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Drawing the PDB: Protein−Ligand Complexes in Two Dimensions

https://doi.org/10.1021/ml100164p
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What this work says

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

inferredcites →https://doi.org/10.1002/9780470125908.ch6openalex-snapshot
Structure Diagram Generation
inferredcites →https://doi.org/10.1002/cmdc.200700010openalex-snapshot
From Modeling to Medicinal Chemistry: Automatic Generation of Two‐Dimensional Complex Diagrams
inferredcites →https://doi.org/10.1002/pro.5560050621openalex-snapshot
Tumor marker disaccharide D‐Gal‐β1,3‐GalNAc complexed to heat‐labile enterotoxin from Escherichia coli
inferredcites →https://doi.org/10.1002/prot.21818openalex-snapshot
Modeling of metal interaction geometries for protein–ligand docking
inferredcites →https://doi.org/10.1007/978-3-540-78246-9_38openalex-snapshot
KNIME: The Konstanz Information Miner
inferredcites →https://doi.org/10.1016/s1097-2765(00)00037-xopenalex-snapshot
Structural Basis for Discrimination of 3-Phosphoinositides by Pleckstrin Homology Domains
inferredcites →https://doi.org/10.1021/ci7001473openalex-snapshot
2D Depiction of Protein−Ligand Complexes
inferredcites →https://doi.org/10.1038/nmeth.1410openalex-snapshot
Single-gene transgenic mouse strains for reprogramming adult somatic cells
inferredcites →https://doi.org/10.1038/nmeth.1427openalex-snapshot
Visualization of macromolecular structures
inferredcites →https://doi.org/10.1038/nmeth.1436openalex-snapshot
Visualization of omics data for systems biology
inferredcites →https://doi.org/10.1038/nsb1203-980openalex-snapshot
Announcing the worldwide Protein Data Bank
inferredcites →https://doi.org/10.1039/b716535hopenalex-snapshot
Crystal structure of coelenterazine-binding protein from Renilla muelleri at 1.7 Å: Why it is not a calcium-regulated photoprotein
inferredcites →https://doi.org/10.1073/pnas.96.17.9459openalex-snapshot
Cation-π interactions in structural biology
inferredcites →https://doi.org/10.1074/jbc.273.25.15458openalex-snapshot
π-Stacking Interactions
inferredcites →https://doi.org/10.1074/jbc.m403319200openalex-snapshot
Structural Basis for the Autoinhibition and STI-571 Inhibition of c-Kit Tyrosine Kinase
inferredcites →https://doi.org/10.1093/acprof:oso/9780198509707.001.0001openalex-snapshot
The Weak Hydrogen Bond
inferredcites →https://doi.org/10.1093/bioinformatics/bth214openalex-snapshot
Ligand Depot: a data warehouse for ligands bound to macromolecules
inferredcites →https://doi.org/10.1093/bioinformatics/btl150openalex-snapshot
Molecular complexes at a glance: automated generation of two-dimensional complex diagrams
inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot
The Protein Data Bank
inferredcites →https://doi.org/10.1093/protein/8.2.127openalex-snapshot
LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions
inferredcites →https://doi.org/10.1186/1758-2946-1-13openalex-snapshot
Fast automated placement of polar hydrogen atoms in protein-ligand complexes
inferredcites →https://doi.org/10.1198/tas.2009.0033openalex-snapshot
The History of the Cluster Heat Map
inferredcites →https://doi.org/10.1351/pac200880020277openalex-snapshot
Graphical representation standards for chemical structure diagrams (IUPAC Recommendations 2008)

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CYP154A18 from the endophytic Streptomyces cavourensis YBQ59: A monooxygenase for selective hydroxylation of monoterpene and aliphatic alcohols
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inferred← citeshttps://doi.org/10.1016/j.molstruc.2020.128459openalex-snapshot
A machine learning approach to discriminate MR1 binders: The importance of the phenol and carbonyl fragments
inferred← citeshttps://doi.org/10.1016/j.molstruc.2022.132569openalex-snapshot
A novel dual three and five-component reactions between dimedone, aryl aldehydes, and 1-naphthylamine: synthesis and computational studies
inferred← citeshttps://doi.org/10.1016/j.molstruc.2022.133029openalex-snapshot
Spectroscopic, electrochemical, and some theoretical studies on the interactional of neuraminidase inhibitor zanamivir with double helix deoxyribonucleic acid
inferred← citeshttps://doi.org/10.1016/j.molstruc.2024.139773openalex-snapshot
Serial triphenylpropionic acid and N,N'-chelator mixed ligands Cu(II) complexes: Structure and biological properties
inferred← citeshttps://doi.org/10.1016/j.molstruc.2026.147221openalex-snapshot
Synthesis, structure and evaluation of antifungal and cytoprotective activities of caffeine–azole hybrids
inferred← citeshttps://doi.org/10.1016/j.molstruc.2026.147688openalex-snapshot
Synthesis and structural characterization of squaric acid derivatives containing 3,4,5-trimethoxyphenyl; crystal structures and preliminary biological evaluation
inferred← citeshttps://doi.org/10.1016/j.neurot.2025.e00803openalex-snapshot
Simvastatin-induced neuroprotective effect after brain injury is mediated by mitochondrial protection through modulation of the 18 kDa translocator protein
inferred← citeshttps://doi.org/10.1016/j.pbiomolbio.2014.05.006openalex-snapshot
Polypharmacology rescored: Protein–ligand interaction profiles for remote binding site similarity assessment
inferred← citeshttps://doi.org/10.1016/j.polymer.2014.11.003openalex-snapshot
Conformational characteristics and configurational properties of poly(ethylene succinate) and poly(butylene succinate) and structure–property–function relationships of representative biodegradable polyesters
inferred← citeshttps://doi.org/10.1016/j.toxicon.2016.12.007openalex-snapshot
Structural and binding studies of a C-type galactose-binding lectin from Bothrops jararacussu snake venom
inferred← citeshttps://doi.org/10.1016/j.toxrep.2021.07.015openalex-snapshot
Toxicity evaluation of Eleutherine plicata Herb. extracts and possible cell death mechanism
inferred← citeshttps://doi.org/10.1016/j.vetpar.2023.110001openalex-snapshot
Molecular interaction analysis of the lignans from Piper cubeba in complex with Haemonchus contortus phosphomethyltransferase
inferred← citeshttps://doi.org/10.1016/j.ymeth.2014.09.009openalex-snapshot
A new crystal structure fragment-based pharmacophore method for G protein-coupled receptors
inferred← citeshttps://doi.org/10.1017/9781108774956openalex-snapshot
Quantum Chemistry Simulation of Biological Molecules
inferred← citeshttps://doi.org/10.1021/acs.analchem.7b04813openalex-snapshot
Highly Specific near-Infrared Fluorescent Probe for the Real-Time Detection of β‑Glucuronidase in Various Living Cells and Animals
inferred← citeshttps://doi.org/10.1021/acs.chemrestox.8b00188openalex-snapshot
Mechanisms of Fumonisin B1 Toxicity: A Computational Perspective beyond the Ceramide Synthases Inhibition
inferred← citeshttps://doi.org/10.1021/acs.jafc.1c03901openalex-snapshot
Crystal Structure of a Sucrose-6-phosphate Hydrolase from Lactobacillus gasseri with Potential Applications in Fructan Production and the Food Industry
inferred← citeshttps://doi.org/10.1021/acs.jafc.4c06711openalex-snapshot
Toxicity and Glutathione S-Transferase-Catalyzed Metabolism of R-/S-Metolachlor in Rice
inferred← citeshttps://doi.org/10.1021/acs.jafc.5c03323openalex-snapshot
A Novel High-Throughput Colorimetric Assay to Assess Glutathione S -Transferase-Catalyzed Herbicide Metabolism
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00235openalex-snapshot
On-the-Fly Integration of Data from a Spin-Diffusion-Based NMR Experiment into Protein–Ligand Docking
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00323openalex-snapshot
Discriminative Chemical Patterns: Automatic and Interactive Design
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c01927openalex-snapshot
Structure-Aware Heterogeneous Information Fusion Framework for Protein–Ligand Binding Affinity Prediction
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c02587openalex-snapshot
UniDock-Pro: A Unified GPU-Accelerated Platform for High-Throughput Structure-Based, Ligand-Based, and Synergistic Hybrid Virtual Screening
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00163openalex-snapshot
PL-PatchSurfer2: Improved Local Surface Matching-Based Virtual Screening Method That Is Tolerant to Target and Ligand Structure Variation
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00391openalex-snapshot
Simulation-Based Algorithm for Two-Dimensional Chemical Structure Diagram Generation of Complex Molecules and Ligand–Protein Interactions
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00753openalex-snapshot
Comparison of the Predictive Performance and Interpretability of Random Forest and Linear Models on Benchmark Data Sets
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00350openalex-snapshot
Protein Family-Specific Models Using Deep Neural Networks and Transfer Learning Improve Virtual Screening and Highlight the Need for More Data
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00757openalex-snapshot
Conservation and Relevance of Pharmacophore Point Types
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.5c01788openalex-snapshot
Discovery of First-in-Class Carbonic Anhydrase/Histone Deacetylase Dual Inhibitors with Antiproliferative Activity in Cancer Cells
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.6b01755openalex-snapshot
Fibroblast Activation Protein α Activated Tripeptide Bufadienolide Antitumor Prodrug with Reduced Cardiotoxicity
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.7b01601openalex-snapshot
A–C Estrogens as Potent and Selective Estrogen Receptor-Beta Agonists (SERBAs) to Enhance Memory Consolidation under Low-Estrogen Conditions
inferred← citeshttps://doi.org/10.1021/acs.jnatprod.5b00132openalex-snapshot
Inhibitory Effects of Highly Oxygenated Lanostane Derivatives from the Fungus Ganoderma lucidum on P-Glycoprotein and α-Glucosidase
inferred← citeshttps://doi.org/10.1021/acs.jnatprod.8b00889openalex-snapshot
Inhibitory Properties of ATP-Competitive Coumestrol and Boldine Are Correlated to Different Modulations of CK2 Flexibility
inferred← citeshttps://doi.org/10.1021/acs.joc.3c00815openalex-snapshot
Synthesis and Hemolytic Activity of Bile Acid-Indole Bioconjugates Linked by Triazole
inferred← citeshttps://doi.org/10.1021/acsbiomedchemau.1c00016openalex-snapshot
Identification of a BAZ2A Bromodomain Hit Compound by Fragment Joining
inferred← citeshttps://doi.org/10.1021/acschembio.7b00175openalex-snapshot
Rational Design of Novel Allosteric Dihydrofolate Reductase Inhibitors Showing Antibacterial Effects on Drug-Resistant Escherichia coli Escape Variants
inferred← citeshttps://doi.org/10.1021/acschemneuro.4c00008openalex-snapshot
2-Butoxytetrahydrofuran, Isolated from Holothuria scabra, Attenuates Aggregative and Oxidative Properties of α-Synuclein and Alleviates Its Toxicity in a Transgenic Caenorhabditis elegans Model of Parkinson’s Disease
inferred← citeshttps://doi.org/10.1021/acsomega.5c04674openalex-snapshot
Galactofuranosidases: From the Initial Activity Detection to the First Crystalline Structure
inferred← citeshttps://doi.org/10.1021/acsomega.6c05946openalex-snapshot
Functional and Structural Characterization of the Erythrina fusca Seed Lectin EFusL: A GalNAc-Binding Lectin with Specificity for Tumor-Associated O-Glycans
inferred← citeshttps://doi.org/10.1021/acsomega.9b00008openalex-snapshot
Synthesis, Derivatization, and Structural Analysis of Phosphorylated Mono-, Di-, and Trifluorinated d -Gluco-heptuloses by Glucokinase: Tunable Phosphoglucomutase Inhibition
inferred← citeshttps://doi.org/10.1021/acssynbio.6c00245openalex-snapshot
Engineering Orthogonal Quorum-Sensing Circuits Using LuxR-Type Systems in Yeast Consortia
inferred← citeshttps://doi.org/10.1021/ci300331dopenalex-snapshot
Simple Structure-Based Approach for Predicting the Activity of Inhibitors of Beta-Secretase (BACE1) Associated with Alzheimer’s Disease
inferred← citeshttps://doi.org/10.1021/ci500405gopenalex-snapshot
A Virtual Screening Approach For Identifying Plants with Anti H5N1 Neuraminidase Activity
inferred← citeshttps://doi.org/10.1038/s41467-024-50933-6openalex-snapshot
Deciphering the allosteric regulation of mycobacterial inosine-5′-monophosphate dehydrogenase
inferred← citeshttps://doi.org/10.1038/s41467-024-54208-yopenalex-snapshot
Late-stage (radio)fluorination of alkyl phosphonates via electrophilic activation
inferred← citeshttps://doi.org/10.1038/s41467-024-55536-9openalex-snapshot
Next generation thiazolyl ketone inhibitors of cytosolic phospholipase A2 α for targeted cancer therapy
inferred← citeshttps://doi.org/10.1038/s41598-018-20325-0openalex-snapshot
Inhibition of the checkpoint protein PD-1 by the therapeutic antibody pembrolizumab outlined by quantum chemistry
inferred← citeshttps://doi.org/10.1038/s41598-023-30310-xopenalex-snapshot
Accurate prediction by AlphaFold2 for ligand binding in a reductive dehalogenase and implications for PFAS (per- and polyfluoroalkyl substance) biodegradation
inferred← citeshttps://doi.org/10.1038/s41598-023-45175-3openalex-snapshot
Targeting allosteric binding site in methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) to identify natural product inhibitors via structure-based computational approach
inferred← citeshttps://doi.org/10.1038/s41598-024-59933-4openalex-snapshot
HBCVTr: an end-to-end transformer with a deep neural network hybrid model for anti-HBV and HCV activity predictor from SMILES
inferred← citeshttps://doi.org/10.1038/s41598-024-66861-wopenalex-snapshot
Docking analysis of phenolic acid and flavonoids with selected TAS2R receptors and in vitro experiment
inferred← citeshttps://doi.org/10.1038/s41598-024-84609-4openalex-snapshot
Isolation, identification, and characterisation of the malachite green detoxifying bacterial strain Bacillus pacificus ROC1 and the azoreductase AzrC
inferred← citeshttps://doi.org/10.1038/s41598-025-06104-8openalex-snapshot
Chiral pyrimidinyl-piperazine carboxamide derivatives as potent yeast α-glucosidase inhibitors
inferred← citeshttps://doi.org/10.1038/s41598-025-88746-2openalex-snapshot
Characteristics of Plasmodium vivax apicomplexan amino acid transporter 8 (PvApiAT8) in the cationic amino acid transport
inferred← citeshttps://doi.org/10.1039/c4ib00140kopenalex-snapshot
C. pseudotuberculosis Phop confers virulence and may be targeted by natural compounds
inferred← citeshttps://doi.org/10.1039/c4ib00175copenalex-snapshot
Modelling ligand selectivity of serine proteases using integrative proteochemometric approaches improves model performance and allows the multi-target dependent interpretation of features
inferred← citeshttps://doi.org/10.1039/c4md00236aopenalex-snapshot
Synthesis of new betulinic acid–peptide conjugates and in vivo and in silico studies of the influence of peptide moieties on the triterpenoid core activity
inferred← citeshttps://doi.org/10.1039/c5ra04395fopenalex-snapshot
Quantum molecular modelling of ibuprofen bound to human serum albumin
inferred← citeshttps://doi.org/10.1039/c5ra12253hopenalex-snapshot
Microbial transformation of diosgenin by Cunninghamella blakesleana AS 3.970 and potential inhibitory effects on P-glycoprotein of its metabolites
inferred← citeshttps://doi.org/10.1039/c6md00292gopenalex-snapshot
Design, synthesis and biological activity evaluation of novel conjugated sialic acid and pentacyclic triterpene derivatives as anti-influenza entry inhibitors
inferred← citeshttps://doi.org/10.1039/c6ra25206kopenalex-snapshot
Quantum binding energy features of the T3-785 collagen-like triple-helical peptide
inferred← citeshttps://doi.org/10.1039/c7ay01433copenalex-snapshot
Characterization of phenolic acids binding to thrombin using frontal affinity chromatography and molecular docking
inferred← citeshttps://doi.org/10.1039/d0cp04415fopenalex-snapshot
A quantum biochemistry investigation of the protein–protein interactions for the description of allosteric modulation on biomass-degrading chimera
inferred← citeshttps://doi.org/10.1039/d0cp05322hopenalex-snapshot
In silico approach of modified melanoma peptides and their immunotherapeutic potential
inferred← citeshttps://doi.org/10.1039/d0fo02276dopenalex-snapshot
Rutin present in Alibertia edulis extract acts on human platelet aggregation through inhibition of cyclooxygenase/thromboxane
inferred← citeshttps://doi.org/10.1039/d0ra02339fopenalex-snapshot
Synthesis, acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) activities, and molecular docking studies of a novel compound based on combination of flurbiprofen and isoniazide
inferred← citeshttps://doi.org/10.1039/d1cb00046bopenalex-snapshot
Mechanisms of allosteric and mixed mode aromatase inhibitors
inferred← citeshttps://doi.org/10.1039/d4dt02714kopenalex-snapshot
Rhenium( i ) and technetium( i ) complexes with megazol derivatives: towards the development of a theranostic platform for Chagas disease
inferred← citeshttps://doi.org/10.1039/d4ra06461eopenalex-snapshot
In vivo and in silico evaluation of the phytoalexin-eliciting activity in common bean ( Phaseolus vulgaris L.) of jasmonoyl- l -isoleucine analogs having a pyrazolidin-3-one ring
inferred← citeshttps://doi.org/10.1039/d4ra08330jopenalex-snapshot
2-Amino-4,6-diarylpyrimidines as potential chronic myeloid leukemia cell inhibitors targeting anti-ABL1 kinase: microwave-assisted synthesis, biological evaluation, molecular docking, and dynamics studies
inferred← citeshttps://doi.org/10.1039/d6ra01605gopenalex-snapshot
Sustainable nanomedicine from olive leaf waste: biosynthesized ZnONPs with mechanistic validation against hepatocellular carcinoma
inferred← citeshttps://doi.org/10.1063/5.0019088openalex-snapshot
A workflow for exploring ligand dissociation from a macromolecule: Efficient random acceleration molecular dynamics simulation and interaction fingerprint analysis of ligand trajectories
inferred← citeshttps://doi.org/10.1073/pnas.1211614109openalex-snapshot
Unique thrombin inhibition mechanism by anophelin, an anticoagulant from the malaria vector
inferred← citeshttps://doi.org/10.1073/pnas.1602382113openalex-snapshot
Gram-negative trimeric porins have specific LPS binding sites that are essential for porin biogenesis
inferred← citeshttps://doi.org/10.1074/jbc.m116.743948openalex-snapshot
The Mechanism by Which Arabinoxylanases Can Recognize Highly Decorated Xylans
inferred← citeshttps://doi.org/10.1080/00397911.2020.1780613openalex-snapshot
Carbon-SO3H: An efficient catalyst for the synthesis of biscoumarin under ambient reaction conditions and their in silico studies
inferred← citeshttps://doi.org/10.1080/03602532.2024.2329928openalex-snapshot
Investigating the association between CYP2J2 inhibitors and QT prolongation: a literature review
inferred← citeshttps://doi.org/10.1080/07391102.2015.1051115openalex-snapshot
Insights into the structure and inhibition ofGiardia intestinalisarginine deiminase: homology modeling, docking, and molecular dynamics studies
inferred← citeshttps://doi.org/10.1080/07391102.2016.1166454openalex-snapshot
Identification of abelson tyrosine kinase inhibitors as potential therapeutics for Alzheimer’s disease using multiple e-pharmacophore modeling and molecular dynamics
inferred← citeshttps://doi.org/10.1080/07391102.2018.1491422openalex-snapshot
Delineating the active site architecture of G9a lysine methyltransferase through substrate and inhibitor binding mode analysis: a molecular dynamics study
inferred← citeshttps://doi.org/10.1080/07391102.2018.1540362openalex-snapshot
Multicomplex-based pharmacophore modeling in conjunction with multi-target docking and molecular dynamics simulations for the identification of PfDHFR inhibitors
inferred← citeshttps://doi.org/10.1080/07391102.2019.1644197openalex-snapshot
A profound computational study to prioritize the natural compound inhibitors against the P. falciparum orotidine-5-monophosphate decarboxylase enzyme
inferred← citeshttps://doi.org/10.1080/07391102.2019.1655480openalex-snapshot
Potential novel inhibitors against emerging zoonotic pathogen Nipah virus: a virtual screening and molecular dynamics approach
inferred← citeshttps://doi.org/10.1080/07391102.2019.1696709openalex-snapshot
Natural analogues inhibiting selective cyclin-dependent kinase protein isoforms: a computational perspective
inferred← citeshttps://doi.org/10.1080/07391102.2020.1763839openalex-snapshot
Discovery of new potential CDK2/VEGFR2 type II inhibitors by fragmentation and virtual screening of natural products
inferred← citeshttps://doi.org/10.1080/07391102.2020.1806110openalex-snapshot
Identification of the natural compound inhibitors against Plasmodium falciparum plasmepsin-II via common feature based screening and molecular dynamics simulations
inferred← citeshttps://doi.org/10.1080/07391102.2021.1900916openalex-snapshot
Methoxylated flavonols from Vellozia dasypus Seub ethyl acetate active myeloperoxidase extract: in vitro and in silico assays
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