Research graph
References from Assessing the Generalizability of Machine Learning and Physics-Based Methods with DNA-Encoded Libraries. Local targets link to admitted publications; unresolved targets remain external evidence.
Principles of Early Drug Discovery
10.1111/j.1476-5381.2010.01127.x · 2011 · External reference
Improving the Generalizability of Protein-Ligand Binding Predictions with AI-Bind
10.1038/s41467-023-37572-z · 2023 · External reference
Molecular Docking: A Powerful Approach for Structure-Based Drug Discovery
10.2174/157340911795677602 · 2011 · External reference
Recent Advances in Ligand-Based Drug Design: Relevance and Utility of the Conformationally Sampled Pharmacophore Approach
10.2174/157340911793743547 · 2011 · External reference
A Brief Review of Protein-Ligand Interaction Prediction
10.1016/j.csbj.2022.06.004 · 2022 · External reference
Highly Accurate Protein Structure Prediction with AlphaFold
10.1038/s41586-021-03819-2 · 2021 · External reference
Accurate Structure Prediction of Biomolecular Interactions with AlphaFold 3
10.1038/s41586-024-07487-w · 2024 · External reference
10.1101/2025.06.14.659707
10.1101/2025.06.14.659707 · External reference
Unresolved reference
External reference
State-Specific Protein–ligand Complex Structure Prediction with a Multiscale Deep Generative Model
10.1038/s42256-024-00792-z · 2024 · External reference
The Importance of the Domain of Applicability in QSAR Modeling
10.1016/j.jmgm.2008.01.002 · 2008 · External reference
Decoding the Limits of Deep Learning in Molecular Docking for Drug Discovery
10.1039/d5sc05395a · 2025 · External reference
Chemical Composition of DNA-Encoded Libraries, Past Present and Future
10.1039/c9ob00581a · 2019 · External reference
DNA-Encoded Chemical Libraries: A Comprehensive Review with Succesful Stories and Future Challenges
10.1021/acsptsci.1c00118 · 2021 · External reference
DNA-Encoded Chemical Libraries
10.1038/s43586-021-00084-5 · 2022 · External reference
Screening of DNA-Encoded Small Molecule Libraries inside a Living Cell
10.1021/jacs.0c09213 · 2021 · External reference
Design, Synthesis and Selection of DNA-Encoded Small-Molecule Libraries
10.1038/nchembio.211 · 2009 · External reference
DNA-Encoded Chemical Libraries - Achievements and Remaining Challenges
10.1002/1873-3468.13068 · 2018 · External reference
Design Concepts for DNA-Encoded Library Synthesis
10.1016/j.bmc.2021.116189 · 2021 · External reference
DNA-Encoded Library Hit Confirmation: Bridging the Gap between on-DNA and off-DNA Chemistry
10.1021/acsmedchemlett.1c00156 · 2021 · External reference
Challenges and Prospects of DNA-Encoded Library Data Interpretation
10.1021/acs.chemrev.4c00284 · 2024 · External reference
Toward Generalizable Predictive Models for DNA-Encoded Libraries
10.1016/j.drudis.2026.104629 · 2026 · External reference
Widespread False Negatives in DNA-Encoded Library Data: How Linker Effects Impair Machine Learning-Based Lead Prediction
10.1039/d5sc00844a · 2025 · External reference
Evaluation of DNA Encoded Library and Machine Learning Model Combinations for Hit Discovery
10.1038/s44386-025-00007-4 · 2025 · External reference
Machine Learning on DNA-Encoded Libraries: A New Paradigm for Hit Finding
10.1021/acs.jmedchem.0c00452 · 2020 · External reference
Enabling Open Machine Learning of Deoxyribonucleic Acid-Encoded Library Selections to Accelerate the Discovery of Small Molecule Protein Binders
10.1021/acs.jmedchem.5c01972 · 2025 · External reference
Building Block-Based Binding Predictions for DNA-Encoded Libraries
10.1021/acs.jcim.3c00588 · 2023 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
Randomness in DNA Encoded Library Selection Data Can Be Modeled for More Reliable Enrichment Calculation
10.1177/2472555218757718 · 2018 · External reference
Simulated Screens of DNA Encoded Libraries: The Potential Influence of Chemical Synthesis Fidelity on Interpretation of Structure-Activity Relationships
10.1021/acscombsci.6b00001 · 2016 · External reference
Force Field Optimization Guided by Small Molecule Crystal Lattice Data Enables Consistent Sub-Angstrom Protein-Ligand Docking
10.1021/acs.jctc.0c01184 · 2021 · External reference
RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite
10.1371/journal.pone.0020161 · 2011 · External reference
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening
10.1021/jm030644s · 2004 · External reference
Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein-Ligand Complexes
10.1021/jm051256o · 2006 · External reference
Unresolved reference
External reference
SMILES, a Chemical Language and Information System. 1. Introduction to Methodology and Encoding Rules
10.1021/ci00057a005 · 1988 · External reference
Extended-Connectivity Fingerprints
10.1021/ci100050t · 2010 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
Large-Scale Chemical Language Representations Capture Molecular Structure and Properties
10.1038/s42256-022-00580-7 · 2022 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
Interpretation of QSAR Models by Coloring Atoms according to Changes in Predicted Activity: How Robust Is It?
10.1021/acs.jcim.8b00825 · 2019 · External reference
Reoptimization of MDL Keys for Use in Drug Discovery
10.1021/ci010132r · 2002 · External reference
The Properties of Known Drugs. 1. Molecular Frameworks
10.1021/jm9602928 · 1996 · External reference
ZINC20-A Free Ultralarge-Scale Chemical Database for Ligand Discovery
10.1021/acs.jcim.0c00675 · 2020 · External reference
10.21105/joss.00861
10.21105/joss.00861 · External reference
10.18653/v1/2021.eacl-main.156
10.18653/v1/2021.eacl-main.156 · External reference
10.64898/2026.06.29.735309
10.64898/2026.06.29.735309 · External reference
10.1021/acs.jcim.6c00332
10.1021/acs.jcim.6c00332 · External reference
Using RosettaLigand for Small Molecule Docking into Comparative Models
10.1371/journal.pone.0050769 · 2012 · External reference
RosettaLigand Docking with Full Ligand and Receptor Flexibility
10.1016/j.jmb.2008.11.010 · 2009 · External reference
D3R Grand Challenge 4: Blind Prediction of Protein-Ligand Poses, Affinity Rankings, and Relative Binding Free Energies
10.1007/s10822-020-00289-y · 2020 · External reference
More Protein-Ligand Data Are Needed for AlphaFold-like Models to Enable Drug Discovery
10.1016/j.sbi.2026.103257 · 2026 · External reference
10.1101/2025.07.29.667267
10.1101/2025.07.29.667267 · External reference
A Computational Community Blind Challenge on Pan-Coronavirus Drug Discovery Data
10.1021/acs.jcim.5c02106 · 2026 · External reference
Investigating Whether Deep Learning Models for Co-Folding Learn the Physics of Protein-Ligand Interactions
10.1038/s41467-025-63947-5 · 2025 · External reference
Evaluating Generalization in Protein-Ligand Cofolding Methods
10.1038/s41594-026-01797-5 · 2026 · External reference
10.64898/2025.12.25.696505
10.64898/2025.12.25.696505 · External reference
Benchmarking Sets for Molecular Docking
10.1021/jm0608356 · 2006 · External reference
On Evaluating Molecular-Docking Methods for Pose Prediction and Enrichment Factors
10.1021/ci0503255 · 2006 · External reference
Comparative Evaluation of Eight Docking Tools for Docking and Virtual Screening Accuracy
10.1002/prot.20149 · 2004 · External reference
Comparative Assessment of Scoring Functions: The CASF-2016 Update
10.1021/acs.jcim.8b00545 · 2019 · External reference
Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy
10.1021/ci900056c · 2009 · External reference
PLIP 2025: Introducing Protein-Protein Interactions to the Protein-Ligand Interaction Profiler
10.1093/nar/gkaf361 · 2025 · External reference
Building Block-Centric Approach to DNA-Encoded Library Design
10.1021/acs.jcim.4c00232 · 2024 · External reference
Unresolved reference
External reference
Comparing Structural Fingerprints Using a Literature-Based Similarity Benchmark
10.1186/s13321-016-0148-0 · 2016 · External reference
Unresolved reference
External reference
Drug Discovery with DNA-Encoded Chemical Libraries
10.1021/bc1001483 · 2010 · External reference
Structural Insights into Binding of Inhibitors to Soluble Epoxide Hydrolase Gained by Fragment Screening and X-Ray Crystallography
10.1016/j.bmc.2014.03.001 · 2014 · External reference
DNA-Encoded Library-Enabled Discovery of Proximity-Inducing Small Molecules
10.1038/s41589-023-01458-4 · 2024 · External reference
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
10.1021/ct400341p · 2013 · External reference
ProDy: Protein Dynamics Inferred from Theory and Experiments
10.1093/bioinformatics/btr168 · 2011 · External reference
DNA-Encoded Chemical Libraries - Achievements and Remaining Challenges
10.1002/1873-3468.13068 · ExternalCitation · doi-reference
Comparative Evaluation of Eight Docking Tools for Docking and Virtual Screening Accuracy
10.1002/prot.20149 · ExternalCitation · doi-reference
D3R Grand Challenge 4: Blind Prediction of Protein-Ligand Poses, Affinity Rankings, and Relative Binding Free Energies
10.1007/s10822-020-00289-y · ExternalCitation · doi-reference
Structural Insights into Binding of Inhibitors to Soluble Epoxide Hydrolase Gained by Fragment Screening and X-Ray Crystallography
10.1016/j.bmc.2014.03.001 · ExternalCitation · doi-reference
Design Concepts for DNA-Encoded Library Synthesis
10.1016/j.bmc.2021.116189 · ExternalCitation · doi-reference
A Brief Review of Protein-Ligand Interaction Prediction
10.1016/j.csbj.2022.06.004 · ExternalCitation · doi-reference
Toward Generalizable Predictive Models for DNA-Encoded Libraries
10.1016/j.drudis.2026.104629 · ExternalCitation · doi-reference
RosettaLigand Docking with Full Ligand and Receptor Flexibility
10.1016/j.jmb.2008.11.010 · ExternalCitation · doi-reference
The Importance of the Domain of Applicability in QSAR Modeling
10.1016/j.jmgm.2008.01.002 · ExternalCitation · doi-reference
More Protein-Ligand Data Are Needed for AlphaFold-like Models to Enable Drug Discovery
10.1016/j.sbi.2026.103257 · ExternalCitation · doi-reference
Challenges and Prospects of DNA-Encoded Library Data Interpretation
10.1021/acs.chemrev.4c00284 · ExternalCitation · doi-reference
ZINC20-A Free Ultralarge-Scale Chemical Database for Ligand Discovery
10.1021/acs.jcim.0c00675 · ExternalCitation · doi-reference
Building Block-Based Binding Predictions for DNA-Encoded Libraries
10.1021/acs.jcim.3c00588 · ExternalCitation · doi-reference
Building Block-Centric Approach to DNA-Encoded Library Design
10.1021/acs.jcim.4c00232 · ExternalCitation · doi-reference
A Computational Community Blind Challenge on Pan-Coronavirus Drug Discovery Data
10.1021/acs.jcim.5c02106 · ExternalCitation · doi-reference
10.1021/acs.jcim.6c00332
10.1021/acs.jcim.6c00332 · ExternalCitation · doi-reference
Comparative Assessment of Scoring Functions: The CASF-2016 Update
10.1021/acs.jcim.8b00545 · ExternalCitation · doi-reference
Interpretation of QSAR Models by Coloring Atoms according to Changes in Predicted Activity: How Robust Is It?
10.1021/acs.jcim.8b00825 · ExternalCitation · doi-reference
Force Field Optimization Guided by Small Molecule Crystal Lattice Data Enables Consistent Sub-Angstrom Protein-Ligand Docking
10.1021/acs.jctc.0c01184 · ExternalCitation · doi-reference
Machine Learning on DNA-Encoded Libraries: A New Paradigm for Hit Finding
10.1021/acs.jmedchem.0c00452 · ExternalCitation · doi-reference
Enabling Open Machine Learning of Deoxyribonucleic Acid-Encoded Library Selections to Accelerate the Discovery of Small Molecule Protein Binders
10.1021/acs.jmedchem.5c01972 · ExternalCitation · doi-reference
Simulated Screens of DNA Encoded Libraries: The Potential Influence of Chemical Synthesis Fidelity on Interpretation of Structure-Activity Relationships
10.1021/acscombsci.6b00001 · ExternalCitation · doi-reference
DNA-Encoded Library Hit Confirmation: Bridging the Gap between on-DNA and off-DNA Chemistry
10.1021/acsmedchemlett.1c00156 · ExternalCitation · doi-reference
DNA-Encoded Chemical Libraries: A Comprehensive Review with Succesful Stories and Future Challenges
10.1021/acsptsci.1c00118 · ExternalCitation · doi-reference
Drug Discovery with DNA-Encoded Chemical Libraries
10.1021/bc1001483 · ExternalCitation · doi-reference
SMILES, a Chemical Language and Information System. 1. Introduction to Methodology and Encoding Rules
10.1021/ci00057a005 · ExternalCitation · doi-reference
Reoptimization of MDL Keys for Use in Drug Discovery
10.1021/ci010132r · ExternalCitation · doi-reference
On Evaluating Molecular-Docking Methods for Pose Prediction and Enrichment Factors
10.1021/ci0503255 · ExternalCitation · doi-reference
Extended-Connectivity Fingerprints
10.1021/ci100050t · ExternalCitation · doi-reference
Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy
10.1021/ci900056c · ExternalCitation · doi-reference
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
10.1021/ct400341p · ExternalCitation · doi-reference
Screening of DNA-Encoded Small Molecule Libraries inside a Living Cell
10.1021/jacs.0c09213 · ExternalCitation · doi-reference
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening
10.1021/jm030644s · ExternalCitation · doi-reference
Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein-Ligand Complexes
10.1021/jm051256o · ExternalCitation · doi-reference
Benchmarking Sets for Molecular Docking
10.1021/jm0608356 · ExternalCitation · doi-reference
The Properties of Known Drugs. 1. Molecular Frameworks
10.1021/jm9602928 · ExternalCitation · doi-reference
Design, Synthesis and Selection of DNA-Encoded Small-Molecule Libraries
10.1038/nchembio.211 · ExternalCitation · doi-reference
Improving the Generalizability of Protein-Ligand Binding Predictions with AI-Bind
10.1038/s41467-023-37572-z · ExternalCitation · doi-reference
Investigating Whether Deep Learning Models for Co-Folding Learn the Physics of Protein-Ligand Interactions
10.1038/s41467-025-63947-5 · ExternalCitation · doi-reference
Highly Accurate Protein Structure Prediction with AlphaFold
10.1038/s41586-021-03819-2 · ExternalCitation · doi-reference
Accurate Structure Prediction of Biomolecular Interactions with AlphaFold 3
10.1038/s41586-024-07487-w · ExternalCitation · doi-reference
DNA-Encoded Library-Enabled Discovery of Proximity-Inducing Small Molecules
10.1038/s41589-023-01458-4 · ExternalCitation · doi-reference
Evaluating Generalization in Protein-Ligand Cofolding Methods
10.1038/s41594-026-01797-5 · ExternalCitation · doi-reference
Large-Scale Chemical Language Representations Capture Molecular Structure and Properties
10.1038/s42256-022-00580-7 · ExternalCitation · doi-reference
State-Specific Protein–ligand Complex Structure Prediction with a Multiscale Deep Generative Model
10.1038/s42256-024-00792-z · ExternalCitation · doi-reference
DNA-Encoded Chemical Libraries
10.1038/s43586-021-00084-5 · ExternalCitation · doi-reference
Evaluation of DNA Encoded Library and Machine Learning Model Combinations for Hit Discovery
10.1038/s44386-025-00007-4 · ExternalCitation · doi-reference
Chemical Composition of DNA-Encoded Libraries, Past Present and Future
10.1039/c9ob00581a · ExternalCitation · doi-reference
Widespread False Negatives in DNA-Encoded Library Data: How Linker Effects Impair Machine Learning-Based Lead Prediction
10.1039/d5sc00844a · ExternalCitation · doi-reference
Decoding the Limits of Deep Learning in Molecular Docking for Drug Discovery
10.1039/d5sc05395a · ExternalCitation · doi-reference
ProDy: Protein Dynamics Inferred from Theory and Experiments
10.1093/bioinformatics/btr168 · ExternalCitation · doi-reference
PLIP 2025: Introducing Protein-Protein Interactions to the Protein-Ligand Interaction Profiler
10.1093/nar/gkaf361 · ExternalCitation · doi-reference
10.1101/2025.06.14.659707
10.1101/2025.06.14.659707 · ExternalCitation · doi-reference
10.1101/2025.07.29.667267
10.1101/2025.07.29.667267 · ExternalCitation · doi-reference
Principles of Early Drug Discovery
10.1111/j.1476-5381.2010.01127.x · ExternalCitation · doi-reference
Randomness in DNA Encoded Library Selection Data Can Be Modeled for More Reliable Enrichment Calculation
10.1177/2472555218757718 · ExternalCitation · doi-reference
Comparing Structural Fingerprints Using a Literature-Based Similarity Benchmark
10.1186/s13321-016-0148-0 · ExternalCitation · doi-reference
RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite
10.1371/journal.pone.0020161 · ExternalCitation · doi-reference
Using RosettaLigand for Small Molecule Docking into Comparative Models
10.1371/journal.pone.0050769 · ExternalCitation · doi-reference
10.18653/v1/2021.eacl-main.156
10.18653/v1/2021.eacl-main.156 · ExternalCitation · doi-reference
10.21105/joss.00861
10.21105/joss.00861 · ExternalCitation · doi-reference
Recent Advances in Ligand-Based Drug Design: Relevance and Utility of the Conformationally Sampled Pharmacophore Approach
10.2174/157340911793743547 · ExternalCitation · doi-reference
Molecular Docking: A Powerful Approach for Structure-Based Drug Discovery
10.2174/157340911795677602 · ExternalCitation · doi-reference
10.64898/2025.12.25.696505
10.64898/2025.12.25.696505 · ExternalCitation · doi-reference
10.64898/2026.06.29.735309
10.64898/2026.06.29.735309 · ExternalCitation · doi-reference
