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Reducing Docking Score Variations Arising from Input Differences

https://doi.org/10.1021/ci100204x
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Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/(sici)1096-987x(199604)17:5/6<490::aid-jcc1>3.0.co;2-popenalex-snapshot
Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94
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Difficulties with multiple time stepping and fast multipole algorithm in molecular dynamics
inferredcites →https://doi.org/10.1002/(sici)1096-987x(199905)20:7<720::aid-jcc7>3.0.co;2-xopenalex-snapshot
MMFF VI. MMFF94s option for energy minimization studies
inferredcites →https://doi.org/10.1006/jcph.1993.1220openalex-snapshot
Dangers of Multiple Time Step Methods
inferredcites →https://doi.org/10.1006/jcph.1999.6202openalex-snapshot
Masking Resonance Artifacts in Force-Splitting Methods for Biomolecular Simulations by Extrapolative Langevin Dynamics
inferredcites →https://doi.org/10.1007/s10822-007-9154-7openalex-snapshot
The effect of numerical error on the reproducibility of molecular geometry optimizations
inferredcites →https://doi.org/10.1007/s10822-007-9165-4openalex-snapshot
Can we use docking and scoring for hit-to-lead optimization?
inferredcites →https://doi.org/10.1016/j.drudis.2008.06.006openalex-snapshot
Limitations and lessons in the use of X-ray structural information in drug design
inferredcites →https://doi.org/10.1016/j.drudis.2009.01.003openalex-snapshot
Managing protein flexibility in docking and its applications
inferredcites →https://doi.org/10.1016/j.drudis.2009.03.013openalex-snapshot
Targeted scoring functions for virtual screening
inferredcites →https://doi.org/10.1021/ci0200671openalex-snapshot
Fuzzy Clustering as a Means of Selecting Representative Conformers and Molecular Alignments
inferredcites →https://doi.org/10.1021/ci0601214openalex-snapshot
Are Automated Molecular Dynamics Simulations and Binding Free Energy Calculations Realistic Tools in Lead Optimization? An Evaluation of the Linear Interaction Energy (LIE) Method
inferredcites →https://doi.org/10.1021/ci9000629openalex-snapshot
Effect of Input Differences on the Results of Docking Calculations
inferredcites →https://doi.org/10.1021/jm050362nopenalex-snapshot
A Critical Assessment of Docking Programs and Scoring Functions
inferredcites →https://doi.org/10.1021/jm060763iopenalex-snapshot
Contribution of Conformer Focusing to the Uncertainty in Predicting Free Energies for Protein−Ligand Binding
inferredcites →https://doi.org/10.1021/jm060999mopenalex-snapshot
Prediction of Protein−Ligand Interactions. Docking and Scoring: Successes and Gaps
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/jm8016464openalex-snapshot
Structural Artifacts in Protein−Ligand X-ray Structures: Implications for the Development of Docking Scoring Functions
inferredcites →https://doi.org/10.1023/a:1015941316283openalex-snapshot
Identifying potential binding modes and explaining partitioning behavior using flexible alignments and multidimensional scaling
inferredcites →https://doi.org/10.1038/nrd1549openalex-snapshot
Docking and scoring in virtual screening for drug discovery: methods and applications
inferredcites →https://doi.org/10.1063/1.476737openalex-snapshot
Extrapolation versus impulse in multiple-timestepping schemes. II. Linear analysis and applications to Newtonian and Langevin dynamics

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

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A Structure‐Activity Investigation of the Fungal Metabolite (−)‐TAN‐2483B: Inhibition of Bruton's Tyrosine Kinase
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Latest developments in molecular docking: 2010–2011 in review
inferred← citeshttps://doi.org/10.1007/s10822-012-9570-1openalex-snapshot
Variability in docking success rates due to dataset preparation
inferred← citeshttps://doi.org/10.1016/j.drudis.2015.07.012openalex-snapshot
Development of HIV-1 integrase inhibitors: recent molecular modeling perspectives
inferred← citeshttps://doi.org/10.1021/ci200598mopenalex-snapshot
Numerical Errors and Chaotic Behavior in Docking Simulations
inferred← citeshttps://doi.org/10.1021/ci300298dopenalex-snapshot
Numerical Errors in Minimization Based Binding Energy Calculations
inferred← citeshttps://doi.org/10.1021/ci400285zopenalex-snapshot
Improved Ligand Binding Energies Derived from Molecular Dynamics: Replicate Sampling Enhances the Search of Conformational Space
inferred← citeshttps://doi.org/10.1021/jm501740aopenalex-snapshot
The Discovery of Orally Bioavailable Tyrosine Threonine Kinase (TTK) Inhibitors: 3-(4-(heterocyclyl)phenyl)-1H-indazole-5-carboxamides as Anticancer Agents
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On the energy minimization of large molecules
inferred← citeshttps://doi.org/10.32463/rphs.2018.v04i01.05openalex-snapshot
Molecular Docking an Enchanted Way in The Discovery of Novel Molecule in Designing Drug: A Focused Review
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