the Validation of Protein−Ligand Docking Performance

inferredcites →https://doi.org/10.1021/jm101020zopenalex-snapshot

Quo Vadis, Virtual Screening? A Comprehensive Survey of Prospective Applications

inferredcites →https://doi.org/10.1021/jm200558uopenalex-snapshot

Docking Performance of Fragments and Druglike Compounds

inferredcites →https://doi.org/10.1021/jm200590kopenalex-snapshot

Structure-Based Design of Pseudopeptidic Inhibitors for SIRT1 and SIRT2

inferredcites →https://doi.org/10.1021/jm300687eopenalex-snapshot

Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking

inferredcites →https://doi.org/10.1021/jm3012068openalex-snapshot

Principles and Applications of Halogen Bonding in Medicinal Chemistry and Chemical Biology

inferredcites →https://doi.org/10.1021/jm301488qopenalex-snapshot

Design, Synthesis, and Biological Evaluation of Novel Deguelin-Based Heat Shock Protein 90 (HSP90) Inhibitors Targeting Proliferation and Angiogenesis

inferredcites →https://doi.org/10.1021/jm9004708openalex-snapshot

Heat Shock Protein 90: Inhibitors in Clinical Trials

inferredcites →https://doi.org/10.1021/jm901013aopenalex-snapshot

Constrained Peptidomimetics Reveal Detailed Geometric Requirements of Covalent Prolyl Oligopeptidase Inhibitors

inferredcites →https://doi.org/10.1021/jm901137jopenalex-snapshot

New Substructure Filters for Removal of Pan Assay Interference Compounds (PAINS) from Screening Libraries and for Their Exclusion in Bioassays

inferredcites →https://doi.org/10.1038/nature06526openalex-snapshot

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inferredcites →https://doi.org/10.1038/nature11700openalex-snapshot

The NAD-dependent deacetylase SIRT2 is required for programmed necrosis

inferredcites →https://doi.org/10.1038/nrd3139openalex-snapshot

Virtual screening: an endless staircase?

inferredcites →https://doi.org/10.1038/nrd892openalex-snapshot

The druggable genome

inferredcites →https://doi.org/10.1073/pnas.0805326105openalex-snapshot

Targeted rescue of a destabilized mutant of p53 by an in silico screened drug

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SIRT2 inhibition achieves neuroprotection by decreasing sterol biosynthesis

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Kinetic mechanism of p53 oncogenic mutant aggregation and its inhibition

inferredcites →https://doi.org/10.1073/pnas.1215060109openalex-snapshot

Lithocholic acid is an endogenous inhibitor of MDM4 and MDM2

inferredcites →https://doi.org/10.1073/pnas.96.18.9997openalex-snapshot

The maximal affinity of ligands

inferredcites →https://doi.org/10.1093/bioinformatics/18.1.130openalex-snapshot

The Binding Database: data management and interface design

inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot

The Protein Data Bank

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/10.1093/nar/gkp456openalex-snapshot

PubChem: a public information system for analyzing bioactivities of small molecules

inferredcites →https://doi.org/10.1093/nar/gkr777openalex-snapshot

ChEMBL: a large-scale bioactivity database for drug discovery

inferredcites →https://doi.org/10.1096/fasebj.9.8.7768349openalex-snapshot

The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification 1

inferredcites →https://doi.org/10.1101/gr.2160004openalex-snapshot

Genomic Analysis of the Nuclear Receptor Family: New Insights Into Structure, Regulation, and Evolution From the Rat Genome

inferredcites →https://doi.org/10.1110/ps.21302openalex-snapshot

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Structure-Based Virtual Screening for Drug Discovery: a Problem-Centric Review

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BindingDB and ChEMBL: online compound databases for drug discovery

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Molecular Recognition in the Case of Flexible Targets

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BindingDB: A Web-Accessible Molecular Recognition Database

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Docking-Based Virtual Screening: Recent Developments

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Structure-Based Virtual Ligand Screening: Recent Success Stories

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R: A Language and Environment for Statistical Computing

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Water Network-Augmented Two-State Model for Protein–Ligand Binding Affinity Prediction

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BigBind: Learning from Nonstructural Data for Structure-Based Virtual Screening

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Evaluation of AlphaFold2 Structures for Hit Identification across Multiple Scenarios

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XDock: A General Docking Method for Modeling Protein–Ligand and Nucleic Acid–Ligand Interactions

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Benchmarking Data Sets for the Evaluation of Virtual Ligand Screening Methods: Review and Perspectives

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pROC-Chemotype Plots Enhance the Interpretability of Benchmarking Results in Structure-Based Virtual Screening

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Three-Dimensional Similarity in Molecular Docking: Prioritizing Ligand Poses on the Basis of Experimental Binding Modes

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Improved Prediction of Drug–Protein Interactions through Physics-Based Few-Shot Learning

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Bioactivity Deep Learning for Complex Structure-Free Compound-Protein Interaction Prediction

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HitScreen: A Sequence-Based Drug Virtual Screening Approach Using Data Augmentation and Protein Language Models

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Cosolvent-Based Molecular Dynamics for Ensemble Docking: Practical Method for Generating Druggable Protein Conformations

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Struct2Query: Structure-Guided Virtual Screening via Composite-Molecule ROCS Queries Derived from Protein Pocket Similarity

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The Last Mile Problem: A Critical Assessment of Physics-Based and AI Tools for Small Molecule Binding Prediction in Virtual Screening

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Systematic Evaluation of Graph Neural Networks for Ligand-Based Virtual Screening on ChEMBL Datasets

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Maximal Unbiased Benchmarking Data Sets for Human Chemokine Receptors and Comparative Analysis

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Improved Method of Structure-Based Virtual Screening via Interaction-Energy-Based Learning

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In Need of Bias Control: Evaluating Chemical Data for Machine Learning in Structure-Based Virtual Screening

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The Development of Target-Specific Machine Learning Models as Scoring Functions for Docking-Based Target Prediction

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Assessing the Performance of Mixed Strategies To Combine Lipophilic Molecular Similarity and Docking in Virtual Screening

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InteractionGraphNet: A Novel and Efficient Deep Graph Representation Learning Framework for Accurate Protein–Ligand Interaction Predictions

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TocoDecoy: A New Approach to Design Unbiased Datasets for Training and Benchmarking Machine-Learning Scoring Functions

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Boosting Protein–Ligand Binding Pose Prediction and Virtual Screening Based on Residue–Atom Distance Likelihood Potential and Graph Transformer

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Topology-Based and Conformation-Based Decoys Database: An Unbiased Online Database for Training and Benchmarking Machine-Learning Scoring Functions

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Folding-Based End-To-End Chemical Drug Design with Uncertainty Estimation: Tackling Hallucination in the Post-GPT Era

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Harnessing Glutamine-117 Plasticity toward Structure-Based Identification of Triazole IL-17 Inhibitors

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Utility of the Morgan Fingerprint in Structure-Based Virtual Ligand Screening

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Compound Ranking Based on Fuzzy Three-Dimensional Similarity Improves the Performance of Docking into Homology Models of G-Protein-Coupled Receptors

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Accounting for Target Flexibility and Water Molecules by Docking to Ensembles of Target Structures: The HCV NS5B Palm Site I Inhibitors Case Study

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Docking Ligands into Flexible and Solvated Macromolecules. 7. Impact of Protein Flexibility and Water Molecules on Docking-Based Virtual Screening Accuracy

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Application of the 4D Fingerprint Method with a Robust Scoring Function for Scaffold-Hopping and Drug Repurposing Strategies

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Comparative Modeling and Benchmarking Data Sets for Human Histone Deacetylases and Sirtuin Families

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MetalloDock: Decoding Metalloprotein–Ligand Interactions via Physics-Aware Deep Learning for Metalloprotein Drug Discovery

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Discovery of Covalent Ligands with AlphaFold3

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ProMol_Func: A Structure-Free Deep Learning Model for Virtual Screening

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Graph-based deep learning approach for high-throughput protein-DNA interaction scoring

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Sequence-based drug design as a concept in computational drug design

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Targeting JMJD1C to selectively disrupt tumor Treg cell fitness enhances antitumor immunity

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SurfDock is a surface-informed diffusion generative model for reliable and accurate protein–ligand complex prediction

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A practical guide to machine-learning scoring for structure-based virtual screening

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Facilitating structure-based drug discovery with an artificial intelligence-driven virtual screening platform

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Generic protein–ligand interaction scoring by integrating physical prior knowledge and data augmentation modelling

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Benchmarking AI-powered docking methods from the perspective of virtual screening

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Efficient and accurate large library ligand docking with KarmaDock

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Performance of machine-learning scoring functions in structure-based virtual screening

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Machine Learning Approaches to Chemical Space Exploration

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Improved method of structure-based virtual screening based on ensemble learning

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MetalProGNet: a structure-based deep graph model for metalloprotein–ligand interaction predictions

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PIGNet2: a versatile deep learning-based protein–ligand interaction prediction model for binding affinity scoring and virtual screening

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A generalized protein–ligand scoring framework with balanced scoring, docking, ranking and screening powers

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CarsiDock: a deep learning paradigm for accurate protein–ligand docking and screening based on large-scale pre-training

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Synthesis and elucidation of strained galactopyronose esters as selective cyclooxygenase-2 inhibitor: a comprehensive computational approach

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PharmacoNet: deep learning-guided pharmacophore modeling for ultra-large-scale virtual screening

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Modeling protein–ligand interactions for drug discovery in the era of deep learning

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Decoding the limits of deep learning in molecular docking for drug discovery

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Unlocking the application potential of AlphaFold3-like approaches in virtual screening

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Optimising drug activity using docking-informed machine learning

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How to Valorize Biodiversity? Letʼs Go Hashing, Extracting, Filtering, Mining, Fishing

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Machine learning classification can reduce false positives in structure-based virtual screening

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Targeting p53-MDM2 interactions to identify small molecule inhibitors for cancer therapy: beyond “Failure to rescue”

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Structural Docking Studies of COX-II Inhibitory Activity for Metabolites Derived fromCorchorus olitoriusandVitis vinifera

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Structure-guided approach on the role of substitution on amide-linked bipyrazoles and its effect on their anti-inflammatory activity

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AlphaFold and what is next: bridging functional, systems and structural biology

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Getting the most out of PubChem for virtual screening

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Guided structure-based ligand identification and design via artificial intelligence modeling

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On the application of artificial intelligence in virtual screening

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Hybridization of isatin and benzoxazolinone via a diethyl spacer: a new scaffold for breast cancer drug discovery

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Beware of the generic machine learning-based scoring functions in structure-based virtual screening

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The impact of compound library size on the performance of scoring functions for structure-based virtual screening

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Reducing false positive rate of docking-based virtual screening by active learning

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Improving drug-target affinity prediction via feature fusion and knowledge distillation

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ML-PLIC: a web platform for characterizing protein–ligand interactions and developing machine learning-based scoring functions

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Protein language models are performant in structure-free virtual screening

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Topological deep learning for drug–target interaction, virtual screening, and docking scoring: a practical, benchmark-driven review

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Generating property-matched decoy molecules using deep learning

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PLATE-VS: a web server for protein–ligand assay curation and cross-target virtual screening datasets

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Drug design and repurposing with a sequence-to-drug paradigm

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EquiScore: A generic protein-ligand interaction scoring method integrating physical prior knowledge with data augmentation modeling

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Simpatico: accurate and ultra-fast virtual drug screening with atomic embeddings

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Small Molecule Approach to RNA Targeting Binder Discovery (SMARTBind) Using Deep Learning Without Structural Input

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A Protein-Context Enhanced Master Slave Framework for Zero-Shot Drug Target Interaction Prediction

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Interaction-Based Inductive Bias in Graph Neural Networks: Enhancing Protein-Ligand Binding Affinity Predictions From 3D Structures

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Enrichment Assessment of Multiple Virtual Screening Strategies for Toll‐Like Receptor 8 Agonists Based on a Maximal Unbiased Benchmarking Data Set

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In-Silico Predictions of Drug Resistance in Lung Cancers with EGFR Mutation

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Performance Studies on Distributed Virtual Screening

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Use of DEKOIS 2.0 to gain insights for virtual screening

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Probing the impact of protein and ligand preparation procedures on chemotype enrichment in structure-based virtual screening using DEKOIS 2.0 benchmark sets

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Applying DEKOIS 2.0 in structure-based virtual screening to probe the impact of preparation procedures and score normalization

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11th German Conference on Chemoinformatics (GCC 2015)

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Rocker: Open source, easy-to-use tool for AUC and enrichment calculations and ROC visualization

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DLIGAND2: an improved knowledge-based energy function for protein–ligand interactions using the distance-scaled, finite, ideal-gas reference state

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DockStream: a docking wrapper to enhance de novo molecular design

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Confidence bands and hypothesis tests for hit enrichment curves

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Efficient decoy selection to improve virtual screening using machine learning models

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DockM8: an all-in-one open-source platform for consensus virtual screening in drug design

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Design and Synthesis of Novel Quinazoline Derivatives and Their Evaluation as PI3Ks Inhibitors

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Fully Flexible Docking of Medium Sized Ligand Libraries with RosettaLigand

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Evaluating the structure-based virtual screening performance of SARS-CoV-2 main protease: A benchmarking approach and a multistage screening example against the wild-type and Omicron variants

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From ranking to decision: TASC-VS for calibration-aware top-k virtual screening

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Confidence Bands and Hypothesis Tests for Hit Enrichment Curves

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Small-Molecule Intervention At The Dimerization Interface Of Survivin By Novel Rigidized Scaffolds

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Benchmarking the Structure-Based Virtual Screening Performance of Wild-Type and Resistant PfDHFR Using Docking and Machine Learning Re-Scoring

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Standards for Computational Methods in Drug Design and Discovery: Simplified Guidance for Authors and Reviewers

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Virtual Screening Meets Deep Learning

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Enhancing Semiempirical Quantum Mechanical Scoring with Machine Learning: a new scoring function that accounts for both the enthalpic and entropic contributions to the ligand binding free energy

inferred← citeshttps://doi.org/10.26434/chemrxiv-2022-68n6h-v2openalex-snapshot

Enhancing Semiempirical Quantum Mechanical Scoring with Machine Learning: a new scoring function that accounts for both the enthalpic and entropic contributions to the ligand binding free energy

inferred← citeshttps://doi.org/10.33774/chemrxiv-2021-qvhmlopenalex-snapshot

DockStream: A Docking Wrapper to Enhance De Novo Molecular Design

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Supporting SARS-CoV-2 Papain-Like Protease Drug Discovery: In silico Methods and Benchmarking

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Non-Extensive Fragmentation of Natural Products and Pharmacophore-Based Virtual Screening as a Practical Approach to Identify Novel Promising Chemical Scaffolds

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Yin-yang in drug discovery: rethinking de novo design and development of predictive models

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Decoys Selection in Benchmarking Datasets: Overview and Perspectives

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Empirical Scoring Functions for Structure-Based Virtual Screening: Applications, Critical Aspects, and Challenges

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miDruglikeness: Subdivisional Drug-Likeness Prediction Models Using Active Ensemble Learning Strategies

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The Roles of the NLRP3 Inflammasome in Neurodegenerative and Metabolic Diseases and in Relevant Advanced Therapeutic Interventions

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Key Topics in Molecular Docking for Drug Design

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Benchmarking Data Sets from PubChem BioAssay Data: Current Scenario and Room for Improvement

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Comprehensive Survey of Recent Drug Discovery Using Deep Learning

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The Impact of Data on Structure-Based Binding Affinity Predictions Using Deep Neural Networks

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vScreenML v2.0: Improved Machine Learning Classification for Reducing False Positives in Structure-Based Virtual Screening

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Comprehensive Survey of Consensus Docking for High-Throughput Virtual Screening

inferred← citeshttps://doi.org/10.3390/molecules28031296openalex-snapshot

In Silico Targeting of Fascin Protein for Cancer Therapy: Benchmarking, Virtual Screening and Molecular Dynamics Approaches

inferred← citeshttps://doi.org/10.3390/ph17080992openalex-snapshot

Do Molecular Fingerprints Identify Diverse Active Drugs in Large-Scale Virtual Screening? (No)

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ComTarget: Small-Molecule Target Prediction with Combinatorial Modeling

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A Guide to In Silico Drug Design

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Strategies of Virtual Screening in Medicinal Chemistry

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Strategies of Virtual Screening in Medicinal Chemistry

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Synthesis, Evaluation and Modeling of Some Triazolothienopyrimidinones as Anti-Inflammatory and Antimicrobial Agents

inferred← citeshttps://doi.org/10.48550/arxiv.2001.03207openalex-snapshot

Split Optimization for Protein/Ligand Binding Models

inferred← citeshttps://doi.org/10.6084/m9.figshare.20400853openalex-snapshot

Additional file 1 of Confidence bands and hypothesis tests for hit enrichment curves

inferred← citeshttps://doi.org/10.70675/6c487b82zef74z4584z8ffaz2a1793756009openalex-snapshot

Identification of new therapeutic targets for cystic fibrosis using systems biology and chemogenomics approaches

inferred← citeshttps://doi.org/10.70675/c9cacc57zdf38z489bzacf8z0d5ecf73c80copenalex-snapshot

Development of new virtual screening methods and novel unbiased benchmarking data sets

inferred← citeshttps://doi.org/10.70675/d5fdc018z1d3fz4af2zb794zae806588d521openalex-snapshot

Development of novel algorithms for data-driven prediction of interactions between proteins and small molecules

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