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Exploring Structure–Activity Relationships with Three‐Dimensional Matched Molecular Pairs—A Review

https://doi.org/10.1002/cmdc.201700628

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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/cmdc.201100179openalex-snapshot

From Activity Cliffs to Target‐Specific Scoring Models and Pharmacophore Hypotheses

inferredcites →https://doi.org/10.1002/minf.201200020openalex-snapshot

Prospective Prediction of Antitarget Activity by Matched Molecular Pairs Analysis

inferredcites →https://doi.org/10.1002/minf.201500010openalex-snapshot

Cross‐Mapping of Protein – Ligand Binding Data Between ChEMBL and PDBbind

inferredcites →https://doi.org/10.1006/jmbi.1996.0477openalex-snapshot

A Fast Flexible Docking Method using an Incremental Construction Algorithm

inferredcites →https://doi.org/10.1007/s10822-007-9106-2openalex-snapshot

Outliers in SAR and QSAR: Is unusual binding mode a possible source of outliers?

inferredcites →https://doi.org/10.1016/j.bmcl.2011.05.091openalex-snapshot

Discovery of pyrrolo[2,1-f][1,2,4]triazine C6-ketones as potent, orally active p38α MAP kinase inhibitors

inferredcites →https://doi.org/10.1016/j.chembiol.2007.03.011openalex-snapshot

Molecular Similarity Analysis Uncovers Heterogeneous Structure-Activity Relationships and Variable Activity Landscapes

inferredcites →https://doi.org/10.1016/j.csbj.2016.12.003openalex-snapshot

Matched Molecular Pair Analysis in Short: Algorithms, Applications and Limitations

inferredcites →https://doi.org/10.1021/acs.jcim.7b00335openalex-snapshot

Turbocharging Matched Molecular Pair Analysis: Optimizing the Identification and Analysis of Pairs

inferredcites →https://doi.org/10.1021/ci0100806openalex-snapshot

The Most Common Chemical Replacements in Drug-Like Compounds

inferredcites →https://doi.org/10.1021/ci0503208openalex-snapshot

Molecular Transformations as a Way of Finding and Exploiting Consistent Local QSAR

inferredcites →https://doi.org/10.1021/ci060117sopenalex-snapshot

On Outliers and Activity CliffsWhy QSAR Often Disappoints

inferredcites →https://doi.org/10.1021/ci100258popenalex-snapshot

Lead Optimization Using Matched Molecular Pairs: Inclusion of Contextual Information for Enhanced Prediction of hERG Inhibition, Solubility, and Lipophilicity

inferredcites →https://doi.org/10.1021/ci200254kopenalex-snapshot

A Data Mining Method To Facilitate SAR Transfer

inferredcites →https://doi.org/10.1021/ci2004658openalex-snapshot

Freely Available Conformer Generation Methods: How Good Are They?

inferredcites →https://doi.org/10.1021/ci300158vopenalex-snapshot

Systematic Identification and Classification of Three-Dimensional Activity Cliffs

inferredcites →https://doi.org/10.1021/ci300481dopenalex-snapshot

Systematic Assessment of Compound Series with SAR Transfer Potential

inferredcites →https://doi.org/10.1021/ci400201kopenalex-snapshot

3D Matched Pairs: Integrating Ligand- and Structure-Based Knowledge for Ligand Design and Receptor Annotation

inferredcites →https://doi.org/10.1021/ci500080qopenalex-snapshot

Comparative Assessment of Scoring Functions on an Updated Benchmark: 1. Compilation of the Test Set

inferredcites →https://doi.org/10.1021/ci500245dopenalex-snapshot

OOMMPPAA: A Tool To Aid Directed Synthesis by the Combined Analysis of Activity and Structural Data

inferredcites →https://doi.org/10.1021/ci5005256openalex-snapshot

VAMMPIRE-LORD: A Web Server for Straightforward Lead Optimization Using Matched Molecular Pairs

inferredcites →https://doi.org/10.1021/ci7004093openalex-snapshot

Structure−Activity Landscape Index: Identifying and Quantifying Activity Cliffs

inferredcites →https://doi.org/10.1021/ci9000053openalex-snapshot

Comparative Assessment of Scoring Functions on a Diverse Test Set

inferredcites →https://doi.org/10.1021/ci900450mopenalex-snapshot

Computationally Efficient Algorithm to Identify Matched Molecular Pairs (MMPs) in Large Data Sets

inferredcites →https://doi.org/10.1021/jm0002634openalex-snapshot

Flexible Alignment of Small Molecules

inferredcites →https://doi.org/10.1021/jm020056zopenalex-snapshot

Probing the ATP Ribose-Binding Domain of Cyclin-Dependent Kinases 1 and 2 withO6-Substituted Guanine Derivatives

inferredcites →https://doi.org/10.1021/jm030580lopenalex-snapshot

The PDBbind Database: Collection of Binding Affinities for Protein−Ligand Complexes with Known Three-Dimensional Structures

inferredcites →https://doi.org/10.1021/jm040163oopenalex-snapshot

A Shape-Based 3-D Scaffold Hopping Method and Its Application to a Bacterial Protein−Protein Interaction

inferredcites →https://doi.org/10.1021/jm048957qopenalex-snapshot

The PDBbind Database: Methodologies and Updates

inferredcites →https://doi.org/10.1021/jm400223yopenalex-snapshot

VAMMPIRE: A Matched Molecular Pairs Database for Structure-Based Drug Design and Optimization

inferredcites →https://doi.org/10.1021/jm5009264openalex-snapshot

Comprehensive Analysis of Three-Dimensional Activity Cliffs Formed by Kinase Inhibitors with Different Binding Modes and Cliff Mapping of Structural Analogues

inferredcites →https://doi.org/10.1023/a:1016399411208openalex-snapshot

Flexible docking under pharmacophore type constraints

inferredcites →https://doi.org/10.1038/nrd4128openalex-snapshot

Chemical predictive modelling to improve compound quality

inferredcites →https://doi.org/10.1038/nsb842openalex-snapshot

Structure-based design of a potent purine-based cyclin-dependent kinase inhibitor

inferredcites →https://doi.org/10.1039/c5ra01730kopenalex-snapshot

Identification and analysis of the currently available high-confidence three-dimensional activity cliffs

inferredcites →https://doi.org/10.1039/c5ra01732gopenalex-snapshot

Extension of three-dimensional activity cliff information through systematic mapping of active analogs

inferredcites →https://doi.org/10.1093/nar/gkr777openalex-snapshot

ChEMBL: a large-scale bioactivity database for drug discovery

inferredcites →https://doi.org/10.1186/1758-2946-5-26openalex-snapshot

Open-source platform to benchmark fingerprints for ligand-based virtual screening

inferredcites →https://doi.org/10.1208/s12248-012-9322-0openalex-snapshot

Structure-Based Virtual Screening for Drug Discovery: a Problem-Centric Review

inferredcites →https://doi.org/10.4155/fmc-2016-0203openalex-snapshot

Practical Applications of Matched Series Analysis: Sar Transfer, Binding Mode Suggestion and Data Point Validation

What points at this work

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

inferred← citeshttps://doi.org/10.1016/b978-0-12-409547-2.14703-1openalex-snapshot

Chemometrics for QSAR Modeling

inferred← citeshttps://doi.org/10.1016/j.csbj.2021.02.018openalex-snapshot

Structure-based molecular modeling in SAR analysis and lead optimization

inferred← citeshttps://doi.org/10.1016/j.ejmech.2018.11.074openalex-snapshot

Discovery of potent and selective inhibitors of the Escherichia coli M1-aminopeptidase via multicomponent solid-phase synthesis of tetrazole-peptidomimetics

inferred← citeshttps://doi.org/10.1016/j.ejmech.2023.116049openalex-snapshot

Camptothecin structure simplification elaborated new imidazo[2,1-b]quinazoline derivative as a human topoisomerase I inhibitor with efficacy against bone cancer cells and colon adenocarcinoma

inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00290openalex-snapshot

Performance of Relative Binding Free Energy Calculations on an Automatically Generated Dataset of Halogen–Deshalogen Matched Molecular Pairs

inferred← citeshttps://doi.org/10.1021/acs.jmedchem.2c01787openalex-snapshot

Matched Molecular Pair Analysis in Drug Discovery: Methods and Recent Applications

inferred← citeshttps://doi.org/10.1021/acsomega.2c00173openalex-snapshot

Visualization of Topological Pharmacophore Space with Graph Edit Distance

inferred← citeshttps://doi.org/10.1101/2023.11.16.567496openalex-snapshot

PanScreen: A Comprehensive Approach to Off-Target Liability Assessment

inferred← citeshttps://doi.org/10.1371/journal.pone.0296010openalex-snapshot

Secondary metabolites of Trichoderma spp. as EGFR tyrosine kinase inhibitors: Evaluation of anticancer efficacy through computational approach

inferred← citeshttps://doi.org/10.1371/journal.pone.0302105openalex-snapshot

Exploration of Type III effector Xanthomonas outer protein Q (XopQ) inhibitor from Picrasma quassioides as an antibacterial agent using chemoinformatics analysis

inferred← citeshttps://doi.org/10.3390/biomedicines13092202openalex-snapshot

Integrated Virtual Screening for Anti-Caries Compounds from Neem: Dual-Target Inhibition of Biofilm Formation and Bacterial DNA Replication

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