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Theoretical and computational approaches to ligand-based drug discovery

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What this work says

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

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Handbook of Molecular Descriptors

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Basic Overview of Chemoinformatics.

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Generating Optimal Linear PLS Estimations (GOLPE): An Advanced Chemometric Tool for Handling 3D‐QSAR Problems

inferredcites →https://doi.org/10.1007/978-3-658-19771-1_5openalex-snapshot

Methodology and preliminary results

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Automatic search for maximum similarity between molecular electrostatic potential distributions

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OVID and SUPER: Two overlap programs for drug design

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Chemical forces in terms of the electron density

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Chemoinformatics: a new field with a long tradition

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Pattern recognition based on color-coded quantum mechanical surfaces for molecular alignment

inferredcites →https://doi.org/10.1007/s10822-006-9087-6openalex-snapshot

PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results

inferredcites →https://doi.org/10.1007/s10822-006-9100-0openalex-snapshot

Pushing the boundaries of 3D-QSAR

inferredcites →https://doi.org/10.1007/s10822-008-9188-5openalex-snapshot

A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE)

inferredcites →https://doi.org/10.1016/0003-9861(84)90136-xopenalex-snapshot

Papain hydrolysis of X-phenyl-N-methanesulfonyl glycinates: A quantitative structure-activity relationship and molecular graphics analysis

inferredcites →https://doi.org/10.1016/j.drudis.2008.12.006openalex-snapshot

Molecular fields in drug discovery: getting old or reaching maturity?

inferredcites →https://doi.org/10.1016/s0026-895x(25)14861-xopenalex-snapshot

Molecular Orbital Calculation of Preferred Conformations of Acetylcholine, Muscarine, and Muscarone

inferredcites →https://doi.org/10.1016/s0065-7743(08)61101-xopenalex-snapshot

Glossary of Terms Used in Medicinal Chemistry (IUPAC Recommendations 1997)

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The support vector machine under test

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Linking CoMFA and protein homology models of enzyme–inhibitor interactions: an application to non-steroidal aromatase inhibitors

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Protein flexibility and drug design: how to hit a moving target

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Chemography: The Art of Navigating in Chemical Space

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A Quantum Mechanical/Neural Net Model for Boiling Points with Error Estimation

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Structure-Based Pharmacophore Design and Virtual Screening for Novel Angiotensin Converting Enzyme 2 Inhibitors

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On Outliers and Activity CliffsWhy QSAR Often Disappoints

inferredcites →https://doi.org/10.1021/ci600387ropenalex-snapshot

Graph-Based Molecular Alignment (GMA)

inferredcites →https://doi.org/10.1021/ci700332kopenalex-snapshot

The Trouble with QSAR (or How I Learned To Stop Worrying and Embrace Fallacy)

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

Structure−Activity Landscape Index: Identifying and Quantifying Activity Cliffs

inferredcites →https://doi.org/10.1021/ci800009uopenalex-snapshot

SAMFA: Simplifying Molecular Description for 3D-QSAR

inferredcites →https://doi.org/10.1021/ci8001414openalex-snapshot

Assessing How Well a Modeling Protocol Captures a Structure−Activity Landscape

inferredcites →https://doi.org/10.1021/ci9000508openalex-snapshot

CAUTION: Popular “Benchmark” Data Sets Do Not Distinguish the Merits of 3D QSAR Methods

inferredcites →https://doi.org/10.1021/ci950273ropenalex-snapshot

Identification of Common Functional Configurations Among Molecules

inferredcites →https://doi.org/10.1021/ci990131nopenalex-snapshot

QM/NN QSPR Models with Error Estimation: Vapor Pressure and LogP

inferredcites →https://doi.org/10.1021/cr950066qopenalex-snapshot

Bioisosterism: A Rational Approach in Drug Design

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/ja01280a022openalex-snapshot

The Effect of Structure upon the Reactions of Organic Compounds. Benzene Derivatives

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

Flexible Alignment of Small Molecules

inferredcites →https://doi.org/10.1021/jm00042a012openalex-snapshot

Comparative Molecular Field Analysis Using GRID Force-Field and GOLPE Variable Selection Methods in a Study of Inhibitors of Glycogen Phosphorylase b

inferredcites →https://doi.org/10.1021/jm00050a010openalex-snapshot

Molecular Similarity Indices in a Comparative Analysis (CoMSIA) of Drug Molecules to Correlate and Predict Their Biological Activity

inferredcites →https://doi.org/10.1021/jm000986nopenalex-snapshot

Multiple-Conformation and Protonation-State Representation in 4D-QSAR: The Neurokinin-1 Receptor System

inferredcites →https://doi.org/10.1021/jm00113a022openalex-snapshot

Applications of neural networks in quantitative structure-activity relationships of dihydrofolate reductase inhibitors

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/jm00155a005openalex-snapshot

A quantitative structure-activity relationship and molecular graphics analysis of hydrophobic effects in the interactions of inhibitors with alcohol dehydrogenase

inferredcites →https://doi.org/10.1021/jm00334a001openalex-snapshot

A Mathematical Contribution to Structure-Activity Studies

inferredcites →https://doi.org/10.1021/jm00377a009openalex-snapshot

Structure-activity relationship of the ficin hydrolysis of phenyl hippurates. Comparison with papain, actinidin, and bromelain

inferredcites →https://doi.org/10.1021/jm011005popenalex-snapshot

5D-QSAR: The Key for Simulating Induced Fit?

inferredcites →https://doi.org/10.1021/jm020155copenalex-snapshot

Do Structurally Similar Molecules Have Similar Biological Activity?

inferredcites →https://doi.org/10.1021/jm0210616openalex-snapshot

Field Interaction and Geometrical Overlap: A New Simplex and Experimental Design Based Computational Procedure for Superposing Small Ligand Molecules

inferredcites →https://doi.org/10.1021/jm0497141openalex-snapshot

A Comparison of Methods for Modeling Quantitative Structure−Activity Relationships

inferredcites →https://doi.org/10.1021/jm050185qopenalex-snapshot

Combining Protein Modeling and 6D-QSAR. Simulating the Binding of Structurally Diverse Ligands to the Estrogen Receptor

inferredcites →https://doi.org/10.1021/jm060167oopenalex-snapshot

Do Structurally Similar Ligands Bind in a Similar Fashion?

inferredcites →https://doi.org/10.1021/jm8009958openalex-snapshot

Four-Dimensional Docking: A Fast and Accurate Account of Discrete Receptor Flexibility in Ligand Docking

inferredcites →https://doi.org/10.1021/jm900817uopenalex-snapshot

Three-Dimensional Pharmacophore Methods in Drug Discovery

inferredcites →https://doi.org/10.1021/jm970015gopenalex-snapshot

Comparative Molecular Field Analysis of Haptens Docked to the Multispecific Antibody IgE(Lb4)

inferredcites →https://doi.org/10.1021/jm9810607openalex-snapshot

Self-Organizing Molecular Field Analysis: A Tool for Structure−Activity Studies

inferredcites →https://doi.org/10.1021/jp902968mopenalex-snapshot

Efficient Free Energy Calculations for Compounds with Multiple Stable Conformations Separated by High Energy Barriers

inferredcites →https://doi.org/10.1038/nbt1519openalex-snapshot

Protein promiscuity and its implications for biotechnology

inferredcites →https://doi.org/10.1038/nsb1203-980openalex-snapshot

Announcing the worldwide Protein Data Bank

inferredcites →https://doi.org/10.1063/1.2888998openalex-snapshot

Hamiltonian replica exchange molecular dynamics using soft-core interactions

inferredcites →https://doi.org/10.1073/pnas.89.23.11322openalex-snapshot

Drug design by machine learning: the use of inductive logic programming to model the structure-activity relationships of trimethoprim analogues binding to dihydrofolate reductase.

inferredcites →https://doi.org/10.1073/pnas.93.1.438openalex-snapshot

Structure-activity relationships derived by machine learning: the use of atoms and their bond connectivities to predict mutagenicity by inductive logic programming.

inferredcites →https://doi.org/10.1080/10629360008033231openalex-snapshot

Partial Least Squares Modeling and Genetic Algorithm Optimization in Quantitative Structure-Activity Relationships

inferredcites →https://doi.org/10.1080/10629360902949567openalex-snapshot

How not to develop a quantitative structure–activity or structure–property relationship (QSAR/QSPR)

inferredcites →https://doi.org/10.1111/j.1747-0285.2007.00605.xopenalex-snapshot

Atomic Property Fields: Generalized 3D Pharmacophoric Potential for Automated Ligand Superposition, Pharmacophore Elucidation and 3D QSAR

inferredcites →https://doi.org/10.2751/jcac.2.29openalex-snapshot

Novel alignment method of small molecules using Hopfield Neural Network

inferredcites →https://doi.org/10.2751/jcac.3.63openalex-snapshot

Application of novel molecular alignment method using Hopfield Neural Network to 3D-QSAR

inferredcites →https://doi.org/10.3109/10799899909036635openalex-snapshot

Chance Favors the Prepared Mind - From Serendipity to Rational Drug Design

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

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GA(M)E-QSAR: A Novel, Fully Automatic Genetic-Algorithm-(Meta)-Ensembles Approach for Binary Classification in Ligand-Based Drug Design

inferred← citeshttps://doi.org/10.1021/om400721vopenalex-snapshot

3D-QSAR as a Tool for Understanding and Improving Single-Site Polymerization Catalysts. A Review

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Identification of candidate drugs using tensor-decomposition-based unsupervised feature extraction in integrated analysis of gene expression between diseases and DrugMatrix datasets

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Planejamento e sintese de compostos potencialmente ligantes dos receptores 5-HT2C e H4

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Trends in application of advancing computational approaches in GPCR ligand discovery

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Drug candidate identification based on gene expression of treated cells using tensor decomposition-based unsupervised feature extraction for large-scale data

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Computational methods for the design of potent aromatase inhibitors

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Fragment Based Drug Design: From Experimental to Computational Approaches

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Structure-Based Virtual Screening in Tuberculosis Drug Discovery Pharmacological Constraints Failure Modes and Translational Lessons

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Recent Advances on P-Glycoprotein (ABCB1) Transporter Modelling with In Silico Methods

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Focused Chemical Libraries – Design and Enrichment: An Example of Protein–Protein Interaction Chemical Space

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