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The Application of Statistical Methods to Cognate Docking: A Path Forward?
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/prot.20497openalex-snapshot
Comparing protein–ligand docking programs is difficult
inferredcites →https://doi.org/10.1007/bf02295996openalex-snapshot
Note on the Sampling Error of the Difference Between Correlated Proportions or Percentages
inferredcites →https://doi.org/10.1007/s10822-007-9166-3openalex-snapshot
How to do an evaluation: pitfalls and traps
inferredcites →https://doi.org/10.1007/s10822-011-9531-0openalex-snapshot
Substantial improvements in large-scale redocking and screening using the novel HYDE scoring function
inferredcites →https://doi.org/10.1007/s10822-011-9533-yopenalex-snapshot
Surflex-Dock: Docking benchmarks and real-world application
inferredcites →https://doi.org/10.1007/s10822-012-9547-0openalex-snapshot
Docking and scoring with ICM: the benchmarking results and strategies for improvement
inferredcites →https://doi.org/10.1007/s10822-012-9549-yopenalex-snapshot
Lead Finder docking and virtual screening evaluation with Astex and DUD test sets
inferredcites →https://doi.org/10.1007/s10822-012-9551-4openalex-snapshot
Pose prediction and virtual screening performance of GOLD scoring functions in a standardized test
inferredcites →https://doi.org/10.1007/s10822-012-9565-yopenalex-snapshot
Evaluation of DOCK 6 as a pose generation and database enrichment tool
inferredcites →https://doi.org/10.1007/s10822-012-9570-1openalex-snapshot
Variability in docking success rates due to dataset preparation
inferredcites →https://doi.org/10.1007/s10822-012-9575-9openalex-snapshot
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
inferredcites →https://doi.org/10.1007/s10822-012-9584-8openalex-snapshot
FRED and HYBRID docking performance on standardized datasets
inferredcites →https://doi.org/10.1016/j.drudis.2012.06.011openalex-snapshot
Essential considerations for using protein–ligand structures in drug discovery
inferredcites →https://doi.org/10.1016/j.pmrj.2010.07.482openalex-snapshot
The Importance of Accounting for Correlated Observations
inferredcites →https://doi.org/10.1017/s0140525x98281167openalex-snapshot
We need statistical thinking, not statistical rituals
inferredcites →https://doi.org/10.1021/ci049970mopenalex-snapshot
Assessment of Docking Poses: Interactions-Based Accuracy Classification (IBAC) versus Crystal Structure Deviations
inferredcites →https://doi.org/10.1021/ci0500177openalex-snapshot
A Discussion of Measures of Enrichment in Virtual Screening: Comparing the Information Content of Descriptors with Increasing Levels of Sophistication
inferredcites →https://doi.org/10.1021/ci0503255openalex-snapshot
On Evaluating Molecular-Docking Methods for Pose Prediction and Enrichment Factors
inferredcites →https://doi.org/10.1021/ci100031xopenalex-snapshot
Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database
inferredcites →https://doi.org/10.1021/ci100161zopenalex-snapshot
Protein Kinases: Docking and Homology Modeling Reliability
inferredcites →https://doi.org/10.1021/ci1001982openalex-snapshot
Docking Validation Resources: Protein Family and Ligand Flexibility Experiments
inferredcites →https://doi.org/10.1021/ci100436popenalex-snapshot
FRED Pose Prediction and Virtual Screening Accuracy
inferredcites →https://doi.org/10.1021/ci300314kopenalex-snapshot
Conformer Generation with OMEGA: Learning from the Data Set and the Analysis of Failures
inferredcites →https://doi.org/10.1021/ci300411bopenalex-snapshot
Current Assessment of Docking into GPCR Crystal Structures and Homology Models: Successes, Challenges, and Guidelines
inferredcites →https://doi.org/10.1021/ci7000346openalex-snapshot
Comparative Performance of Several Flexible Docking Programs and Scoring Functions: Enrichment Studies for a Diverse Set of Pharmaceutically Relevant Targets
inferredcites →https://doi.org/10.1021/ci800084xopenalex-snapshot
An Alternative Method for the Evaluation of Docking Performance: RSR vs RMSD
inferredcites →https://doi.org/10.1021/ci8004176openalex-snapshot
Docking Ligands into Flexible and Solvated Macromolecules. 3. Impact of Input Ligand Conformation, Protein Flexibility, and Water Molecules on the Accuracy of Docking Programs
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/ci9001074openalex-snapshot
GARD: A Generally Applicable Replacement for RMSD
inferredcites →https://doi.org/10.1021/jm0493818openalex-snapshot
Ph4Dock: Pharmacophore-Based Protein−Ligand Docking
inferredcites →https://doi.org/10.1021/jm051197eopenalex-snapshot
MolDock: A New Technique for High-Accuracy Molecular Docking
inferredcites →https://doi.org/10.1021/jm0603365openalex-snapshot
Comparison of Shape-Matching and Docking as Virtual Screening Tools
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/jm200558uopenalex-snapshot
Docking Performance of Fragments and Druglike Compounds
inferredcites →https://doi.org/10.1080/00031305.1973.10478966openalex-snapshot
Graphs in Statistical Analysis
inferredcites →https://doi.org/10.1080/00401706.1989.10488618openalex-snapshot
Statistical Power Analysis for the Behavioral Sciences
inferredcites →https://doi.org/10.1080/01621459.1987.10478410openalex-snapshot
Better Bootstrap Confidence Intervals
inferredcites →https://doi.org/10.1107/s0108767390010224openalex-snapshot
Improved methods for building protein models in electron density maps and the location of errors in these models
inferredcites →https://doi.org/10.1107/s0907444902003931openalex-snapshot
Rearrangement of Cruickshank's formulae for the diffraction-component precision index
inferredcites →https://doi.org/10.1107/s0907444904013253openalex-snapshot
The Uppsala Electron-Density Server
inferredcites →https://doi.org/10.1107/s0907444999016364openalex-snapshot
Validation of protein crystal structures
inferredcites →https://doi.org/10.2307/1269179openalex-snapshot
Mathematical Statistics and Data Analysis
inferredcites →https://doi.org/10.2307/2983604openalex-snapshot
Contingency Tables Involving Small Numbers and the χ2 Test
inferredcites →https://doi.org/10.2307/3001968openalex-snapshot
Individual Comparisons by Ranking Methods
inferredcites →https://doi.org/10.3758/bf03193146openalex-snapshot
G*Power 3: A flexible statistical power analysis program for the social, behavioral, and biomedical sciences
inferredcites →https://doi.org/10.5465/ambpp.1985.4978223openalex-snapshot
In Search of Power: A Statistical Power Analysis of Contemporary Research in Strategic Management.
inferredcites →https://doi.org/10.5860/choice.46-0372openalex-snapshot
The cult of statistical significance: how the standard error costs us jobs, justice, and lives
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/minf.201501025openalex-snapshot
GLIMPSED: An Improved Docking Protocol for Cognate Docking
inferred← citeshttps://doi.org/10.1007/978-1-4939-7465-8_18openalex-snapshot
Ligand-Based Methods in GPCR Computer-Aided Drug Design
inferred← citeshttps://doi.org/10.1007/s10822-015-9856-1openalex-snapshot
Ligand- and receptor-based docking with LiBELa
inferred← citeshttps://doi.org/10.1007/s10822-016-9923-2openalex-snapshot
A pose prediction approach based on ligand 3D shape similarity
inferred← citeshttps://doi.org/10.1007/s12038-026-00588-wopenalex-snapshot
Structure evaluation coupled with all-atom molecular dynamics and advanced quantum mechanical DFT revealed kaempferol as a potent binding flavonol for the epigenetic-target HDAC9
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00358openalex-snapshot
Decisions with Confidence: Application to the Conformation Sampling of Molecules in the Solid State
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00142openalex-snapshot
POSIT: Flexible Shape-Guided Docking For Pose Prediction
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00613openalex-snapshot
High-Quality Dataset of Protein-Bound Ligand Conformations and Its Application to Benchmarking Conformer Ensemble Generators
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00221openalex-snapshot
Conformation Generation: The State of the Art
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00391openalex-snapshot
Estimating Electron Density Support for Individual Atoms and Molecular Fragments in X-ray Structures
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00536openalex-snapshot
Successful Identification of Cardiac Troponin Calcium Sensitizers Using a Combination of Virtual Screening and ROC Analysis of Known Troponin C Binders
inferred← citeshttps://doi.org/10.1021/ci5003735openalex-snapshot
Improving Docking Results via Reranking of Ensembles of Ligand Poses in Multiple X-ray Protein Conformations with MM-GBSA
inferred← citeshttps://doi.org/10.1021/ci500662dopenalex-snapshot
Evidence of Water Molecules—A Statistical Evaluation of Water Molecules Based on Electron Density
inferred← citeshttps://doi.org/10.1080/07391102.2022.2159529openalex-snapshot
In silico selection of aptamers for bacterial toxins detection
inferred← citeshttps://doi.org/10.1186/s13321-019-0346-7openalex-snapshot
Binding mode information improves fragment docking
inferred← citeshttps://doi.org/10.3390/ijms21155183openalex-snapshot
Assessing Molecular Docking Tools to Guide Targeted Drug Discovery of CD38 Inhibitors
inferred← citeshttps://doi.org/10.3390/molecules22010136openalex-snapshot
The Performance of Several Docking Programs at Reproducing Protein–Macrolide-Like Crystal Structures
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