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Encoding Protein–Ligand Interaction Patterns in Fingerprints and Graphs

https://doi.org/10.1021/ci300566n
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What this work says

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

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Extended Summary: BIOSTER-a database of structurally analogous compounds
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A fast method of molecular shape comparison: A simple application of a Gaussian description of molecular shape
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Current Protocols in Bioinformatics
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Structure‐Based Approaches to Target Fishing and Ligand Profiling
inferredcites →https://doi.org/10.1002/minf.201100026openalex-snapshot
Identification of Nonpeptide Oxytocin Receptor Ligands by Receptor‐Ligand Fingerprint Similarity Search
inferredcites →https://doi.org/10.1007/bf00991836openalex-snapshot
Cliques of a graph-variations on the Bron-Kerbosch algorithm
inferredcites →https://doi.org/10.1007/s10822-005-9019-xopenalex-snapshot
Molecular shape and electrostatics in the encoding of relevant chemical information
inferredcites →https://doi.org/10.1007/s10822-006-9072-0openalex-snapshot
Identification of target-specific bioisosteric fragments from ligand–protein crystallographic data
inferredcites →https://doi.org/10.1007/s10822-008-9196-5openalex-snapshot
Recommendations for evaluation of computational methods
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Similarity-based virtual screening using 2D fingerprints
inferredcites →https://doi.org/10.1021/ci010132ropenalex-snapshot
Reoptimization of MDL Keys for Use in Drug Discovery
inferredcites →https://doi.org/10.1021/ci049870gopenalex-snapshot
Expanded Interaction Fingerprint Method for Analyzing Ligand Binding Modes in Docking and Structure-Based Drug Design
inferredcites →https://doi.org/10.1021/ci050006dopenalex-snapshot
Virtual Screen for Ligands of Orphan G Protein-Coupled Receptors
inferredcites →https://doi.org/10.1021/ci0503964openalex-snapshot
The Quest for Bioisosteric Replacements
inferredcites →https://doi.org/10.1021/ci050420dopenalex-snapshot
Knowledge-Based Interaction Fingerprint Scoring: A Simple Method for Improving the Effectiveness of Fast Scoring Functions
inferredcites →https://doi.org/10.1021/ci100050topenalex-snapshot
Extended-Connectivity Fingerprints
inferredcites →https://doi.org/10.1021/ci200264hopenalex-snapshot
Computational Screening for Active Compounds Targeting Protein Sequences: Methodology and Experimental Validation
inferredcites →https://doi.org/10.1021/ci300034xopenalex-snapshot
PROLIX: Rapid Mining of Protein–Ligand Interactions in Large Crystal Structure Databases
inferredcites →https://doi.org/10.1021/ci3000776openalex-snapshot
Pharmacophore Fingerprint-Based Approach to Binding Site Subpocket Similarity and Its Application to Bioisostere Replacement
inferredcites →https://doi.org/10.1021/ci300184xopenalex-snapshot
Comparison and Druggability Prediction of Protein–Ligand Binding Sites from Pharmacophore-Annotated Cavity Shapes
inferredcites →https://doi.org/10.1021/ci600342eopenalex-snapshot
Optimizing Fragment and Scaffold Docking by Use of Molecular Interaction Fingerprints
inferredcites →https://doi.org/10.1021/ci600426eopenalex-snapshot
Evaluating Virtual Screening Methods: Good and Bad Metrics for the “Early Recognition” Problem
inferredcites →https://doi.org/10.1021/ci800064zopenalex-snapshot
Hot-Spots-Guided Receptor-Based Pharmacophores (HS-Pharm): A Knowledge-Based Approach to Identify Ligand-Anchoring Atoms in Protein Cavities and Prioritize Structure-Based Pharmacophores
inferredcites →https://doi.org/10.1021/ci800229qopenalex-snapshot
Ligand-Target Interaction-Based Weighting of Substructures for Virtual Screening
inferredcites →https://doi.org/10.1021/ci8003094openalex-snapshot
Computational Fragment-Based Approach at PDB Scale by Protein Local Similarity
inferredcites →https://doi.org/10.1021/ci800322yopenalex-snapshot
Similarity Searching Using Fingerprints of Molecular Fragments Involved in Protein−Ligand Interactions
inferredcites →https://doi.org/10.1021/ci800447gopenalex-snapshot
Development and Validation of a Novel Protein−Ligand Fingerprint To Mine Chemogenomic Space: Application to G Protein-Coupled Receptors and Their Ligands
inferredcites →https://doi.org/10.1021/ci900043ropenalex-snapshot
APIF: A New Interaction Fingerprint Based on Atom Pairs and Its Application to Virtual Screening
inferredcites →https://doi.org/10.1021/ci970429iopenalex-snapshot
RECAPRetrosynthetic Combinatorial Analysis Procedure: A Powerful New Technique for Identifying Privileged Molecular Fragments with Useful Applications in Combinatorial Chemistry
inferredcites →https://doi.org/10.1021/ci9800211openalex-snapshot
Chemical Similarity Searching
inferredcites →https://doi.org/10.1021/ci990263gopenalex-snapshot
Similarity Searching in Files of Three-Dimensional Chemical Structures: Analysis of the BIOSTER Database Using Two-Dimensional Fingerprints and Molecular Field Descriptors
inferredcites →https://doi.org/10.1021/j100011a016openalex-snapshot
A Gaussian Description of Molecular Shape
inferredcites →https://doi.org/10.1021/jm020406hopenalex-snapshot
Surflex: Fully Automatic Flexible Molecular Docking Using a Molecular Similarity-Based Search Engine
inferredcites →https://doi.org/10.1021/jm030331xopenalex-snapshot
Structural Interaction Fingerprint (SIFt): A Novel Method for Analyzing Three-Dimensional Protein−Ligand Binding Interactions
inferredcites →https://doi.org/10.1021/jm049092jopenalex-snapshot
Virtual Screening Workflow Development Guided by the “Receiver Operating Characteristic” Curve Approach. Application to High-Throughput Docking on Metabotropic Glutamate Receptor Subtype 4
inferredcites →https://doi.org/10.1021/jm049312topenalex-snapshot
Interaction Profiles of Protein Kinase−Inhibitor Complexes and Their Application to Virtual Screening
inferredcites →https://doi.org/10.1021/jm050381xopenalex-snapshot
Knowledge-Based Design of Target-Focused Libraries Using Protein−Ligand Interaction Constraints
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/jm300687eopenalex-snapshot
Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking
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/jm9806998openalex-snapshot
New 4-Point Pharmacophore Method for Molecular Similarity and Diversity Applications: Overview of the Method and Applications, Including a Novel Approach to the Design of Combinatorial Libraries Containing Privileged Substructures
inferredcites →https://doi.org/10.1021/jp953707uopenalex-snapshot
A Gaussian Description of Molecular Shape
inferredcites →https://doi.org/10.1023/a:1007996124545openalex-snapshot
Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
inferredcites →https://doi.org/10.1038/nrd3139openalex-snapshot
Virtual screening: an endless staircase?
inferredcites →https://doi.org/10.1093/bioinformatics/btq140openalex-snapshot
A CROC stronger than ROC: measuring, visualizing and optimizing early retrieval
inferredcites →https://doi.org/10.1093/bioinformatics/btr120openalex-snapshot
sc-PDB: a database for identifying variations and multiplicity of ‘druggable’ binding sites in proteins
inferredcites →https://doi.org/10.1093/nar/gks1059openalex-snapshot
SwissBioisostere: a database of molecular replacements for ligand design
inferredcites →https://doi.org/10.1107/s0108767305015266openalex-snapshot
Rapid calculation of RMSDs using a quaternion-based characteristic polynomial
inferredcites →https://doi.org/10.1111/j.1747-0285.2008.00762.xopenalex-snapshot
CREDO: A Protein–Ligand Interaction Database for Drug Discovery
inferredcites →https://doi.org/10.1111/j.1747-0285.2010.01007.xopenalex-snapshot
Computational Methodologies for Compound Database Searching that Utilize Experimental Protein–Ligand Interaction Information
inferredcites →https://doi.org/10.1145/362342.362367openalex-snapshot
Algorithm 457: finding all cliques of an undirected graph

What points at this work

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

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Molecular Interaction Fingerprints
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SiteMine: Large‐scale binding site similarity searching in protein structure databases
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IChem: A Versatile Toolkit for Detecting, Comparing, and Predicting Protein–Ligand Interactions
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AQDnet: Deep Neural Network for Protein–Ligand Docking Simulation
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sc-PDB-Frag: A Database of Protein–Ligand Interaction Patterns for Bioisosteric Replacements
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VirtuousPocketome: a computational tool for screening protein–ligand complexes to identify similar binding sites
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HDBind: encoding of molecular structure with hyperdimensional binary representations
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Binding site characterization – similarity, promiscuity, and druggability
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Insights into the stereoselectivity of human SETD7 methyltransferase
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Computational representations of protein–ligand interfaces for structure-based virtual screening
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Site2Vec: a reference frame invariant algorithm for vector embedding of protein–ligand binding sites
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Protein language models are performant in structure-free virtual screening
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The role of drug profiles as similarity metrics: applications to repurposing, adverse effects detection and drug–drug interactions
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Binding site matching in rational drug design: algorithms and applications
inferred← citeshttps://doi.org/10.1093/bioinformatics/btaf284openalex-snapshot
Mapping the space of protein binding sites with sequence-based protein language models
inferred← citeshttps://doi.org/10.1093/nar/gku928openalex-snapshot
sc-PDB: a 3D-database of ligandable binding sites—10 years on
inferred← citeshttps://doi.org/10.1093/nar/gkv315openalex-snapshot
PLIP: fully automated protein–ligand interaction profiler
inferred← citeshttps://doi.org/10.1101/2025.06.08.658499openalex-snapshot
Simpatico: accurate and ultra-fast virtual drug screening with atomic embeddings
inferred← citeshttps://doi.org/10.1109/tcbb.2017.2756879openalex-snapshot
Discovery of Functional Motifs from the Interface Region of Oligomeric Proteins Using Frequent Subgraph Mining
inferred← citeshttps://doi.org/10.1109/tpami.2024.3400515openalex-snapshot
Interaction-Based Inductive Bias in Graph Neural Networks: Enhancing Protein-Ligand Binding Affinity Predictions From 3D Structures
inferred← citeshttps://doi.org/10.1126/scisignal.aal2869openalex-snapshot
CCR5 adopts three homodimeric conformations that control cell surface delivery
inferred← citeshttps://doi.org/10.1186/s12859-017-1750-5openalex-snapshot
Enhance the performance of current scoring functions with the aid of 3D protein-ligand interaction fingerprints
inferred← citeshttps://doi.org/10.1186/s12859-018-2206-2openalex-snapshot
Sequence-based prediction of physicochemical interactions at protein functional sites using a function-and-interaction-annotated domain profile database
inferred← citeshttps://doi.org/10.1186/s12859-020-3347-7openalex-snapshot
visGReMLIN: graph mining-based detection and visualization of conserved motifs at 3D protein-ligand interface at the atomic level
inferred← citeshttps://doi.org/10.1186/s12859-022-04995-2openalex-snapshot
A multilayer dynamic perturbation analysis method for predicting ligand–protein interactions
inferred← citeshttps://doi.org/10.1186/s13321-018-0264-0openalex-snapshot
A novel interaction fingerprint derived from per atom score contributions: exhaustive evaluation of interaction fingerprint performance in docking based virtual screening
inferred← citeshttps://doi.org/10.1186/s13321-018-0302-yopenalex-snapshot
Life beyond the Tanimoto coefficient: similarity measures for interaction fingerprints
inferred← citeshttps://doi.org/10.1186/s13321-019-0346-7openalex-snapshot
Binding mode information improves fragment docking
inferred← citeshttps://doi.org/10.1186/s13321-021-00545-9openalex-snapshot
2D SIFt: a matrix of ligand-receptor interactions
inferred← citeshttps://doi.org/10.1186/s13321-022-00654-zopenalex-snapshot
One class classification for the detection of β2 adrenergic receptor agonists using single-ligand dynamic interaction data
inferred← citeshttps://doi.org/10.1186/s13321-023-00795-9openalex-snapshot
Structure-based, deep-learning models for protein-ligand binding affinity prediction
inferred← citeshttps://doi.org/10.1186/s13321-024-00822-3openalex-snapshot
Systematic analysis, aggregation and visualisation of interaction fingerprints for molecular dynamics simulation data
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1006483openalex-snapshot
A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs)
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1009783openalex-snapshot
fingeRNAt—A novel tool for high-throughput analysis of nucleic acid-ligand interactions
inferred← citeshttps://doi.org/10.1371/journal.pone.0233089openalex-snapshot
Structure-based drug repositioning explains ibrutinib as VEGFR2 inhibitor
inferred← citeshttps://doi.org/10.14499/indonesianjpharm27iss3pp163openalex-snapshot
OPTIMIZING STRUCTURE-BASED VIRTUAL SCREENING PROTOCOL TO IDENTIFY PHYTOCHEMICALS AS CYCLOOXYGENASE-2 INHIBITORS
inferred← citeshttps://doi.org/10.14499/indonesianjpharm28iss2pp100openalex-snapshot
Computer-aided Design of Chalcone Derivatives as Lead Compounds Targeting Acetylcholinesterase
inferred← citeshttps://doi.org/10.2174/0109298673266470231023110841openalex-snapshot
Drug Repurposing: Insights into Current Advances and Future Applications
inferred← citeshttps://doi.org/10.22146/ijc.24172openalex-snapshot
Binary Quantitative Structure-Activity Relationship Analysis to Increase the Predictive Ability of Structure-Based Virtual Screening Campaigns Targeting Cyclooxygenase-2
inferred← citeshttps://doi.org/10.26434/chemrxiv-2023-h76kdopenalex-snapshot
Rational Screening of Mn(II) Metal-Ligand Complexes for Using as MRI Contrast Agents Using Machine Learning
inferred← citeshttps://doi.org/10.26434/chemrxiv-2023-h76kd-v2openalex-snapshot
Rational Screening of Mn(II) Metal-Ligand Complexes for Using as MRI Contrast Agents Using Machine Learning
inferred← citeshttps://doi.org/10.30598//ijcr.2023.11-budopenalex-snapshot
Study of Anthocyanin Molecule Blocking as Anti-Hypertensive through the Pathway of the Renin-Angiotensin-Aldosterone System (RAAS)
inferred← citeshttps://doi.org/10.3389/fchem.2019.00324openalex-snapshot
Deep Neural Network Classifier for Virtual Screening Inhibitors of (S)-Adenosyl-L-Methionine (SAM)-Dependent Methyltransferase Family
inferred← citeshttps://doi.org/10.3389/fchem.2021.662688openalex-snapshot
Applications of Virtual Screening in Bioprospecting: Facts, Shifts, and Perspectives to Explore the Chemo-Structural Diversity of Natural Products
inferred← citeshttps://doi.org/10.3389/fchem.2023.1089714openalex-snapshot
Mining the Protein Data Bank to inspire fragment library design
inferred← citeshttps://doi.org/10.3389/frhem.2024.1305741openalex-snapshot
De novo drug design through artificial intelligence: an introduction
inferred← citeshttps://doi.org/10.3390/biom14010072openalex-snapshot
Fingerprinting Interactions between Proteins and Ligands for Facilitating Machine Learning in Drug Discovery
inferred← citeshttps://doi.org/10.3390/ijms161226202openalex-snapshot
Proteins and Their Interacting Partners: An Introduction to Protein–Ligand Binding Site Prediction Methods
inferred← citeshttps://doi.org/10.3390/ijms21124380openalex-snapshot
Benchmarking Data Sets from PubChem BioAssay Data: Current Scenario and Room for Improvement
inferred← citeshttps://doi.org/10.3390/ijms22094435openalex-snapshot
Deep Learning in Virtual Screening: Recent Applications and Developments
inferred← citeshttps://doi.org/10.3390/ijms232012462openalex-snapshot
Estimating the Similarity between Protein Pockets
inferred← citeshttps://doi.org/10.3390/ijms24119289openalex-snapshot
Roles of Virtual Screening and Molecular Dynamics Simulations in Discovering and Understanding Antimalarial Drugs
inferred← citeshttps://doi.org/10.3390/molecules23020456openalex-snapshot
Structural Insights into σ1 Receptor Interactions with Opioid Ligands by Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.3390/molecules24142610openalex-snapshot
Local Interaction Density (LID), a Fast and Efficient Tool to Prioritize Docking Poses
inferred← citeshttps://doi.org/10.3390/molecules25204723openalex-snapshot
Merging Ligand-Based and Structure-Based Methods in Drug Discovery: An Overview of Combined Virtual Screening Approaches
inferred← citeshttps://doi.org/10.3390/molecules26154625openalex-snapshot
MolADI: A Web Server for Automatic Analysis of Protein–Small Molecule Dynamic Interactions
inferred← citeshttps://doi.org/10.3390/molecules26227025openalex-snapshot
The Structural Determinants for α1-Adrenergic/Serotonin Receptors Activity among Phenylpiperazine-Hydantoin Derivatives
inferred← citeshttps://doi.org/10.4018/978-1-5225-0115-2.ch005openalex-snapshot
Protein Ligand Interaction Fingerprints
inferred← citeshttps://doi.org/10.4018/978-1-5225-1762-7.ch041openalex-snapshot
Protein Ligand Interaction Fingerprints
inferred← citeshttps://doi.org/10.48550/arxiv.1701.08086openalex-snapshot
Sequence-based prediction of function site and protein-ligand interaction by a functionally annotated domain profile database
inferred← citeshttps://doi.org/10.5772/intechopen.100109openalex-snapshot
Using the Structural Kinome to Systematize Kinase Drug Discovery
inferred← citeshttps://doi.org/10.6084/m9.figshare.11979093openalex-snapshot
Additional file 1 of visGReMLIN: graph mining-based detection and visualization of conserved motifs at 3D protein-ligand interface at the atomic level
inferred← citeshttps://doi.org/10.6084/m9.figshare.16590419openalex-snapshot
Additional file 1 of 2D SIFt: a matrix of ligand-receptor interactions
inferred← citeshttps://doi.org/10.6084/m9.figshare.21485795openalex-snapshot
Additional file 1 of A multilayer dynamic perturbation analysis method for predicting ligand–protein interactions
inferred← citeshttps://doi.org/10.6084/m9.figshare.26660296openalex-snapshot
Additional file 1 of Structure-based, deep-learning models for protein-ligand binding affinity prediction
inferred← citeshttps://doi.org/10.6084/m9.figshare.26692564openalex-snapshot
Additional file 1 of Systematic analysis, aggregation and visualisation of interaction fingerprints for molecular dynamics simulation data
inferred← citeshttps://doi.org/10.64898/2026.04.17.719144openalex-snapshot
Large-scale analysis of ligand binding mode similarities in the PDB using interaction fingerprints
inferred← citeshttps://doi.org/10.70675/00fff70azab21z46edz8364z60031c95c00fopenalex-snapshot
Applications of proteochemometrics (PCM) : from species extrapolation to cell-line sensitivity modelling
inferred← citeshttps://doi.org/10.70675/a5e2d86fz9977z404bzb480z3ad03b663b7bopenalex-snapshot
Modélisation du récepteur aux chimiokines C-C de type 5 : caractérisation des états conformationnels et conception rationnelle de modulateurs de la dimérisation
inferred← citeshttps://doi.org/10.70675/c9cacc57zdf38z489bzacf8z0d5ecf73c80copenalex-snapshot
Development of new virtual screening methods and novel unbiased benchmarking data sets
inferred← citeshttps://doi.org/10.70675/ff9e5fd3za154z4b07zb082z0544574f7124openalex-snapshot
Rational design of bioactive molecules for antibiotic purposes
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