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Construction and Test of Ligand Decoy Sets Using MDock: Community Structure–Activity Resource Benchmarks for Binding Mode Prediction
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Critical evaluation of search algorithms for automated molecular docking and database screening
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Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method
inferredcites →https://doi.org/10.1002/jcc.10128openalex-snapshot
Fast, efficient generation of high‐quality atomic charges. AM1‐BCC model: II. Parameterization and validation
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UCSF Chimera—A visualization system for exploratory research and analysis
inferredcites →https://doi.org/10.1002/jcc.20290openalex-snapshot
The Amber biomolecular simulation programs
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An iterative knowledge‐based scoring function to predict protein–ligand interactions: I. Derivation of interaction potentials
inferredcites →https://doi.org/10.1002/jcc.20505openalex-snapshot
An iterative knowledge‐based scoring function to predict protein–ligand interactions: II. Validation of the scoring function
inferredcites →https://doi.org/10.1002/jcc.20893openalex-snapshot
Assessment of programs for ligand binding affinity prediction
inferredcites →https://doi.org/10.1002/jcc.540130412openalex-snapshot
Automated docking with grid‐based energy evaluation
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A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
inferredcites →https://doi.org/10.1002/prot.20149openalex-snapshot
Comparative evaluation of eight docking tools for docking and virtual screening accuracy
inferredcites →https://doi.org/10.1002/prot.20497openalex-snapshot
Comparing protein–ligand docking programs is difficult
inferredcites →https://doi.org/10.1002/prot.21086openalex-snapshot
ROSETTALIGAND: Protein–small molecule docking with full side‐chain flexibility
inferredcites →https://doi.org/10.1002/prot.21214openalex-snapshot
Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking
inferredcites →https://doi.org/10.1007/s10822-006-9060-4openalex-snapshot
Development and validation of a modular, extensible docking program: DOCK 5
inferredcites →https://doi.org/10.1007/s10822-007-9163-6openalex-snapshot
Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection—What can we learn from earlier mistakes?
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/s10822-008-9196-5openalex-snapshot
Recommendations for evaluation of computational methods
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A geometric approach to macromolecule-ligand interactions
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Iterative partial equalization of orbital electronegativity—a rapid access to atomic charges
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On Evaluating Molecular-Docking Methods for Pose Prediction and Enrichment Factors
inferredcites →https://doi.org/10.1021/ci2000727openalex-snapshot
Scoring and Lessons Learned with the CSAR Benchmark Using an Improved Iterative Knowledge-Based Scoring Function
inferredcites →https://doi.org/10.1021/jm0003992openalex-snapshot
Detailed Analysis of Scoring Functions for Virtual Screening
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/jm0203783openalex-snapshot
Comparative Evaluation of 11 Scoring Functions for Molecular Docking
inferredcites →https://doi.org/10.1021/jm030489hopenalex-snapshot
Assessing Scoring Functions for Protein−Ligand Interactions
inferredcites →https://doi.org/10.1021/jm050362nopenalex-snapshot
A Critical Assessment of Docking Programs and Scoring Functions
inferredcites →https://doi.org/10.1021/jm0608356openalex-snapshot
Benchmarking Sets for Molecular Docking
inferredcites →https://doi.org/10.1021/jm9006966openalex-snapshot
Automated Docking Screens: A Feasibility Study
inferredcites →https://doi.org/10.1021/jm980536jopenalex-snapshot
A General and Fast Scoring Function for Protein−Ligand Interactions: A Simplified Potential Approach
inferredcites →https://doi.org/10.1023/a:1011115820450openalex-snapshot
DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
inferredcites →https://doi.org/10.1023/b:jcam.0000017496.76572.6fopenalex-snapshot
Comparative study of several algorithms for flexible ligand docking
inferredcites →https://doi.org/10.1039/c0cp00151aopenalex-snapshot
Scoring functions and their evaluation methods for protein–ligand docking: recent advances and future directions
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Efficient molecular docking of NMR structures: Application to HIV‐1 protease
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Advances and Challenges in Protein-Ligand Docking
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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A nonredundant structure dataset for benchmarking protein‐RNA computational docking
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Improving scoring-docking-screening powers of protein-ligand scoring functions using random forest
inferred← citeshttps://doi.org/10.1002/jmr.2266openalex-snapshot
Latest developments in molecular docking: 2010–2011 in review
inferred← citeshttps://doi.org/10.1007/s10822-019-00185-0openalex-snapshot
Predicting protein–ligand binding modes for CELPP and GC3: workflows and insight
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00895openalex-snapshot
Holo Protein Conformation Generation from Apo Structures by Ligand Binding Site Refinement
inferred← citeshttps://doi.org/10.1021/acs.jcim.4c00855openalex-snapshot
XDock: A General Docking Method for Modeling Protein–Ligand and Nucleic Acid–Ligand Interactions
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00275openalex-snapshot
HybridDock: A Hybrid Protein–Ligand Docking Protocol Integrating Protein- and Ligand-Based Approaches
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00142openalex-snapshot
Hierarchical Flexible Peptide Docking by Conformer Generation and Ensemble Docking of Peptides
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00329openalex-snapshot
Novel Consensus Docking Strategy to Improve Ligand Pose Prediction
inferred← citeshttps://doi.org/10.1021/acs.jctc.6b00090openalex-snapshot
An Atomistic Statistically Effective Energy Function for Computational Protein Design
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Structure-Based and Multiple Potential Three-Dimensional Quantitative Structure–Activity Relationship (SB-MP-3D-QSAR) for Inhibitor Design
inferred← citeshttps://doi.org/10.1021/ci400045vopenalex-snapshot
Automated Large-Scale File Preparation, Docking, and Scoring: Evaluation of ITScore and STScore Using the 2012 Community Structure–Activity Resource Benchmark
inferred← citeshttps://doi.org/10.1021/ci4000486openalex-snapshot
CSAR Data Set Release 2012: Ligands, Affinities, Complexes, and Docking Decoys
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Quantum and molecular modelling of abrocitinib as a potential disruptor of cell polarity in colorectal cancer
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Comprehensive assessment of flexible-ligand docking algorithms: current effectiveness and challenges
inferred← citeshttps://doi.org/10.1186/s13321-017-0246-7openalex-snapshot
Efficient conformational ensemble generation of protein-bound peptides
inferred← citeshttps://doi.org/10.2174/1381612811319120005openalex-snapshot
Scoring Functions for Prediction of Protein-Ligand Interactions
inferred← citeshttps://doi.org/10.2174/1389203724666230315121434openalex-snapshot
Dynamic Play between Human N-α-acetyltransferase D and H4-mutant Histones: Molecular Dynamics Study
inferred← citeshttps://doi.org/10.2174/1389557520666200204121129openalex-snapshot
Consensus Analyses in Molecular Docking Studies Applied to Medicinal Chemistry
inferred← citeshttps://doi.org/10.3390/molecules190710150openalex-snapshot
Challenges, Applications, and Recent Advances of Protein-Ligand Docking in Structure-Based Drug Design
inferred← citeshttps://doi.org/10.4018/978-1-5225-0115-2.ch001openalex-snapshot
Molecular Docking at a Glance
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Molecular Docking at a Glance
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