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Quantum Chemical Associations Ligand−Residue: Their Role to Predict Flavonoid Binding Sites in Proteins

https://doi.org/10.1021/ci900358z
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking
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Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small molecule
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Drug Discovery Research: New Frontiers in the Post-Genomic Era
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Spectroscopic and molecular modeling studies on the binding of the flavonoid luteolin and human serum albumin
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UCSF Chimera—A visualization system for exploratory research and analysis
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Geometric and chemical patterns of interaction in protein–ligand complexes and their application in docking
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Principles of docking: An overview of search algorithms and a guide to scoring functions
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Comparison of protein active site structures for functional annotation of proteins and drug design
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Molecular simulations bring new insights into flavonoid/quercetinase interaction modes
inferredcites →https://doi.org/10.1002/prot.22170openalex-snapshot
Principles of flexible protein–protein docking
inferredcites →https://doi.org/10.1002/qua.20391openalex-snapshot
Essential amino acids interacting with flavonoids: A theoretical approach
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Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen
inferredcites →https://doi.org/10.1007/s10822-008-9168-9openalex-snapshot
Multiple protein structures and multiple ligands: effects on the apparent goodness of virtual screening results
inferredcites →https://doi.org/10.1007/s10822-008-9189-4openalex-snapshot
Community benchmarks for virtual screening
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The role of quantum mechanics in structure-based drug design
inferredcites →https://doi.org/10.1016/j.jmb.2007.03.062openalex-snapshot
Crystal Structures of Multidrug Binding Protein TtgR in Complex with Antibiotics and Plant Antimicrobials
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Exploring protein–ligand recognition with Binding MOAD
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Understanding the Selectivity of Genistein for Human Estrogen Receptor-β Using X-Ray Crystallography and Computational Methods
inferredcites →https://doi.org/10.1016/j.theochem.2007.05.036openalex-snapshot
Theoretical affinity order among flavonoids and amino acid residues: An approach to understand flavonoid–protein interactions
inferredcites →https://doi.org/10.1016/s0022-2836(02)01408-0openalex-snapshot
Relibase: Design and Development of a Database for Comprehensive Analysis of Protein–Ligand Interactions
inferredcites →https://doi.org/10.1016/s0022-2836(02)01409-2openalex-snapshot
Utilising Structural Knowledge in Drug Design Strategies: Applications Using Relibase
inferredcites →https://doi.org/10.1016/s0959-440x(00)00105-6openalex-snapshot
Recent advances in structure-based rational drug design
inferredcites →https://doi.org/10.1016/s1367-5931(00)00217-9openalex-snapshot
High-throughput docking for lead generation
inferredcites →https://doi.org/10.1021/bi049162oopenalex-snapshot
Crystal Structure of Quinone Reductase 2 in Complex with Resveratrol ,
inferredcites →https://doi.org/10.1021/ci050372xopenalex-snapshot
sc-PDB: an Annotated Database of Druggable Binding Sites from the Protein Data Bank
inferredcites →https://doi.org/10.1021/ci600253eopenalex-snapshot
A Common Reference Framework for Analyzing/Comparing Proteins and Ligands. Fingerprints for Ligands And Proteins (FLAP): Theory and Application
inferredcites →https://doi.org/10.1021/ci700052xopenalex-snapshot
Comparison of Topological, Shape, and Docking Methods in Virtual Screening
inferredcites →https://doi.org/10.1021/ci800298zopenalex-snapshot
Empirical Scoring Functions for Advanced Protein−Ligand Docking with PLANTS
inferredcites →https://doi.org/10.1021/cr800188vopenalex-snapshot
Advances in Solution- and Solid-Phase Synthesis toward the Generation of Natural Product-like Libraries
inferredcites →https://doi.org/10.1021/ja042666popenalex-snapshot
Pairwise Decomposition of Residue Interaction Energies Using Semiempirical Quantum Mechanical Methods in Studies of Protein−Ligand Interaction
inferredcites →https://doi.org/10.1021/ja981176sopenalex-snapshot
A Theoretical Approach to Analytical Properties of 2,4-Diamino-5-phenylthiazole in Water Solution. Tautomerism and Dependence on pH
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/jm701500eopenalex-snapshot
Comprehensive Mechanistic Analysis of Hits from High-Throughput and Docking Screens against β-Lactamase
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/10.1038/385602a0openalex-snapshot
Crystal structure of the Src family tyrosine kinase Hck
inferredcites →https://doi.org/10.1038/nchembio.155openalex-snapshot
Molecular docking and ligand specificity in fragment-based inhibitor discovery
inferredcites →https://doi.org/10.1039/b905779jopenalex-snapshot
MMH-2 as a new approach for the prediction of intermolecular interactions: the crystal packing of acetamide
inferredcites →https://doi.org/10.1073/pnas.0706290104openalex-snapshot
Mechanism of inhibition of bovine F 1 -ATPase by resveratrol and related polyphenols
inferredcites →https://doi.org/10.1073/pnas.262506299openalex-snapshot
Anaerobic enzyme⋅substrate structures provide insight into the reaction mechanism of the copper-dependent quercetin 2,3-dioxygenase
inferredcites →https://doi.org/10.1093/bioinformatics/btg243openalex-snapshot
Protein Ligand Database (PLD): additional understanding of the nature and specificity of protein–ligand complexes
inferredcites →https://doi.org/10.1093/bioinformatics/btl524openalex-snapshot
Inherent limitations in protein–protein docking procedures
inferredcites →https://doi.org/10.1093/nar/29.1.221openalex-snapshot
PDBsum: summaries and analyses of PDB structures
inferredcites →https://doi.org/10.1093/nar/gki059openalex-snapshot
PDB-Ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures
inferredcites →https://doi.org/10.1093/nar/gkj062openalex-snapshot
SitesBase: a database for structure-based protein-ligand binding site comparisons
inferredcites →https://doi.org/10.1107/s0907444998007100openalex-snapshot
Databases in Protein Crystallography
inferredcites →https://doi.org/10.1147/sj.402.0360openalex-snapshot
Large-scale virtual screening for discovering leads in the postgenomic era
inferredcites →https://doi.org/10.1158/1535-7163.mct-06-0397openalex-snapshot
Characterization of a potent and selective small-molecule inhibitor of the PIM1 kinase
inferredcites →https://doi.org/10.2174/138920306778559412openalex-snapshot
eHiTS: An Innovative Approach to the Docking and Scoring Function Problems
inferredcites →https://doi.org/10.2174/1573409054367682openalex-snapshot
Scope and Limitation of Ligand Docking: Methods, Scoring Functions and Protein Targets
inferredcites →https://doi.org/10.2210/pdb3ckl/pdbopenalex-snapshot
Crystal structure of human cytosolic sulfotransferase SULT1B1 in complex with PAP and resveratrol
inferredcites →https://doi.org/10.3892/ijmm.12.4.415openalex-snapshot
Inhibition of lipoxygenase by (-)-epigallocatechin gallate: X-ray analysis at 2.1 Å reveals degradation of EGCG and shows soybean LOX-3 complex with EGC instead

What points at this work

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

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Polyphenols bind to low density lipoprotein at biologically relevant concentrations that are protective for heart disease
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Sourcing the affinity of flavonoids for the glycogen phosphorylase inhibitor site via crystallography, kinetics and QM/MM-PBSA binding studies: Comparison of chrysin and flavopiridol
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Using DFT methodology for more reliable predictive models: Design of inhibitors of Golgi α-Mannosidase II
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An approach based on Density Functional Theory (DFT) calculations to assess the Candida antarctica lipase B selectivity in rutin, isoquercitrin and quercetin acetylation
inferred← citeshttps://doi.org/10.1021/acs.jafc.8b06674openalex-snapshot
Binding of Plant Polyphenols to Serum Albumin and LDL: Healthy Implications for Heart Disease
inferred← citeshttps://doi.org/10.1021/acsomega.8b01776openalex-snapshot
Naringin–Chalcone Bioflavonoid-Protected Nanocolloids: Mode of Flavonoid Adsorption, a Determinant for Protein Extraction
inferred← citeshttps://doi.org/10.1021/jf300424wopenalex-snapshot
Bioevaluation of Human Serum Albumin–Hesperidin Bioconjugate: Insight into Protein Vector Function and Conformation
inferred← citeshttps://doi.org/10.1039/c2cp42174gopenalex-snapshot
Cross-talk between amino acid residues and flavonoid derivatives: insights into their chemical recognition
inferred← citeshttps://doi.org/10.1080/07391102.2021.2011785openalex-snapshot
Analysis and prediction pathways of natural products and their cytotoxicity against HeLa cell line protein using docking, molecular dynamics and ADMET
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Signal Transduction and Molecular Targets of Selected Flavonoids
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Complementation of the embryo-lethal T-DNA insertion mutant of AUXIN-BINDING-PROTEIN 1 (ABP1) with abp1 point mutated versions reveals crosstalk of ABP1 and phytochromes
inferred← citeshttps://doi.org/10.1105/tpc.15.00726openalex-snapshot
TWISTED DWARF1 Mediates the Action of Auxin Transport Inhibitors on Actin Cytoskeleton Dynamics
inferred← citeshttps://doi.org/10.1371/journal.pone.0038261openalex-snapshot
Prediction of Molecular Targets of Cancer Preventing Flavonoid Compounds Using Computational Methods
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Structural Analysis of Flavonoids and Related Compounds - A Review of Spectroscopic Applications
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