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MMP-Cliffs: Systematic Identification of Activity Cliffs on the Basis of Matched Molecular Pairs

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What this work says

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

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Chemoinformatics in Drug Discovery

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Navigating structure–activity landscapes

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On Outliers and Activity CliffsWhy QSAR Often Disappoints

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Chemical Substitutions That Introduce Activity Cliffs Across Different Compound Classes and Biological Targets

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Assessing the Confidence Level of Public Domain Compound Activity Data and the Impact of Alternative Potency Measurements on SAR Analysis

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Structure−Activity Landscape Index: Identifying and Quantifying Activity Cliffs

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Characterization of Activity Landscapes Using 2D and 3D Similarity Methods: Consensus Activity Cliffs

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

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Searching Techniques for Databases of Two- and Three-Dimensional Chemical Structures

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Activity Landscape Representations for Structure−Activity Relationship Analysis

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Local Structural Changes, Global Data Views: Graphical Substructure−Activity Relationship Trailing

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Exploring Activity Cliffs in Medicinal Chemistry

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BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities

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ChEMBL: a large-scale bioactivity database for drug discovery

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Comprehensive Analysis of Single‐ and Multi‐Target Activity Cliffs Formed by Currently Available Bioactive Compounds

What points at this work

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inferred← citeshttps://doi.org/10.1080/17460441.2018.1465926openalex-snapshot

Progress with modeling activity landscapes in drug discovery

inferred← citeshttps://doi.org/10.1080/17460441.2019.1593371openalex-snapshot

Duality of activity cliffs in drug discovery

inferred← citeshttps://doi.org/10.1093/bib/bbag548openalex-snapshot

MMP2Mol: a matched molecular pairs-based framework for ligand-based de novo drug design

inferred← citeshttps://doi.org/10.1101/2023.10.06.561266openalex-snapshot

Cheminformatics analysis of multi-target structure-activity landscape of environmental chemicals binding to human endocrine receptors

inferred← citeshttps://doi.org/10.1111/cbdd.12115openalex-snapshot

Activity Cliffs: Facts or Artifacts?

inferred← citeshttps://doi.org/10.1111/cbdd.12605openalex-snapshot

Identification of Interaction Hot Spots in Structures of Drug Targets on the Basis of Three‐Dimensional Activity Cliff Information

inferred← citeshttps://doi.org/10.1111/cbdd.12919openalex-snapshot

Mapping of inhibitors and activity data to the human kinome and exploring promiscuity from a ligand and target perspective

inferred← citeshttps://doi.org/10.1111/cbdd.13147openalex-snapshot

In silico ligand‐based modeling of hBACE ‐1 inhibitors

inferred← citeshttps://doi.org/10.1111/cbdd.13985openalex-snapshot

Systematic identification of activity cliffs with dual‐atom replacements and their rationalization on the basis of single‐atom replacement analogs and X‐ray structures

inferred← citeshttps://doi.org/10.1186/s13321-020-00473-0openalex-snapshot

Memory-assisted reinforcement learning for diverse molecular de novo design

inferred← citeshttps://doi.org/10.1186/s13321-021-00526-yopenalex-snapshot

“Molecular Anatomy”: a new multi-dimensional hierarchical scaffold analysis tool

inferred← citeshttps://doi.org/10.1186/s13321-022-00676-7openalex-snapshot

Large-scale prediction of activity cliffs using machine and deep learning methods of increasing complexity

inferred← citeshttps://doi.org/10.1186/s13321-023-00733-9openalex-snapshot

Explaining compound activity predictions with a substructure-aware loss for graph neural networks

inferred← citeshttps://doi.org/10.1186/s13321-025-01006-3openalex-snapshot

Activity cliff-aware reinforcement learning for de novo drug design

inferred← citeshttps://doi.org/10.1208/s12248-014-9567-xopenalex-snapshot

Formation of Activity Cliffs Is Accompanied by Systematic Increases in Ligand Efficiency from Lowly to Highly Potent Compounds

inferred← citeshttps://doi.org/10.1208/s12248-014-9621-8openalex-snapshot

Many Approved Drugs Have Bioactive Analogs With Different Target Annotations

inferred← citeshttps://doi.org/10.1208/s12248-015-9737-5openalex-snapshot

Structural and Activity Profile Relationships Between Drug Scaffolds

inferred← citeshttps://doi.org/10.1208/s12248-017-0066-8openalex-snapshot

Structure-Promiscuity Relationship Puzzles—Extensively Assayed Analogs with Large Differences in Target Annotations

inferred← citeshttps://doi.org/10.12688/f1000research.12370.1openalex-snapshot

Towards a systematic assessment of assay interference: Identification of extensively tested compounds with high assay promiscuity

inferred← citeshttps://doi.org/10.12688/f1000research.2-199.v1openalex-snapshot

Advancing the activity cliff concept

inferred← citeshttps://doi.org/10.12688/f1000research.3-36.v1openalex-snapshot

Matched molecular pair-based data sets for computer-aided medicinal chemistry

inferred← citeshttps://doi.org/10.12688/f1000research.3788.1openalex-snapshot

Advancing the activity cliff concept, part II

inferred← citeshttps://doi.org/10.12688/f1000research.4057openalex-snapshot

Advancing the activity cliff concept, part II

inferred← citeshttps://doi.org/10.12688/f1000research.6661.1openalex-snapshot

Comprehensive knowledge base of two- and three-dimensional activity cliffs for medicinal and computational chemistry

inferred← citeshttps://doi.org/10.1517/17460441.2015.1019861openalex-snapshot

Activity cliff clusters as a source of structure–activity relationship information

inferred← citeshttps://doi.org/10.1517/17460441.2015.1073257openalex-snapshot

Activity landscape of DNA methyltransferase inhibitors bridges chemoinformatics with epigenetic drug discovery

inferred← citeshttps://doi.org/10.20944/preprints202407.0477.v1openalex-snapshot

Non-Nucleoside Lycorine-Based Analogues as Potential DENV/ZIKV NS5 Dual Inhibitors: Structure-Based Virtual Screening and Chemoinformatic Analysis

inferred← citeshttps://doi.org/10.21203/rs.3.rs-1120840/v1openalex-snapshot

Activity Cliffs As Protein-Related Phenomenon: Investigation Using Machine Learning Against Numerous Protein Kinases

inferred← citeshttps://doi.org/10.2144/fsoa-2019-0040openalex-snapshot

Data Structures for Compound Promiscuity Analysis: Promiscuity cliffs, Pathways and Promiscuity Hubs Formed by Inhibitors of the Human Kinome

inferred← citeshttps://doi.org/10.2144/fsoa-2020-0020openalex-snapshot

Increasing the Public Activity Cliff Knowledge Base With New Categories of Activity Cliffs

inferred← citeshttps://doi.org/10.2174/1381612826666200427111309openalex-snapshot

Bioactivity Prediction Based on Matched Molecular Pair and Matched Molecular Series Methods

inferred← citeshttps://doi.org/10.2751/jcac.16.15openalex-snapshot

A Mini-review on Chemoinformatics Approaches for Drug Discovery

inferred← citeshttps://doi.org/10.3389/fphar.2025.1673688openalex-snapshot

Target fishing: from “needle in haystack” to “precise guidance”--new technology, new strategy and new opportunity

inferred← citeshttps://doi.org/10.3390/biom11111647openalex-snapshot

Data-Driven Analysis of Fluorination of Ligands of Aminergic G Protein Coupled Receptors

inferred← citeshttps://doi.org/10.3390/metabo14100519openalex-snapshot

Non-Nucleoside Lycorine-Based Analogs as Potential DENV/ZIKV NS5 Dual Inhibitors: Structure-Based Virtual Screening and Chemoinformatic Analysis

inferred← citeshttps://doi.org/10.3390/molecules24224185openalex-snapshot

Identifying Promiscuous Compounds with Activity against Different Target Classes

inferred← citeshttps://doi.org/10.3390/molecules26164916openalex-snapshot

Interpretation of Ligand-Based Activity Cliff Prediction Models Using the Matched Molecular Pair Kernel

inferred← citeshttps://doi.org/10.3390/molecules26175253openalex-snapshot

Congenericity of Claimed Compounds in Patent Applications

inferred← citeshttps://doi.org/10.3390/molecules26175291openalex-snapshot

Automatic Identification of Analogue Series from Large Compound Data Sets: Methods and Applications

inferred← citeshttps://doi.org/10.3390/molecules28020490openalex-snapshot

Isomeric Activity Cliffs—A Case Study for Fluorine Substitution of Aminergic G Protein-Coupled Receptor Ligands

inferred← citeshttps://doi.org/10.4155/fmc-2018-0299openalex-snapshot

Second-generation Activity Cliffs Identified on the Basis of Target set-dependent Potency Difference Criteria

inferred← citeshttps://doi.org/10.4155/fmc-2020-0157openalex-snapshot

Evidence for the Presence of Core structure-dependent Activity Cliffs

inferred← citeshttps://doi.org/10.4155/fmc.13.173openalex-snapshot

Chemoinformatic Characterization of Activity and Selectivity Switches of Antiprotozoal Compounds

inferred← citeshttps://doi.org/10.4155/fmc.13.208openalex-snapshot

Improving Data Mining Strategies for Drug Design

inferred← citeshttps://doi.org/10.4155/fmc.14.94openalex-snapshot

Evolution of the Activity Cliff Concept for Structure–Activity Relationship Analysis and Drug Discovery

inferred← citeshttps://doi.org/10.4155/fmc.15.51openalex-snapshot

Activity and Property Landscape Modeling is at the Interface of Chemoinformatics and Medicinal Chemistry

inferred← citeshttps://doi.org/10.4155/fmc.15.89openalex-snapshot

Monitoring Global Growth of Activity Cliff Information over Time and Assessing Activity Cliff Frequencies and Distributions

inferred← citeshttps://doi.org/10.4155/fsoa-2016-0058openalex-snapshot

Analog Series-Based Scaffolds: Computational Design and Exploration of a New Type of Molecular Scaffolds for Medicinal Chemistry

inferred← citeshttps://doi.org/10.4155/fsoa-2017-0001openalex-snapshot

Entering the ‘Big Data’ Era in Medicinal Chemistry: Molecular Promiscuity Analysis Revisited

inferred← citeshttps://doi.org/10.4155/fsoa-2017-0065openalex-snapshot

From Activity Cliffs to Promiscuity Cliffs

inferred← citeshttps://doi.org/10.4155/fsoa-2017-0102openalex-snapshot

Computational Design of New Molecular Scaffolds for Medicinal Chemistry, Part II: Generalization of Analog Series-Based Scaffolds

inferred← citeshttps://doi.org/10.4155/fsoa-2018-0089openalex-snapshot

Systematic Identification of Target Set-Dependent Activity Cliffs

inferred← citeshttps://doi.org/10.5936/csbj.201401003openalex-snapshot

EXPLORING COMPOUND PROMISCUITY PATTERNS AND MULTI-TARGET ACTIVITY SPACES

inferred← citeshttps://doi.org/10.60084/hjas.v4i2.462openalex-snapshot

Activity Cliffs and Machine Learning Generalization in QSAR: Why Similar Molecules Remain Difficult to Predict

inferred← citeshttps://doi.org/10.6084/m9.figshare.13212631openalex-snapshot

Additional file 1 of Memory-assisted reinforcement learning for diverse molecular de novo design

inferred← citeshttps://doi.org/10.6084/m9.figshare.15047880openalex-snapshot

Additional file 1 of “Molecular Anatomy”: a new multi-dimensional hierarchical scaffold analysis tool

inferred← citeshttps://doi.org/10.6084/m9.figshare.26559899openalex-snapshot

Additional file 1 of Large-scale prediction of activity cliffs using machine and deep learning methods of increasing complexity

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