On the public citation graph
Self-Organizing Fuzzy Graphs for Structure-Based Comparison of Protein Pockets
0 signed · 114 inferred · view as graph
Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.
Is this your work? Sign in with ORCID and put your name on the
claims that are yours.
Reference health. See whether every reference in this work resolves to a
known work and none has been retracted — and get a dated CiteStamped
badge you can embed.
What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/anie.200500883openalex-snapshot
Quantification of Cation–π Interactions in Protein–Ligand Complexes: Crystal‐Structure Analysis of Factor Xa Bound to a Quaternary Ammonium Ion Ligand
inferredcites →https://doi.org/10.1002/cbic.200900604openalex-snapshot
Architectural Repertoire of Ligand‐Binding Pockets on Protein Surfaces
inferredcites →https://doi.org/10.1002/cmdc.200800443openalex-snapshot
Homology Model Adjustment and Ligand Screening with a Pseudoreceptor of the Human Histamine H4 Receptor
inferredcites →https://doi.org/10.1002/j.1460-2075.1994.tb06265.xopenalex-snapshot
The active site of yeast aspartyl‐tRNA synthetase: structural and functional aspects of the aminoacylation reaction.
inferredcites →https://doi.org/10.1002/jcc.10086openalex-snapshot
Pattern recognition strategies for molecular surfaces. I. Pattern generation using fuzzy set theory
inferredcites →https://doi.org/10.1002/jcc.20770openalex-snapshot
Shapelets: Possibilities and limitations of shape‐based virtual screening
inferredcites →https://doi.org/10.1002/minf.200900010openalex-snapshot
Automated Docking of Flexible Molecules Into Receptor Binding Sites by Ligand Self‐Organization In Situ
inferredcites →https://doi.org/10.1002/pmic.200800092openalex-snapshot
Form follows function: Shape analysis of protein cavities for receptor‐based drug design
inferredcites →https://doi.org/10.1002/prot.10339openalex-snapshot
A new bioinformatic approach to detect common 3D sites in protein structures
inferredcites →https://doi.org/10.1002/prot.21858openalex-snapshot
A simple and fuzzy method to align and compare druggable ligand‐binding sites
inferredcites →https://doi.org/10.1002/prot.22141openalex-snapshot
Rapid comparison of properties on protein surface
inferredcites →https://doi.org/10.1006/jagm.1999.1062openalex-snapshot
Greedily Finding a Dense Subgraph
inferredcites →https://doi.org/10.1006/jmbi.1999.2562openalex-snapshot
Glycyl-tRNA synthetase uses a negatively charged pit for specific recognition and activation of glycine 1 1Edited by R. Huber
inferredcites →https://doi.org/10.1006/jmbi.2000.3820openalex-snapshot
Complexes of porcine odorant binding protein with odorant molecules belonging to different chemical classes
inferredcites →https://doi.org/10.1006/jmbi.2000.4032openalex-snapshot
Structural basis for isotype selectivity of the human retinoic acid nuclear receptor 1 1Edited by T. Richmond
inferredcites →https://doi.org/10.1006/jmbi.2000.4039openalex-snapshot
Crystal structures of mouse class II alcohol dehydrogenase reveal determinants of substrate specificity and catalytic efficiency 1 1Edited by J. Thornton
inferredcites →https://doi.org/10.1007/978-0-230-37405-8_1openalex-snapshot
Introduction to algorithms
inferredcites →https://doi.org/10.1007/bf00124359openalex-snapshot
A new approach to analysis and display of local lipophilicity/hydrophilicity mapped on molecular surfaces
inferredcites →https://doi.org/10.1007/bf02172039openalex-snapshot
Ecotin: A most adaptable protease inhibitor
inferredcites →https://doi.org/10.1007/bf02575586openalex-snapshot
A note on the derivation of maximal common subgraphs of two directed or undirected graphs
inferredcites →https://doi.org/10.1016/0006-291x(87)91370-2openalex-snapshot
Retinol-binding protein in human serum: Conformational changes induced by retinoic acid binding
inferredcites →https://doi.org/10.1016/0006-291x(92)90842-9openalex-snapshot
Identification of synthetic retinoids with selectivity for human nuclear retinoic acid receptor γ
inferredcites →https://doi.org/10.1016/0022-2836(85)90049-xopenalex-snapshot
Refinement of a molecular model for lamprey hemoglobin from Petromyzon marinus
inferredcites →https://doi.org/10.1016/j.jmb.2004.04.012openalex-snapshot
Recognition of Functional Sites in Protein Structures
inferredcites →https://doi.org/10.1016/j.jmb.2005.11.044openalex-snapshot
Fold Independent Structural Comparisons of Protein–Ligand Binding Sites for Exploring Functional Relationships
inferredcites →https://doi.org/10.1016/s0022-2836(02)00811-2openalex-snapshot
A New Method to Detect Related Function Among Proteins Independent of Sequence and Fold Homology
inferredcites →https://doi.org/10.1016/s0022-2836(02)01337-2openalex-snapshot
Reconstructing the Binding Site of Factor Xa in Trypsin Reveals Ligand-induced Structural Plasticity
inferredcites →https://doi.org/10.1016/s0969-2126(97)00206-2openalex-snapshot
Unusual structure of the oxygen-binding site in the dimeric bacterial hemoglobin from Vitreoscilla sp
inferredcites →https://doi.org/10.1016/s1359-6446(03)02902-7openalex-snapshot
Rediscovering the sweet spot in drug discovery
inferredcites →https://doi.org/10.1016/s1359-6446(03)03008-3openalex-snapshot
Predicting undesirable drug interactions with promiscuous proteins in silico
inferredcites →https://doi.org/10.1016/s1359-6446(05)03624-xopenalex-snapshot
Predicting protein druggability
inferredcites →https://doi.org/10.1021/bi026318gopenalex-snapshot
Aminophosphonate Inhibitors of Dialkylglycine Decarboxylase: Structural Basis for Slow Binding Inhibition,
inferredcites →https://doi.org/10.1021/bi048123+openalex-snapshot
EPR and X-ray Crystallographic Characterization of the Product-Bound Form of the Mn II -Loaded Methionyl Aminopeptidase from Pyrococcus furiosus ,
inferredcites →https://doi.org/10.1021/bi051475bopenalex-snapshot
Role of Q52 in Catalysis of Decarboxylation and Transamination in Dialkylglycine Decarboxylase
inferredcites →https://doi.org/10.1021/bi981848ropenalex-snapshot
Structure-Based Design of Potent Inhibitors of Scytalone Dehydratase: Displacement of a Water Molecule from the Active Site
inferredcites →https://doi.org/10.1021/bi990261popenalex-snapshot
Binding of Biliverdin, Bilirubin, and Thyroid Hormones to Lipocalin-Type Prostaglandin D Synthase
inferredcites →https://doi.org/10.1021/ci0500280openalex-snapshot
Structure-Based Approaches to Improve Selectivity: CDK2−GSK3β Binding Site Analysis
inferredcites →https://doi.org/10.1021/ci700274ropenalex-snapshot
Kernel Approach to Molecular Similarity Based on Iterative Graph Similarity
inferredcites →https://doi.org/10.1021/ci900317xopenalex-snapshot
Rapid Comparison of Protein Binding Site Surfaces with Property Encoded Shape Distributions
inferredcites →https://doi.org/10.1021/ci9003317openalex-snapshot
High-Throughput Virtual Screening of Proteins Using GRID Molecular Interaction Fields
inferredcites →https://doi.org/10.1021/ci900349yopenalex-snapshot
Alignment-Free Ultra-High-Throughput Comparison of Druggable Protein−Ligand Binding Sites
inferredcites →https://doi.org/10.1021/ci900427bopenalex-snapshot
Pharmacophore Screening of the Protein Data Bank for Specific Binding Site Chemistry
inferredcites →https://doi.org/10.1021/ci990307lopenalex-snapshot
Prediction of Physicochemical Parameters by Atomic Contributions
inferredcites →https://doi.org/10.1021/ct800267xopenalex-snapshot
Geometrical Preferences of the Hydrogen Bonds on Protein−Ligand Binding Interface Derived from Statistical Surveys and Quantum Mechanics Calculations
inferredcites →https://doi.org/10.1021/ja00226a005openalex-snapshot
Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins
inferredcites →https://doi.org/10.1021/ja0296733openalex-snapshot
Discovery of a Potent, Selective Protein Tyrosine Phosphatase 1B Inhibitor Using a Linked-Fragment Strategy
inferredcites →https://doi.org/10.1021/ja034440copenalex-snapshot
Discovery of a New Phosphotyrosine Mimetic for PTP1B Using Breakaway Tethering
inferredcites →https://doi.org/10.1021/ja038461iopenalex-snapshot
Thermodynamics of Binding of 2-Methoxy-3-isopropylpyrazine and 2-Methoxy-3-isobutylpyrazine to the Major Urinary Protein
inferredcites →https://doi.org/10.1021/jm00145a002openalex-snapshot
A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
inferredcites →https://doi.org/10.1021/jm048957qopenalex-snapshot
The PDBbind Database: Methodologies and Updates
inferredcites →https://doi.org/10.1021/jp973084fopenalex-snapshot
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
inferredcites →https://doi.org/10.1023/a:1008068904628openalex-snapshot
Feature trees: A new molecular similarity measure based on tree matching
inferredcites →https://doi.org/10.1038/nsb0194-55openalex-snapshot
Analogous inhibitors of elastase do not always bind analogously
inferredcites →https://doi.org/10.1042/bj20031790openalex-snapshot
The periplasmic serine protease inhibitor ecotin protects bacteria against neutrophil elastase
inferredcites →https://doi.org/10.1073/pnas.0812657106openalex-snapshot
Structure-based discovery of β 2 -adrenergic receptor ligands
inferredcites →https://doi.org/10.1073/pnas.0900979106openalex-snapshot
Model structure of APOBEC3C reveals a binding pocket modulating ribonucleic acid interaction required for encapsidation
inferredcites →https://doi.org/10.1073/pnas.97.17.9367openalex-snapshot
Site-directed ligand discovery
inferredcites →https://doi.org/10.1074/jbc.271.2.663openalex-snapshot
Structural Analysis of Monosaccharide Recognition by Rat Liver Mannose-binding Protein
inferredcites →https://doi.org/10.1074/jbc.275.10.7101openalex-snapshot
2-(Oxalylamino)-Benzoic Acid Is a General, Competitive Inhibitor of Protein-tyrosine Phosphatases
inferredcites →https://doi.org/10.1074/jbc.m010368200openalex-snapshot
The Insect Attractant 1-Octen-3-ol Is the Natural Ligand of Bovine Odorant-binding Protein
inferredcites →https://doi.org/10.1074/jbc.m508823200openalex-snapshot
Evolutional Design of a Hyperactive Cysteine- and Methionine-free Mutant of Escherichia coli Dihydrofolate Reductase
inferredcites →https://doi.org/10.1074/mcp.m400159-mcp200openalex-snapshot
Pocketome via Comprehensive Identification and Classification of Ligand Binding Envelopes
inferredcites →https://doi.org/10.1080/01621459.1951.10500769openalex-snapshot
The Kolmogorov-Smirnov Test for Goodness of Fit
inferredcites →https://doi.org/10.1080/01621459.1963.10500845openalex-snapshot
Hierarchical Grouping to Optimize an Objective Function
inferredcites →https://doi.org/10.1093/bioinformatics/bti337openalex-snapshot
Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons
inferredcites →https://doi.org/10.1093/bioinformatics/btm404openalex-snapshot
Clustal W and Clustal X version 2.0
inferredcites →https://doi.org/10.1093/comjnl/45.6.631openalex-snapshot
RASCAL: Calculation of Graph Similarity using Maximum Common Edge Subgraphs
inferredcites →https://doi.org/10.1093/nar/gkm276openalex-snapshot
PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026224openalex-snapshot
A Phylogenetic Analysis of the Lipocalin Protein Family
inferredcites →https://doi.org/10.1093/protein/9.1.69openalex-snapshot
Contribution of a salt bridge to binding affinity and dUMP orientation to catalytic rate: mutation of a substrate-binding arginine in thymidylate synthase
inferredcites →https://doi.org/10.1093/protein/gzg080openalex-snapshot
Common Structural Cliques: a tool for protein structure and function analysis
inferredcites →https://doi.org/10.1101/gr.1239303openalex-snapshot
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
inferredcites →https://doi.org/10.1109/fuzzy.2007.4295409openalex-snapshot
Graph Alignment: Fuzzy Pattern Mining for the Structural Analysis of Protein Active Sites
inferredcites →https://doi.org/10.1110/ps.0368703openalex-snapshot
Identification of protein biochemical functions by similarity search using the molecular surface database eF‐site
inferredcites →https://doi.org/10.1126/science.7604279openalex-snapshot
Interaction of a Peptidomimetic Aminimide Inhibitor with Elastase
inferredcites →https://doi.org/10.1145/321921.321925openalex-snapshot
An Algorithm for Subgraph Isomorphism
inferredcites →https://doi.org/10.1186/1752-153x-1-7openalex-snapshot
PocketPicker: analysis of ligand binding-sites with shape descriptors
inferredcites →https://doi.org/10.2174/0929867023368719openalex-snapshot
The Application of Multi-Component Reactions in Drug Discovery
inferredcites →https://doi.org/10.2174/157340908785747401openalex-snapshot
How to Measure the Similarity Between Protein Ligand-Binding Sites?
inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot
R: A Language and Environment for Statistical Computing
inferredcites →https://doi.org/10.5860/choice.41-5919openalex-snapshot
An introduction to chemoinformatics
inferredcites →https://doi.org/10.82308/22274openalex-snapshot
Conditioned and unconditioned reflexes and inhibition
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/ange.201311162openalex-snapshot
Identifizierung von Pyrrolopyrazinen als polypotente Liganden mit Antimalariawirkung
inferred← citeshttps://doi.org/10.1002/anie.201311162openalex-snapshot
Deorphaning Pyrrolopyrazines as Potent Multi‐Target Antimalarial Agents
inferred← citeshttps://doi.org/10.1002/jcc.22894openalex-snapshot
Virtual screening for compounds that mimic protein–protein interface epitopes
inferred← citeshttps://doi.org/10.1002/minf.201100161openalex-snapshot
A New Method for Mapping the Molecular Surface of a Protein Structure Using a Spherical Self‐Organizing Map
inferred← citeshttps://doi.org/10.1002/minf.201300082openalex-snapshot
Identification of Similar Binding Sites to Detect Distant Polypharmacology
inferred← citeshttps://doi.org/10.1002/minf.201300137openalex-snapshot
Prediction of ProteinProtein Interaction Pocket Using L‐Shaped PLS Approach and Its Visualizations by Generative Topographic Mapping
inferred← citeshttps://doi.org/10.1002/minf.201400028openalex-snapshot
BioGPS: The Music for the Chemo‐ and Bioinformatics Walzer
inferred← citeshttps://doi.org/10.1002/wcms.1529openalex-snapshot
Rational design of allosteric modulators: Challenges and successes
inferred← citeshttps://doi.org/10.1007/978-94-007-5285-6_1openalex-snapshot
SuMo: A Tool for Protein Function Inference Based on 3D Structures Comparisons
inferred← citeshttps://doi.org/10.1007/s11030-018-9881-9openalex-snapshot
Quasi-SMILES: quantitative structure–activity relationships to predict anticancer activity
inferred← citeshttps://doi.org/10.1016/j.csbj.2014.05.004openalex-snapshot
Simple Ligand–Receptor Interaction Descriptor (SILIRID) for alignment-free binding site comparison
inferred← citeshttps://doi.org/10.1016/j.jmb.2020.166751openalex-snapshot
Intrinsically Disordered Protein Ensembles Shape Evolutionary Rates Revealing Conformational Patterns
inferred← citeshttps://doi.org/10.1016/j.pharmthera.2013.01.016openalex-snapshot
Structure and dynamics of molecular networks: A novel paradigm of drug discovery
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00832openalex-snapshot
Advances and Challenges in Computational Target Prediction
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.6b00078openalex-snapshot
Impact of Binding Site Comparisons on Medicinal Chemistry and Rational Molecular Design
inferred← citeshttps://doi.org/10.1021/ci300523ropenalex-snapshot
Subpocket Analysis Method for Fragment-Based Drug Discovery
inferred← citeshttps://doi.org/10.1021/jm200092bopenalex-snapshot
Discovery and Biological Evaluation of a Novel Class of Dual Microsomal Prostaglandin E2Synthase-1/5-lipoxygenase Inhibitors Based on 2-[(4,6-Diphenethoxypyrimidin-2-yl)thio]hexanoic Acid
inferred← citeshttps://doi.org/10.1021/jm401557wopenalex-snapshot
Aminothiazole-Featured Pirinixic Acid Derivatives As Dual 5-Lipoxygenase and Microsomal Prostaglandin E 2 Synthase-1 Inhibitors with Improved Potency and Efficiency in Vivo
inferred← citeshttps://doi.org/10.1039/c2md20242eopenalex-snapshot
On the origins of drug polypharmacology
inferred← citeshttps://doi.org/10.1039/c4sc01443jopenalex-snapshot
Inhibiting Helicobacter pylori HtrA protease by addressing a computationally predicted allosteric ligand binding site
inferred← citeshttps://doi.org/10.1074/jbc.c111.333419openalex-snapshot
Distinct Roles of Secreted HtrA Proteases from Gram-negative Pathogens in Cleaving the Junctional Protein and Tumor Suppressor E-cadherin
inferred← citeshttps://doi.org/10.1074/jbc.m112.383430openalex-snapshot
Identification of UV-protective Activators of Nuclear Factor Erythroid-derived 2-Related Factor 2 (Nrf2) by Combining a Chemical Library Screen with Computer-based Virtual Screening
inferred← citeshttps://doi.org/10.1371/journal.pone.0135246openalex-snapshot
In Silico Adoption of an Orphan Nuclear Receptor NR4A1
inferred← citeshttps://doi.org/10.4155/fmc.11.8openalex-snapshot
Reaction-Driven De Novo Design, Synthesis and Testing of Potential Type II Kinase Inhibitors
inferred← citeshttps://doi.org/10.48160/25913530di17.205openalex-snapshot
Las velocidades de evolución de IDPs son modeladas por los ensembles conformacionales (*)
Editorial review for independent work. ICSAC — the Institute for Complexity
Science and Advanced Computing — runs a structured editorial panel for researchers
publishing outside journals, and publishes on CiteStamp rails. Submission is free
and goes through ORCID: icsacinstitute.org/submit.