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Small Molecule Shape-Fingerprints
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1007/978-94-017-1120-3openalex-snapshot
Computer Simulation of Biomolecular Systems
inferredcites →https://doi.org/10.1016/0167-8655(96)00032-3openalex-snapshot
A fast branch & bound nearest neighbour classifier in metric spaces
inferredcites →https://doi.org/10.1016/0378-3758(89)90033-5openalex-snapshot
Algorithms for clustering data
inferredcites →https://doi.org/10.1016/s1093-3263(02)00204-8openalex-snapshot
Assessing the performance of OMEGA with respect to retrieving bioactive conformations
inferredcites →https://doi.org/10.1021/ci00002a004openalex-snapshot
The development of versions 3 and 4 of the Cambridge Structural Database System
inferredcites →https://doi.org/10.1021/ci00002a005openalex-snapshot
Chemical Abstracts Service Chemical Registry System. 13. Enhanced handling of stereochemistry
inferredcites →https://doi.org/10.1021/ci00007a012openalex-snapshot
Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited
inferredcites →https://doi.org/10.1021/ci00007a013openalex-snapshot
Computer-aided molecular formula determination from mass, proton and carbon-13 NMR spectra
inferredcites →https://doi.org/10.1021/ci000100oopenalex-snapshot
A New Class of Molecular Shape Descriptors. 1. Theory and Properties
inferredcites →https://doi.org/10.1021/ci010132ropenalex-snapshot
Reoptimization of MDL Keys for Use in Drug Discovery
inferredcites →https://doi.org/10.1021/ci960151eopenalex-snapshot
Clustering of Large Databases of Compounds: Using the MDL “Keys” as Structural Descriptors
inferredcites →https://doi.org/10.1021/ci970437zopenalex-snapshot
On the Properties of Bit String-Based Measures of Chemical Similarity
inferredcites →https://doi.org/10.1021/ci980159jopenalex-snapshot
Pharmacophore Fingerprinting. 1. Application to QSAR and Focused Library Design
inferredcites →https://doi.org/10.1021/j100011a016openalex-snapshot
A Gaussian Description of Molecular Shape
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/jm990578nopenalex-snapshot
A Rapid Computational Method for Lead Evolution: Description and Application to α1-Adrenergic Antagonists
inferredcites →https://doi.org/10.1021/jp953707uopenalex-snapshot
A Gaussian Description of Molecular Shape
inferredcites →https://doi.org/10.1023/a:1015930826903openalex-snapshot
Reproducing the conformations of protein-bound ligands: A critical evaluation of several popular conformational searching tools
inferredcites →https://doi.org/10.1148/radiology.143.1.7063747openalex-snapshot
The meaning and use of the area under a receiver operating characteristic (ROC) curve.
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Docking, Scoring, and Virtual Screening in Drug Discovery
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QSAR and Molecular Modeling Approaches for Prediction of Drug Metabolism
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Structural Basis and Computational Modeling of Chiral Drugs
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The Basics of Diversity‐Oriented Synthesis
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Interactive Technologies for Leveraging the Known Chemistry of Anchor Residues to Disrupt Protein Interactions
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Lead Generation Based on Compound Collection Screening
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Similarity methods in chemoinformatics
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Construction of a Shape‐Diverse Fragment Set: Design, Synthesis and Screen against Aurora‐A Kinase
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Shape‐based virtual screening with volumetric aligned molecular shapes
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FRAGMENTISE : A user‐friendly, cross‐platform tool to create and analyze comprehensive small‐molecule fragment databases
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Chemoinformatics applications of cluster analysis
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Smoothed Gaussian molecular fields: an evaluation of molecular alignment problems
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Smoothed Gaussian molecular fields: an evaluation of molecular alignment problems
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Efficient overlay of small organic molecules using 3D pharmacophores
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Design of compound libraries for fragment screening
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Small Molecule Screening Discovers Compounds that Reduce FMRpolyG Protein Aggregates and Splicing Defect Toxicity in Fragile X-Associated Tremor/Ataxia Syndrome
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Library Design: Ligand and Structure-Based Principles for Parallel and Combinatorial Libraries
inferred← citeshttps://doi.org/10.1016/b0-08-045044-x/00257-1openalex-snapshot
Library Design: Reactant and Product-Based Approaches
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Library Design: Reactant and Product-Based Approaches
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Absorption, distribution, metabolism, excretion, and toxicity assessment of drugs using computational tools
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Molecular representations in deep learning
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2D QSAR and similarity studies on cruzain inhibitors aimed at improving selectivity over cathepsin L
inferred← citeshttps://doi.org/10.1016/j.bmc.2021.116119openalex-snapshot
Identification of SARS-CoV-2 viral entry inhibitors using machine learning and cell-based pseudotyped particle assay
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Classifying shape coverage in fragment libraries using a fingerprinting approach
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Streamlining lead discovery by aligning in silico and high-throughput screening
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Fragment library design: efficiently hunting drugs in chemical space
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Molecular similarity analysis in virtual screening: foundations, limitations and novel approaches
inferred← citeshttps://doi.org/10.1016/j.drudis.2013.07.024openalex-snapshot
Rational design of chemical genetic probes of RNA function and lead therapeutics targeting repeating transcripts
inferred← citeshttps://doi.org/10.1016/j.drudis.2016.04.023openalex-snapshot
An improved model for fragment-based lead generation at AstraZeneca
inferred← citeshttps://doi.org/10.1016/j.drudis.2022.103356openalex-snapshot
Concepts and applications of chemical fingerprint for hit and lead screening
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2020.10.136openalex-snapshot
Identification of novel αβ-tubulin modulators with antiproliferative activity directed to cancer therapy using ligand and structure-based virtual screening
inferred← citeshttps://doi.org/10.1016/j.jmgm.2007.03.016openalex-snapshot
Novel DOCK clique driven 3D similarity database search tools for molecule shape matching and beyond: Adding flexibility to the search for ligand kin
inferred← citeshttps://doi.org/10.1016/j.jmgm.2010.08.007openalex-snapshot
Complementing ultrafast shape recognition with an optical isomerism descriptor
inferred← citeshttps://doi.org/10.1016/j.jmgm.2016.03.017openalex-snapshot
Fragment oriented molecular shapes
inferred← citeshttps://doi.org/10.1016/s1574-1400(06)02009-3openalex-snapshot
Chapter 9 Molecular Similarity: Advances in Methods, Applications and Validations in Virtual Screening and QSAR
inferred← citeshttps://doi.org/10.1021/acs.chemrev.5c01081openalex-snapshot
Organic Chemistry as a Catalyst for AI Innovation: Challenges, Methods, and Emerging Paradigms
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00622openalex-snapshot
Improved Scaffold Hopping in Ligand-Based Virtual Screening Using Neural Representation Learning
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00089openalex-snapshot
Mapping Ligand-Shape Space for Protein–Ligand Systems: Distinguishing Key-in-Lock and Hand-in-Glove Proteins
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00796openalex-snapshot
Shape-Restrained Modeling of Protein–Small-Molecule Complexes with High Ambiguity Driven DOCKing
inferred← citeshttps://doi.org/10.1021/acs.jcim.6c00591openalex-snapshot
Struct2Query: Structure-Guided Virtual Screening via Composite-Molecule ROCS Queries Derived from Protein Pocket Similarity
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00528openalex-snapshot
Sparse Generative Topographic Mapping for Both Data Visualization and Clustering
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.5b01409openalex-snapshot
Analysis of Past and Present Synthetic Methodologies on Medicinal Chemistry: Where Have All the New Reactions Gone?
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A Live-Cell NanoBRET Assay to Monitor RNA–Protein Interactions and Their Inhibition by Small Molecules
inferred← citeshttps://doi.org/10.1021/acschembio.6b00253openalex-snapshot
3D Chemical Similarity Networks for Structure-Based Target Prediction and Scaffold Hopping
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Contemporary Computational Applications and Tools in Drug Discovery
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Molecular Similarity Approaches in Chemoinformatics: Early History and Literature Status
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Chemical Correction of Pre-mRNA Splicing Defects Associated with Sequestration of Muscleblind-like 1 Protein by Expanded r(CAG)-Containing Transcripts
inferred← citeshttps://doi.org/10.1021/cb300135hopenalex-snapshot
A Small Molecule That Targets r(CGG)exp and Improves Defects in Fragile X-Associated Tremor Ataxia Syndrome
inferred← citeshttps://doi.org/10.1021/ci1000136openalex-snapshot
SCISSORS: A Linear-Algebraical Technique to Rapidly Approximate Chemical Similarities
inferred← citeshttps://doi.org/10.1021/ci200235eopenalex-snapshot
Anatomy of High-Performance 2D Similarity Calculations
inferred← citeshttps://doi.org/10.1021/ci200282zopenalex-snapshot
Power Keys: A Novel Class of Topological Descriptors Based on Exhaustive Subgraph Enumeration and their Application in Substructure Searching
inferred← citeshttps://doi.org/10.1021/ci200562popenalex-snapshot
Application of Support Vector Machine to Three-Dimensional Shape-Based Virtual Screening Using Comprehensive Three-Dimensional Molecular Shape Overlay with Known Inhibitors
inferred← citeshttps://doi.org/10.1021/ci300030uopenalex-snapshot
Performance Evaluation of 2D Fingerprint and 3D Shape Similarity Methods in Virtual Screening
inferred← citeshttps://doi.org/10.1021/ci400139jopenalex-snapshot
SimG: An Alignment Based Method for Evaluating the Similarity of Small Molecules and Binding Sites
inferred← citeshttps://doi.org/10.1021/ci400731wopenalex-snapshot
Fragment-Based Lead Discovery and Design
inferred← citeshttps://doi.org/10.1021/ci500232gopenalex-snapshot
Atom Pair 2D-Fingerprints Perceive 3D-Molecular Shape and Pharmacophores for Very Fast Virtual Screening of ZINC and GDB-17
inferred← citeshttps://doi.org/10.1021/ci600549qopenalex-snapshot
Selection of Molecules Based on Shape and Electrostatic Similarity: Proof of Concept of “Electroforms”
inferred← citeshttps://doi.org/10.1021/ci7001507openalex-snapshot
Toward High Throughput 3D Virtual Screening Using Spherical Harmonic Surface Representations
inferred← citeshttps://doi.org/10.1021/ci900015bopenalex-snapshot
Unconventional 2D Shape Similarity Method Affords Comparable Enrichment as a 3D Shape Method in Virtual Screening Experiments
inferred← citeshttps://doi.org/10.1021/ci900085dopenalex-snapshot
Quantum Isostere Database: A Web-Based Tool Using Quantum Chemical Topology To Predict Bioisosteric Replacements for Drug Design
inferred← citeshttps://doi.org/10.1021/ci900190zopenalex-snapshot
Alpha Shapes Applied to Molecular Shape Characterization Exhibit Novel Properties Compared to Established Shape Descriptors
inferred← citeshttps://doi.org/10.1021/ci900507gopenalex-snapshot
Comparative Evaluation of 3D Virtual Ligand Screening Methods: Impact of the Molecular Alignment on Enrichment
inferred← citeshttps://doi.org/10.1021/ja210088vopenalex-snapshot
Design of a Bioactive Small Molecule That Targets the Myotonic Dystrophy Type 1 RNA via an RNA Motif–Ligand Database and Chemical Similarity Searching
inferred← citeshttps://doi.org/10.1021/jm0603365openalex-snapshot
Comparison of Shape-Matching and Docking as Virtual Screening Tools
inferred← citeshttps://doi.org/10.1021/jm501660topenalex-snapshot
Small Molecule Binding Sites on the Ras:SOS Complex Can Be Exploited for Inhibition of Ras Activation
inferred← citeshttps://doi.org/10.1021/jm900818sopenalex-snapshot
Molecular Shape and Medicinal Chemistry: A Perspective
inferred← citeshttps://doi.org/10.1038/ncomms1081openalex-snapshot
Diversity-oriented synthesis as a tool for the discovery of novel biologically active small molecules
inferred← citeshttps://doi.org/10.1038/ncomms2119openalex-snapshot
Identifying the preferred RNA motifs and chemotypes that interact by probing millions of combinations
inferred← citeshttps://doi.org/10.1038/s41598-019-53410-zopenalex-snapshot
Discovery of a potent small molecule inhibiting Huntington’s disease (HD) pathogenesis via targeting CAG repeats RNA and Poly Q protein
inferred← citeshttps://doi.org/10.1038/s41598-021-01529-3openalex-snapshot
Piperine analogs arrest c-myc gene leading to downregulation of transcription for targeting cancer
inferred← citeshttps://doi.org/10.1039/9781847558879-00076openalex-snapshot
Pharmacophore-based Virtual Screening in Drug Discovery
inferred← citeshttps://doi.org/10.1039/9781847558879-00120openalex-snapshot
Molecular Similarity Analysis in Virtual Screening
inferred← citeshttps://doi.org/10.1039/c3ob42512fopenalex-snapshot
A modular lead-oriented synthesis of diverse piperazine, 1,4-diazepane and 1,5-diazocane scaffolds
inferred← citeshttps://doi.org/10.1039/c8ob02808gopenalex-snapshot
Bicyclic acetals: biological relevance, scaffold analysis, and applications in diversity-oriented synthesis
inferred← citeshttps://doi.org/10.1073/pnas.1121601109openalex-snapshot
Antiproliferative small-molecule inhibitors of transcription factor LSF reveal oncogene addiction to LSF in hepatocellular carcinoma
inferred← citeshttps://doi.org/10.1074/jbc.m114.589200openalex-snapshot
Discovery of Mycobacterium tuberculosis α-1,4-Glucan Branching Enzyme (GlgB) Inhibitors by Structure- and Ligand-based Virtual Screening
inferred← citeshttps://doi.org/10.1080/07391102.2013.803441openalex-snapshot
Structure- and ligand-based drug design of novel p38-alpha MAPK inhibitors in the fight against the Alzheimer’s disease
inferred← citeshttps://doi.org/10.1080/07391102.2014.908142openalex-snapshot
Development of pharmacophore similarity-based quantitative activity hypothesis and its applicability domain: applied on a diverse data-set of HIV-1 integrase inhibitors
inferred← citeshttps://doi.org/10.1093/bib/bbp023openalex-snapshot
Recent advances in computer-aided drug design
inferred← citeshttps://doi.org/10.1093/chemse/bjaf002openalex-snapshot
Predicting human olfactory perception by odorant structure and receptor activation profile
inferred← citeshttps://doi.org/10.1093/nar/gkq325openalex-snapshot
Frog2: Efficient 3D conformation ensemble generator for small compounds
inferred← citeshttps://doi.org/10.1101/2021.06.10.447890openalex-snapshot
Shape-restrained modelling of protein-small molecule complexes with HADDOCK
inferred← citeshttps://doi.org/10.1101/2024.08.10.607459openalex-snapshot
Efficient clustering of large molecular libraries
inferred← citeshttps://doi.org/10.1146/annurev-biophys-051013-022726openalex-snapshot
Structural Bioinformatics of the Interactome
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Planejamento computacional e avaliação in vitro de novos potenciais inibidores da fosfomanose isomerase (PMI) de interesse para o controle do cancro cítrico
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Planejamento e validação anti-proliferativa e anti-leishmania, de novos híbridos tri-funcionalizados unidos através do anel 1,2,3-triazol e compostos similares
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Quinase p38 alfa como alvo para o planejamento de fármacos em Mal de Alzheimer
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Cyndi: a multi-objective evolution algorithm based method for bioactive molecular conformational generation
inferred← citeshttps://doi.org/10.1186/1471-2105-11-256openalex-snapshot
Binary image representation of a ligand binding site: its application to efficient sampling of a conformational ensemble
inferred← citeshttps://doi.org/10.1186/1752-153x-1-12openalex-snapshot
Fast 3D shape screening of large chemical databases through alignment-recycling
inferred← citeshttps://doi.org/10.1186/1758-2946-3-25openalex-snapshot
PubChem3D: Shape compatibility filtering using molecular shape quadrupoles
inferred← citeshttps://doi.org/10.1186/s13321-014-0051-5openalex-snapshot
Stereoselective virtual screening of the ZINC database using atom pair 3D-fingerprints
inferred← citeshttps://doi.org/10.1186/s13321-017-0208-0openalex-snapshot
The comparison of automated clustering algorithms for resampling representative conformer ensembles with RMSD matrix
inferred← citeshttps://doi.org/10.1186/s13321-018-0268-9openalex-snapshot
Spectrophores as one-dimensional descriptors calculated from three-dimensional atomic properties: applications ranging from scaffold hopping to multi-target virtual screening
inferred← citeshttps://doi.org/10.1371/journal.pone.0134697openalex-snapshot
A Teach-Discover-Treat Application of ZincPharmer: An Online Interactive Pharmacophore Modeling and Virtual Screening Tool
inferred← citeshttps://doi.org/10.14201/gredos.159160openalex-snapshot
Aplicación de nuevas isoxazolidinas quirales en síntesis orientada a la diversidad
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Drug design using comparative molecular surface analysis
inferred← citeshttps://doi.org/10.1517/17460441.1.7.709openalex-snapshot
Discovery strategies in a pharmaceutical setting: the application of computational techniques
inferred← citeshttps://doi.org/10.1517/17460441.3.9.1011openalex-snapshot
Virtual screening of chemical libraries for drug discovery
inferred← citeshttps://doi.org/10.1590/s2175-97902024e23618openalex-snapshot
Rational drug repurposing for alzheimer’s treatment using in-silico ligand and structure-based approaches
inferred← citeshttps://doi.org/10.2174/09298673113209990001openalex-snapshot
Virtual Screening Strategies in Drug Discovery: A Critical Review
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Drug Metabolism in Preclinical Drug Development: A Survey of the Discovery Process, Toxicology, and Computational Tools
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Aurora-A in complex with shape-diverse fragment 39
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Insights into the Development of Chemotherapeutics Targeting PFKFB Enzymes
inferred← citeshttps://doi.org/10.3389/fchem.2018.00229openalex-snapshot
Conformational Sampling of Small Molecules With iCon: Performance Assessment in Comparison With OMEGA
inferred← citeshttps://doi.org/10.3390/ijms23116114openalex-snapshot
Molecular Similarity Perception Based on Machine-Learning Models
inferred← citeshttps://doi.org/10.3797/scipharm.0804-12openalex-snapshot
Chemical Structure Indices in In Silico Molecular Design
inferred← citeshttps://doi.org/10.70675/c62edcc5z1d13z49e5zb18ez2a51ea905a5copenalex-snapshot
Simulation numérique et approche orientée connaissance pour la découverte de nouvelles molécules thérapeutiques
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