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Efficient Virtual Screening Using Multiple Protein Conformations Described as Negative Images of the Ligand-Binding Site
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation
inferredcites →https://doi.org/10.1002/jcc.20289openalex-snapshot
Scalable molecular dynamics with NAMD
inferredcites →https://doi.org/10.1002/jcc.540130311openalex-snapshot
Molecular docking using shape descriptors
inferredcites →https://doi.org/10.1002/prot.10465openalex-snapshot
Improved protein–ligand docking using GOLD
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Molecular docking to ensembles of protein structures 1 1Edited by B. Honig
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Modelling protein docking using shape complementarity, electrostatics and biochemical information 1 1Edited by J. Thornton
inferredcites →https://doi.org/10.1007/bf00124499openalex-snapshot
Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4
inferredcites →https://doi.org/10.1007/s10822-004-3752-4openalex-snapshot
BODIL: a molecular modeling environment for structure-function analysis and drug design
inferredcites →https://doi.org/10.1016/j.jmgm.2005.12.005openalex-snapshot
Automatic atom type and bond type perception in molecular mechanical calculations
inferredcites →https://doi.org/10.1016/j.neuropharm.2009.08.019openalex-snapshot
Exploring kainate receptor pharmacology using molecular dynamics simulations
inferredcites →https://doi.org/10.1016/s0022-2836(05)80038-5openalex-snapshot
Ligand docking to proteins with discrete side-chain flexibility
inferredcites →https://doi.org/10.1016/s0076-6879(97)77028-9openalex-snapshot
[26] Raster3D: Photorealistic molecular graphics
inferredcites →https://doi.org/10.1021/ar000033jopenalex-snapshot
Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models
inferredcites →https://doi.org/10.1021/ci049714+openalex-snapshot
ZINC − A Free Database of Commercially Available Compounds for Virtual Screening
inferredcites →https://doi.org/10.1021/ci049920hopenalex-snapshot
Comparison of 2 D Similarity and 3 D Superposition. Application to Searching a Conformational Drug Database
inferredcites →https://doi.org/10.1021/ci700052xopenalex-snapshot
Comparison of Topological, Shape, and Docking Methods in Virtual Screening
inferredcites →https://doi.org/10.1021/ci700368popenalex-snapshot
Novel Approach to Structure-Based Pharmacophore Search Using Computational Geometry and Shape Matching Techniques
inferredcites →https://doi.org/10.1021/ci800303kopenalex-snapshot
Comparison of Ligand- and Structure-Based Virtual Screening on the DUD Data Set
inferredcites →https://doi.org/10.1021/ci800315dopenalex-snapshot
ShaEP: Molecular Overlay Based on Shape and Electrostatic Potential
inferredcites →https://doi.org/10.1021/ci9002365openalex-snapshot
Improving Virtual Screening Performance against Conformational Variations of Receptors by Shape Matching with Ligand Binding Pocket
inferredcites →https://doi.org/10.1021/ja042260copenalex-snapshot
Representing Receptor Flexibility in Ligand Docking through Relevant Normal Modes
inferredcites →https://doi.org/10.1021/jm040163oopenalex-snapshot
A Shape-Based 3-D Scaffold Hopping Method and Its Application to a Bacterial Protein−Protein Interaction
inferredcites →https://doi.org/10.1021/jm0603365openalex-snapshot
Comparison of Shape-Matching and Docking as Virtual Screening Tools
inferredcites →https://doi.org/10.1021/jm0608356openalex-snapshot
Benchmarking Sets for Molecular Docking
inferredcites →https://doi.org/10.1021/jm8001058openalex-snapshot
Assessment of Scaffold Hopping Efficiency by Use of Molecular Interaction Fingerprints
inferredcites →https://doi.org/10.1021/jm900817uopenalex-snapshot
Three-Dimensional Pharmacophore Methods in Drug Discovery
inferredcites →https://doi.org/10.1023/a:1008124202956openalex-snapshot
Fast prediction and visualization of protein binding pockets with PASS
inferredcites →https://doi.org/10.1038/aps.2009.159openalex-snapshot
Pharmacophore-based virtual screening versus docking-based virtual screening: a benchmark comparison against eight targets
inferredcites →https://doi.org/10.1107/s0021889891004399openalex-snapshot
MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures
inferredcites →https://doi.org/10.1107/s0907444993011333openalex-snapshot
Detection, delineation, measurement and display of cavities in macromolecular structures
inferredcites →https://doi.org/10.1148/radiology.143.1.7063747openalex-snapshot
The meaning and use of the area under a receiver operating characteristic (ROC) curve.
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1007/978-1-0716-1209-5_7openalex-snapshot
Negative Image-Based Screening: Rigid Docking Using Cavity Information
inferred← citeshttps://doi.org/10.1007/978-1-0716-1209-5_8openalex-snapshot
Negative Image-Based Rescoring: Using Cavity Information to Improve Docking Screening
inferred← citeshttps://doi.org/10.1007/s10822-015-9870-3openalex-snapshot
Ultrafast protein structure-based virtual screening with Panther
inferred← citeshttps://doi.org/10.1007/s12035-019-01775-7openalex-snapshot
A Perspective: Active Role of Lipids in Neurotransmitter Dynamics
inferred← citeshttps://doi.org/10.1016/j.jmgm.2015.10.012openalex-snapshot
Case-specific performance of MM-PBSA, MM-GBSA, and SIE in virtual screening
inferred← citeshttps://doi.org/10.1016/j.jmgm.2015.12.006openalex-snapshot
Identification of estrogen receptor α ligands with virtual screening techniques
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c01145openalex-snapshot
Optimization of Cavity-Based Negative Images to Boost Docking Enrichment in Virtual Screening
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00383openalex-snapshot
Getting Docking into Shape Using Negative Image-Based Rescoring
inferred← citeshttps://doi.org/10.1021/acs.molpharmaceut.3c01161openalex-snapshot
Deciphering the Lexicon of Protein Targets: A Review on Multifaceted Drug Discovery in the Era of Artificial Intelligence
inferred← citeshttps://doi.org/10.1021/acsomega.8b00603openalex-snapshot
Discovery of Retinoic Acid-Related Orphan Receptor γt Inverse Agonists via Docking and Negative Image-Based Screening
inferred← citeshttps://doi.org/10.1021/ci1004527openalex-snapshot
Comparison of Virtual High-Throughput Screening Methods for the Identification of Phosphodiesterase-5 Inhibitors
inferred← citeshttps://doi.org/10.1021/ci200168bopenalex-snapshot
Pocket-Space Maps To Identify Novel Binding-Site Conformations in Proteins
inferred← citeshttps://doi.org/10.1080/14756366.2018.1452919openalex-snapshot
Blocking oestradiol synthesis pathways with potent and selective coumarin derivatives
inferred← citeshttps://doi.org/10.1111/cbdd.13446openalex-snapshot
Suitability of MMGBSA for the selection of correct ligand binding modes from docking results
inferred← citeshttps://doi.org/10.1111/cbdd.13584openalex-snapshot
Fragment‐ and negative image‐based screening of phosphodiesterase 10A inhibitors
inferred← citeshttps://doi.org/10.1186/s13321-024-00857-6openalex-snapshot
Building shape-focused pharmacophore models for effective docking screening
inferred← citeshttps://doi.org/10.26434/chemrxiv-2024-dkvf8openalex-snapshot
3D-Pharma, A Ligand-based Virtual Screening toolusing 3D Pharmacophore Fingerprints
inferred← citeshttps://doi.org/10.3389/fphar.2018.00260openalex-snapshot
Improving Docking Performance Using Negative Image-Based Rescoring
inferred← citeshttps://doi.org/10.3390/ijms20112779openalex-snapshot
A Practical Perspective: The Effect of Ligand Conformers on the Negative Image-Based Screening
inferred← citeshttps://doi.org/10.3390/molecules28083420openalex-snapshot
Virtual Screening Strategy to Identify Retinoic Acid-Related Orphan Receptor γt Modulators
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