Research graph
References from Pose Reproduction, Cross Docking, Database Enrichment, and Reverse Docking Benchmarks for DOCK6, Vina, and AutoDock 4 with Emphasis on Approved Drugs. Local targets link to admitted publications; unresolved targets remain external evidence.
Structure-based strategies for drug design and discovery
10.1126/science.257.5073.1078 · 1992 · External reference
The Many Roles of Computation in Drug Discovery
10.1126/science.1096361 · 2004 · External reference
Virtual screening of chemical libraries
10.1038/nature03197 · 2004 · External reference
A geometric approach to macromolecule-ligand interactions
10.1016/0022-2836(82)90153-x · 1982 · External reference
DOCK 6: Impact of new features and current docking performance
10.1002/jcc.23905 · 2015 · External reference
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
10.1002/(sici)1096-987x(19981115)19:14<1639::aid-jcc10>3.0.co;2-b · 1998 · External reference
AutoDock Vina: Improving the Speed and Accuracy of Docking with a New Scoring Function, Efficient Optimization, and Multithreading
10.1002/jcc.21334 · 2010 · External reference
Detailed analysis of grid-based molecular docking: A case study of CDOCKER-A CHARMm-based MD docking algorithm
10.1002/jcc.10306 · 2003 · External reference
eHiTS: an innovative approach to the docking and scoring function problems
10.2174/138920306778559412 · 2006 · External reference
A Fast Flexible Docking Method Using an Incremental Construction Algorithm
10.1006/jmbi.1996.0477 · 1996 · External reference
FRED Pose Prediction and Virtual Screening Accuracy
10.1021/ci100436p · 2011 · External reference
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
10.1021/jm0306430 · 2004 · External reference
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening
10.1021/jm030644s · 2004 · External reference
Improved Protein-Ligand Docking Using GOLD
10.1002/prot.10465 · 2003 · External reference
Diverse, high-quality test set for the validation of protein– ligand docking performance
10.1021/jm061277y · 2007 · External reference
ICM - a new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation
10.1002/jcc.540150503 · 1994 · External reference
Medicinal chemistry and the molecular operating environment (MOE): application of QSAR and molecular docking to drug discovery
10.2174/156802608786786624 · 2008 · External reference
rDock: a fast, versatile and open source program for docking ligands to proteins and nucleic acids
10.1371/journal.pcbi.1003571 · 2014 · External reference
Surflex-Dock: Docking Benchmarks and Real-World Application
10.1007/s10822-011-9533-y · 2012 · External reference
Docking validation resources: protein family and ligand flexibility experiments
10.1021/ci1001982 · 2010 · External reference
Flexible ligand docking using conformational ensembles
10.1002/pro.5560070411 · 1998 · External reference
Comparison of several molecular docking programs: pose prediction and virtual screening accuracy
10.1021/ci900056c · 2009 · External reference
A critical assessment of docking programs and scoring functions
10.1021/jm050362n · 2006 · External reference
Consensus docking: improving the reliability of docking in a virtual screening context
10.1021/ci300399w · 2013 · External reference
Comprehensive evaluation of ten docking programs on a diverse set of protein–ligand complexes: the prediction accuracy of sampling power and scoring power
10.1039/c6cp01555g · 2016 · External reference
Comparative assessment of seven docking programs on a nonredundant metalloprotein subset of the PDBbind refined
10.1021/acs.jcim.9b00346 · 2019 · External reference
Extensive consensus docking evaluation for ligand pose prediction and virtual screening studies
10.1021/ci500424n · 2014 · External reference
The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures
10.1021/jm030580l · 2004 · External reference
Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking
10.1021/jm300687e · 2012 · External reference
Comparing protein–ligand docking programs is difficult
10.1002/prot.20497 · 2005 · External reference
Evaluation of protein-ligand docking methods on peptide-ligand complexes for docking small ligands to peptides
2017 · External reference
How Good Are Current Docking Programs at Nucleic Acid–Ligand Docking? A Comprehensive Evaluation
10.1021/acs.jctc.3c00507 · 2023 · External reference
Benchmarking AlphaFold-enabled molecular docking predictions for antibiotic discovery
10.15252/msb.202211081 · 2022 · External reference
The Protein Data Bank
10.1093/nar/28.1.235 · 2000 · External reference
The Amber biomolecular simulation programs
10.1002/jcc.20290 · 2005 · External reference
Atomic-resolution protein structure determination by cryo-EM
10.1038/s41586-020-2833-4 · 2020 · External reference
Drug discovery in the era of cryo-electron microscopy
10.1016/j.tibs.2021.06.008 · 2022 · External reference
Cryo-electron microscopy: moving beyond X-ray crystal structures for drug receptors and drug development
10.1146/annurev-pharmtox-010919-023545 · 2020 · External reference
Cryo-EM structure and activator screening of human tryptophan hydroxylase 2
10.3389/fphar.2022.907437 · 2022 · External reference
Pushing the limits of computational structure-based drug design with a cryo-EM structure: the Ca2+ channel α2δ-1 subunit as a test case
10.1021/acs.jcim.8b00347 · 2018 · External reference
Structure-based discovery of conformationally selective inhibitors of the serotonin transporter
10.1016/j.cell.2023.04.010 · 2023 · External reference
Atomic resolution cryo electron microscopy of macromolecular complexes
10.1016/b978-0-12-386507-6.00001-4 · 2011 · External reference
DrugCentral 2023 extends human clinical data and integrates veterinary drugs
10.1093/nar/gkac1085 · 2023 · External reference
A comprehensive map of molecular drug targets
10.1038/nrd.2016.230 · 2017 · External reference
DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases
10.1023/a:1011115820450 · 2001 · External reference
PoseBusters: AI-based docking methods fail to generate physically valid poses or generalise to novel sequences
10.1039/d3sc04185a · 2024 · External reference
Implementation of the Hungarian algorithm to account for ligand symmetry and similarity in structure-based design
10.1021/ci400534h · 2014 · External reference
Open Babel: An open chemical toolbox
10.1186/1758-2946-3-33 · 2011 · External reference
FRED and HYBRID docking performance on standardized datasets
10.1007/s10822-012-9584-8 · 2012 · External reference
Lead-and drug-like compounds: the rule-of-five revolution
10.1016/j.ddtec.2004.11.007 · 2004 · External reference
Iterative partial equalization of orbital electronegativity: a rapid access to atomic charges
10.1016/0040-4020(80)80168-2 · 1980 · External reference
Neutral ceramidase-active site inhibitor chemotypes and binding modes
10.1016/j.bioorg.2023.106747 · 2023 · External reference
A semiempirical free energy force field with charge-based desolvation
10.1002/jcc.20634 · 2007 · External reference
Evaluation of DOCK 6 as a pose generation and database enrichment tool
10.1007/s10822-012-9565-y · 2012 · External reference
Structure-activity relationships in purine-based inhibitor binding to HSP90 isoforms
10.1016/j.chembiol.2004.03.033 · 2004 · External reference
PDTD: a web-accessible protein database for drug target identification
10.1186/1471-2105-9-104 · 2008 · External reference
Customizable de novo design strategies for DOCK: Application to HIVgp41 and other therapeutic targets
10.1002/jcc.25052 · 2017 · External reference
A molecular evolution algorithm for ligand design in DOCK.
10.1002/jcc.26993 · 2022 · External reference
Descriptor-Driven de Novo Design Algorithms for DOCK6 Using RDKit
10.1021/acs.jcim.3c01031 · 2023 · External reference
Fragment and torsion biasing algorithms for construction of small organic molecules in proteins using DOCK.
10.1002/jcc.27508 · 2025 · External reference
Expanding the Palette of Molecular Fragments for Small Molecule De Novo Design Through Isosteric Swapping
10.1002/jcc.70312 · 2026 · External reference
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
10.1002/(sici)1096-987x(19981115)19:14<1639::aid-jcc10>3.0.co;2-b · ExternalCitation · doi-reference
Detailed analysis of grid-based molecular docking: A case study of CDOCKER-A CHARMm-based MD docking algorithm
10.1002/jcc.10306 · ExternalCitation · doi-reference
The Amber biomolecular simulation programs
10.1002/jcc.20290 · ExternalCitation · doi-reference
A semiempirical free energy force field with charge-based desolvation
10.1002/jcc.20634 · ExternalCitation · doi-reference
AutoDock Vina: Improving the Speed and Accuracy of Docking with a New Scoring Function, Efficient Optimization, and Multithreading
10.1002/jcc.21334 · ExternalCitation · doi-reference
DOCK 6: Impact of new features and current docking performance
10.1002/jcc.23905 · ExternalCitation · doi-reference
Customizable de novo design strategies for DOCK: Application to HIVgp41 and other therapeutic targets
10.1002/jcc.25052 · ExternalCitation · doi-reference
A molecular evolution algorithm for ligand design in DOCK.
10.1002/jcc.26993 · ExternalCitation · doi-reference
Fragment and torsion biasing algorithms for construction of small organic molecules in proteins using DOCK.
10.1002/jcc.27508 · ExternalCitation · doi-reference
ICM - a new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation
10.1002/jcc.540150503 · ExternalCitation · doi-reference
Expanding the Palette of Molecular Fragments for Small Molecule De Novo Design Through Isosteric Swapping
10.1002/jcc.70312 · ExternalCitation · doi-reference
Flexible ligand docking using conformational ensembles
10.1002/pro.5560070411 · ExternalCitation · doi-reference
Improved Protein-Ligand Docking Using GOLD
10.1002/prot.10465 · ExternalCitation · doi-reference
Comparing protein–ligand docking programs is difficult
10.1002/prot.20497 · ExternalCitation · doi-reference
A Fast Flexible Docking Method Using an Incremental Construction Algorithm
10.1006/jmbi.1996.0477 · ExternalCitation · doi-reference
Surflex-Dock: Docking Benchmarks and Real-World Application
10.1007/s10822-011-9533-y · ExternalCitation · doi-reference
Evaluation of DOCK 6 as a pose generation and database enrichment tool
10.1007/s10822-012-9565-y · ExternalCitation · doi-reference
FRED and HYBRID docking performance on standardized datasets
10.1007/s10822-012-9584-8 · ExternalCitation · doi-reference
A geometric approach to macromolecule-ligand interactions
10.1016/0022-2836(82)90153-x · ExternalCitation · doi-reference
Iterative partial equalization of orbital electronegativity: a rapid access to atomic charges
10.1016/0040-4020(80)80168-2 · ExternalCitation · doi-reference
Atomic resolution cryo electron microscopy of macromolecular complexes
10.1016/b978-0-12-386507-6.00001-4 · ExternalCitation · doi-reference
Neutral ceramidase-active site inhibitor chemotypes and binding modes
10.1016/j.bioorg.2023.106747 · ExternalCitation · doi-reference
Structure-based discovery of conformationally selective inhibitors of the serotonin transporter
10.1016/j.cell.2023.04.010 · ExternalCitation · doi-reference
Structure-activity relationships in purine-based inhibitor binding to HSP90 isoforms
10.1016/j.chembiol.2004.03.033 · ExternalCitation · doi-reference
Lead-and drug-like compounds: the rule-of-five revolution
10.1016/j.ddtec.2004.11.007 · ExternalCitation · doi-reference
Drug discovery in the era of cryo-electron microscopy
10.1016/j.tibs.2021.06.008 · ExternalCitation · doi-reference
Descriptor-Driven de Novo Design Algorithms for DOCK6 Using RDKit
10.1021/acs.jcim.3c01031 · ExternalCitation · doi-reference
Pushing the limits of computational structure-based drug design with a cryo-EM structure: the Ca2+ channel α2δ-1 subunit as a test case
10.1021/acs.jcim.8b00347 · ExternalCitation · doi-reference
Comparative assessment of seven docking programs on a nonredundant metalloprotein subset of the PDBbind refined
10.1021/acs.jcim.9b00346 · ExternalCitation · doi-reference
How Good Are Current Docking Programs at Nucleic Acid–Ligand Docking? A Comprehensive Evaluation
10.1021/acs.jctc.3c00507 · ExternalCitation · doi-reference
Docking validation resources: protein family and ligand flexibility experiments
10.1021/ci1001982 · ExternalCitation · doi-reference
FRED Pose Prediction and Virtual Screening Accuracy
10.1021/ci100436p · ExternalCitation · doi-reference
Consensus docking: improving the reliability of docking in a virtual screening context
10.1021/ci300399w · ExternalCitation · doi-reference
Implementation of the Hungarian algorithm to account for ligand symmetry and similarity in structure-based design
10.1021/ci400534h · ExternalCitation · doi-reference
Extensive consensus docking evaluation for ligand pose prediction and virtual screening studies
10.1021/ci500424n · ExternalCitation · doi-reference
Comparison of several molecular docking programs: pose prediction and virtual screening accuracy
10.1021/ci900056c · ExternalCitation · doi-reference
The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures
10.1021/jm030580l · ExternalCitation · doi-reference
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
10.1021/jm0306430 · 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
A critical assessment of docking programs and scoring functions
10.1021/jm050362n · ExternalCitation · doi-reference
Diverse, high-quality test set for the validation of protein– ligand docking performance
10.1021/jm061277y · ExternalCitation · doi-reference
Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking
10.1021/jm300687e · ExternalCitation · doi-reference
DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases
10.1023/a:1011115820450 · ExternalCitation · doi-reference
Virtual screening of chemical libraries
10.1038/nature03197 · ExternalCitation · doi-reference
A comprehensive map of molecular drug targets
10.1038/nrd.2016.230 · ExternalCitation · doi-reference
Atomic-resolution protein structure determination by cryo-EM
10.1038/s41586-020-2833-4 · ExternalCitation · doi-reference
Comprehensive evaluation of ten docking programs on a diverse set of protein–ligand complexes: the prediction accuracy of sampling power and scoring power
10.1039/c6cp01555g · ExternalCitation · doi-reference
PoseBusters: AI-based docking methods fail to generate physically valid poses or generalise to novel sequences
10.1039/d3sc04185a · ExternalCitation · doi-reference
The Protein Data Bank
10.1093/nar/28.1.235 · ExternalCitation · doi-reference
DrugCentral 2023 extends human clinical data and integrates veterinary drugs
10.1093/nar/gkac1085 · ExternalCitation · doi-reference
The Many Roles of Computation in Drug Discovery
10.1126/science.1096361 · ExternalCitation · doi-reference
Structure-based strategies for drug design and discovery
10.1126/science.257.5073.1078 · ExternalCitation · doi-reference
Cryo-electron microscopy: moving beyond X-ray crystal structures for drug receptors and drug development
10.1146/annurev-pharmtox-010919-023545 · ExternalCitation · doi-reference
PDTD: a web-accessible protein database for drug target identification
10.1186/1471-2105-9-104 · ExternalCitation · doi-reference
Open Babel: An open chemical toolbox
10.1186/1758-2946-3-33 · ExternalCitation · doi-reference
rDock: a fast, versatile and open source program for docking ligands to proteins and nucleic acids
10.1371/journal.pcbi.1003571 · ExternalCitation · doi-reference
Benchmarking AlphaFold-enabled molecular docking predictions for antibiotic discovery
10.15252/msb.202211081 · ExternalCitation · doi-reference
eHiTS: an innovative approach to the docking and scoring function problems
10.2174/138920306778559412 · ExternalCitation · doi-reference
Medicinal chemistry and the molecular operating environment (MOE): application of QSAR and molecular docking to drug discovery
10.2174/156802608786786624 · ExternalCitation · doi-reference
Cryo-EM structure and activator screening of human tryptophan hydroxylase 2
10.3389/fphar.2022.907437 · ExternalCitation · doi-reference
