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Enrichment of Chemical Libraries Docked to Protein Conformational Ensembles and Application to Aldehyde Dehydrogenase 2

https://doi.org/10.1021/ci5002026

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What this work says

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

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Gaussian docking functions

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Knowledge-based scoring function to predict protein-ligand interactions

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The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure

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Discovery of novel regulators of aldehyde dehydrogenase isoenzymes

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CaMKII knockdown attenuates H2O2-induced phosphorylation of ERK1/2, PKB/Akt, and IGF-1R in vascular smooth muscle cells

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sc-PDB: an Annotated Database of Druggable Binding Sites from the Protein Data Bank

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Ligand Identification Scoring Algorithm (LISA)

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Support Vector Regression Scoring of Receptor–Ligand Complexes for Rank-Ordering and Virtual Screening of Chemical Libraries

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DSX: A Knowledge-Based Scoring Function for the Assessment of Protein–Ligand Complexes

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ZINC: A Free Tool to Discover Chemistry for Biology

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ID-Score: A New Empirical Scoring Function Based on a Comprehensive Set of Descriptors Related to Protein–Ligand Interactions

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DrugScore CSD Knowledge-Based Scoring Function Derived from Small Molecule Crystal Data with Superior Recognition Rate of Near-Native Ligand Poses and Better Affinity Prediction

inferredcites →https://doi.org/10.1021/jm0608356openalex-snapshot

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The Protein Data Bank

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CaMKII regulates retinoic acid receptor transcriptional activity and the differentiation of myeloid leukemia cells

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AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening

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Analysis and update of the human aldehyde dehydrogenase (ALDH) gene family

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Open Babel: An open chemical toolbox

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A Novel Anti-Tumor Inhibitor Identified by Virtual Screen with PLK1 Structure and Zebrafish Assay

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Virtual and Biophysical Screening Targeting the γ-Tubulin Complex – A New Target for the Inhibition of Microtubule Nucleation

inferredcites →https://doi.org/10.2174/138945010790711905openalex-snapshot

Z-DNA Binding Proteins as Targets for Structure-Based Virtual Screening

inferredcites →https://doi.org/10.2174/1568026611313070007openalex-snapshot

Molecular Modeling and Ligand Docking for Solute Carrier (SLC) Transporters

What points at this work

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

inferred← citeshttps://doi.org/10.1002/mco2.195openalex-snapshot

Aldehyde dehydrogenase in solid tumors and other diseases: Potential biomarkers and therapeutic targets

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Statistical analysis of EGFR structures’ performance in virtual screening

inferred← citeshttps://doi.org/10.1016/j.imu.2022.100880openalex-snapshot

Molecular modeling in drug discovery

inferred← citeshttps://doi.org/10.1016/j.tips.2019.08.002openalex-snapshot

Aldehyde Dehydrogenase Inhibitors for Cancer Therapeutics

inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00662openalex-snapshot

Discovery of New Estrogen-Related Receptor α Agonists via a Combination Strategy Based on Shape Screening and Ensemble Docking

inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00261openalex-snapshot

Enhancing Virtual Screening Performance of Protein Kinases with Molecular Dynamics Simulations

inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00749openalex-snapshot

The Development of Target-Specific Pose Filter Ensembles To Boost Ligand Enrichment for Structure-Based Virtual Screening

inferred← citeshttps://doi.org/10.1021/acsomega.2c00032openalex-snapshot

Computational Investigation of Structural Basis for Enhanced Binding of Isoflavone Analogues with Mitochondrial Aldehyde Dehydrogenase

inferred← citeshttps://doi.org/10.1021/jacs.5c16359openalex-snapshot

Unlocking Selenium Chemical Space via a Programmable Synthesis Platform Bearing Cannabinoid Receptor Recognition Motifs

inferred← citeshttps://doi.org/10.1038/s41598-017-18332-8openalex-snapshot

Structural ensemble-based docking simulation and biophysical studies discovered new inhibitors of Hsp90 N-terminal domain

inferred← citeshttps://doi.org/10.1080/13543776.2023.2287515openalex-snapshot

A patent review on aldehyde dehydrogenase inhibitors: an overview of small molecule inhibitors from the last decade

inferred← citeshttps://doi.org/10.1093/nar/gkad1084openalex-snapshot

ATLAS: protein flexibility description from atomistic molecular dynamics simulations

inferred← citeshttps://doi.org/10.1111/imm.13016openalex-snapshot

Aldehyde dehydrogenase in regulatory T‐cell development, immunity and cancer

inferred← citeshttps://doi.org/10.1186/s43556-026-00498-1openalex-snapshot

Artificial intelligence and ultra-high performance computing methods and experiments for drug discovery: virtual screening, deep learning, molecular dynamics simulations, ADMET modelling, and experimental validation

inferred← citeshttps://doi.org/10.2174/0929867330666230408200401openalex-snapshot

Aldehyde Dehydrogenases as Promising Targets for Treating Toxic Aldehyde-related Diseases

inferred← citeshttps://doi.org/10.2197/ipsjtbio.18.20openalex-snapshot

Fast and Accurate Comparison of Protein Conformational Ensembles

inferred← citeshttps://doi.org/10.32657/10220/48075openalex-snapshot

Progesterone receptor ligand binding domain : from conformational dynamics to drug discovery

inferred← citeshttps://doi.org/10.3390/cancers15174419openalex-snapshot

Human Aldehyde Dehydrogenases: A Superfamily of Similar Yet Different Proteins Highly Related to Cancer

inferred← citeshttps://doi.org/10.3390/molecules27248773openalex-snapshot

Virtual Screening of FDA-Approved Drugs for Enhanced Binding with Mitochondrial Aldehyde Dehydrogenase

inferred← citeshttps://doi.org/10.3390/molecules28217325openalex-snapshot

Repurposing Drugs for Inhibition against ALDH2 via a 2D/3D Ligand-Based Similarity Search and Molecular Simulation

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