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Toward prediction of functional protein pockets using blind docking and pocket search algorithms

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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/(sici)1096-987x(19981115)19:14<1639::aid-jcc10>3.0.co;2-bopenalex-snapshot
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
inferredcites →https://doi.org/10.1002/jcc.20634openalex-snapshot
A semiempirical free energy force field with charge‐based desolvation
inferredcites →https://doi.org/10.1002/jcc.21202openalex-snapshot
Blind docking of 260 protein–ligand complexes with EADock 2.0
inferredcites →https://doi.org/10.1002/jcc.21256openalex-snapshot
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
inferredcites →https://doi.org/10.1002/prot.21191openalex-snapshot
Strategies for high‐throughput comparative modeling: Applications to leverage analysis in structural genomics and protein family organization
inferredcites →https://doi.org/10.1002/prot.21367openalex-snapshot
EADock: Docking of small molecules into protein active sites with a multiobjective evolutionary optimization
inferredcites →https://doi.org/10.1002/prot.22154openalex-snapshot
Improving accuracy and efficiency of blind protein‐ligand docking by focusing on predicted binding sites
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/s00894-005-0057-zopenalex-snapshot
Acetylcholine nicotinic receptors: finding the putative binding site of allosteric modulators using the “blind docking” approach
inferredcites →https://doi.org/10.1016/j.bmcl.2005.11.097openalex-snapshot
The existence of a second allosteric site on the M1 muscarinic acetylcholine receptor and its implications for drug design
inferredcites →https://doi.org/10.1016/j.cbpa.2008.01.045openalex-snapshot
Structural genomics and drug discovery: all in the family
inferredcites →https://doi.org/10.1016/j.febslet.2006.01.074openalex-snapshot
Blind docking of drug‐sized compounds to proteins with up to a thousand residues
inferredcites →https://doi.org/10.1016/j.sbi.2009.08.002openalex-snapshot
High-throughput crystallography for structural genomics☆
inferredcites →https://doi.org/10.1016/s1093-3263(98)00002-3openalex-snapshot
LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins
inferredcites →https://doi.org/10.1021/ci700388kopenalex-snapshot
Docking of Noncompetitive Inhibitors into Dengue Virus Type 2 Protease: Understanding the Interactions with Allosteric Binding Sites
inferredcites →https://doi.org/10.1021/ja00291a006openalex-snapshot
Computation of molecular volume
inferredcites →https://doi.org/10.1021/jp104983aopenalex-snapshot
Structural and Thermodynamic Characteristics of the Exosite Binding Pocket on the Human BACE1: A Molecular Modeling Approach
inferredcites →https://doi.org/10.1023/a:1008124202956openalex-snapshot
Fast prediction and visualization of protein binding pockets with PASS
inferredcites →https://doi.org/10.1023/a:1016307520660openalex-snapshot
Q-fit: A probabilistic method for docking molecular fragments by sampling low energy conformational space
inferredcites →https://doi.org/10.1038/nrd706openalex-snapshot
High-throughput crystallography for lead discovery in drug design
inferredcites →https://doi.org/10.1073/pnas.0707684105openalex-snapshot
A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation
inferredcites →https://doi.org/10.1073/pnas.0804372105openalex-snapshot
Potentiation of α7 nicotinic acetylcholine receptors via an allosteric transmembrane site
inferredcites →https://doi.org/10.1093/bib/bbp017openalex-snapshot
FINDSITE: a combined evolution/structure-based approach to protein function prediction
inferredcites →https://doi.org/10.1093/bioinformatics/bti315openalex-snapshot
Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites
inferredcites →https://doi.org/10.1093/nar/gkp281openalex-snapshot
SITEHOUND-web: a server for ligand binding site identification in protein structures
inferredcites →https://doi.org/10.1110/ps.0202302openalex-snapshot
Efficient docking of peptides to proteins without prior knowledge of the binding site
inferredcites →https://doi.org/10.1110/ps.0242903openalex-snapshot
Structural genomics: Computational methods for structure analysis
inferredcites →https://doi.org/10.1371/journal.pcbi.1000530openalex-snapshot
The Role of Medical Structural Genomics in Discovering New Drugs for Infectious Diseases
inferredcites →https://doi.org/10.2174/138920306778559386openalex-snapshot
Methods for the Prediction of Protein-Ligand Binding Sites for Structure-Based Drug Design and Virtual Ligand Screening.

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inferred← citeshttps://doi.org/10.1002/advs.202520095openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/fsn3.71695openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.23714openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/mbo3.212openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-1-0716-0528-8_24openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-981-15-6815-2_3openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s00044-018-2138-4openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s10534-020-00235-3openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s10969-011-9110-6openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s12550-018-0321-6openalex-snapshot
Interactions of zearalenone and its reduced metabolites α-zearalenol and β-zearalenol with serum albumins: species differences, binding sites, and thermodynamics
inferred← citeshttps://doi.org/10.1007/s12550-018-0336-zopenalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s13738-026-03489-9openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s13738-026-03597-6openalex-snapshot
Substitution effect in Zn(II) complexes with symmetrical tetradentate Schiff base ligands: experimental vs. theoretical insights
inferred← citeshttps://doi.org/10.1007/s13738-026-03649-xopenalex-snapshot
Synthesis, structural elucidation, electronic properties, and biomolecular docking studies of halogen-substituted aminobenzohydrazone Schiff base ligands
inferred← citeshttps://doi.org/10.1016/bs.apha.2025.02.006openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.bbapap.2012.08.014openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.bbapap.2012.09.007openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.biochi.2013.04.001openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.biochi.2021.10.011openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.biopha.2018.03.146openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.compbiomed.2023.106786openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.ejmech.2011.09.038openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.ica.2025.122910openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.imu.2021.100722openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.isci.2025.112305openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.jphotobiol.2017.03.016openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.jphotobiol.2017.10.021openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.molstruc.2025.142797openalex-snapshot
Spectroscopic, structural, theoretical, and molecular docking studies of Zn(II), Cu(II), and Ni(II) complexes incorporating a symmetrical N2O2 tetradentate Schiff base ligand
inferred← citeshttps://doi.org/10.1016/j.molstruc.2025.143515openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.molstruc.2025.144728openalex-snapshot
Tetradentate Schiff base complexes from 4,5-dimethyl-1,2-phenylenediamine: SC-XRD, HSA, DFT, and molecular docking investigations
inferred← citeshttps://doi.org/10.1016/j.parco.2014.09.008openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.rechem.2025.102902openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.rechem.2025.102909openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.saa.2017.02.047openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.saa.2017.11.015openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.saa.2022.120931openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.talanta.2020.120762openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00574openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acschemneuro.1c00521openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/bi401618yopenalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ct400404qopenalex-snapshot
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inferred← citeshttps://doi.org/10.1038/s41598-017-14840-9openalex-snapshot
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inferred← citeshttps://doi.org/10.1038/s41598-017-16392-4openalex-snapshot
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inferred← citeshttps://doi.org/10.1038/s41598-018-36391-3openalex-snapshot
Effects of point mutations in the binding pocket of the mouse major urinary protein MUP20 on ligand affinity and specificity
inferred← citeshttps://doi.org/10.1039/9781849735377-00171openalex-snapshot
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inferred← citeshttps://doi.org/10.1039/c5ra10761jopenalex-snapshot
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inferred← citeshttps://doi.org/10.1063/4.0000757openalex-snapshot
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inferred← citeshttps://doi.org/10.1073/pnas.1201940109openalex-snapshot
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inferred← citeshttps://doi.org/10.1080/07391102.2019.1580221openalex-snapshot
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inferred← citeshttps://doi.org/10.1080/07391102.2021.1988709openalex-snapshot
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inferred← citeshttps://doi.org/10.1080/07391102.2022.2029564openalex-snapshot
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inferred← citeshttps://doi.org/10.1080/10406638.2024.2399536openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/bib/bbv008openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/bioinformatics/btab525openalex-snapshot
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inferred← citeshttps://doi.org/10.1101/346130openalex-snapshot
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inferred← citeshttps://doi.org/10.1145/2488551.2488584openalex-snapshot
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inferred← citeshttps://doi.org/10.1155/2012/976385openalex-snapshot
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inferred← citeshttps://doi.org/10.1371/journal.pbio.1002146openalex-snapshot
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inferred← citeshttps://doi.org/10.15476/elte.2018.091openalex-snapshot
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inferred← citeshttps://doi.org/10.18632/aging.206227openalex-snapshot
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inferred← citeshttps://doi.org/10.25135/acg.oc.128.2202.2356openalex-snapshot
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inferred← citeshttps://doi.org/10.3390/ijms24021134openalex-snapshot
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inferred← citeshttps://doi.org/10.3390/molecules190710150openalex-snapshot
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inferred← citeshttps://doi.org/10.3390/ph18121777openalex-snapshot
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inferred← citeshttps://doi.org/10.3390/toxins10090353openalex-snapshot
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inferred← citeshttps://doi.org/10.3390/toxins7124871openalex-snapshot
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inferred← citeshttps://doi.org/10.3844/ajbsp.2016.1.9openalex-snapshot
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inferred← citeshttps://doi.org/10.53846/goediss-2927openalex-snapshot
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inferred← citeshttps://doi.org/10.70675/f0567b86z4fdfz4cc8zb716z49ec4d7b8548openalex-snapshot
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inferred← citeshttps://doi.org/10.7476/9786580216123openalex-snapshot
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inferred← citeshttps://doi.org/10.7476/9786580216123.0005openalex-snapshot
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