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Ensemble Docking into Multiple Crystallographically Derived Protein Structures: An Evaluation Based on the Statistical Analysis of Enrichments

https://doi.org/10.1021/ci900407c
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What this work says

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

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Principal Component Analysis
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Combining docking and molecular dynamic simulations in drug design
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Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking
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Energy minimization in low‐frequency normal modes to efficiently allow for global flexibility during systematic protein–protein docking
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Molecular docking to ensembles of protein structures 1 1Edited by B. Honig
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FlexE: efficient molecular docking considering protein structure variations
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Prediction of the binding sites of huperzine A in acetylcholinesterase by docking studies
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How to do an evaluation: pitfalls and traps
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What do we know and when do we know it?
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Improving database enrichment through ensemble docking
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A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE)
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Recommendations for evaluation of computational methods
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Flexible ligand–flexible protein docking in protein kinase systems
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BACE-1 inhibition by a series of ψ[CH2NH] reduced amide isosteres
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β-Secretase (BACE-1) inhibitors: Accounting for 10s loop flexibility using rigid active sites
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Protein Flexibility in Ligand Docking and Virtual Screening to Protein Kinases
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Testing a Flexible-receptor Docking Algorithm in a Model Binding Site
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The Relationship between the Flexibility of Proteins and their Conformational States on Forming Protein–Protein Complexes with an Application to Protein–Protein Docking
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An introduction to ROC analysis
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Functional Plasticity in the Substrate Binding Site of β-Secretase
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Protein flexibility and drug design: how to hit a moving target
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Identification of a Minimal Subset of Receptor Conformations for Improved Multiple Conformation Docking and Two-Step Scoring
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ZINC − A Free Database of Commercially Available Compounds for Virtual Screening
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Docking Ligands into Flexible and Solvated Macromolecules. 1. Development and Validation of FITTED 1.0
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Evaluating Virtual Screening Methods: Good and Bad Metrics for the “Early Recognition” Problem
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Inclusion of Solvation and Entropy in the Knowledge-Based Scoring Function for Protein−Ligand Interactions
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Determination of the Active Site Protonation State of β-Secretase from Molecular Dynamics Simulation and Docking Experiment: Implications for Structure-Based Inhibitor Design
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Representing Receptor Flexibility in Ligand Docking through Relevant Normal Modes
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Exploring Experimental Sources of Multiple Protein Conformations in Structure-Based Drug Design
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Protein Side-Chain Dynamics and Residual Conformational Entropy
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Design and Synthesis of Hydroxyethylene-Based Peptidomimetic Inhibitors of Human β-Secretase
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Unveiling the Full Potential of Flexible Receptor Docking Using Multiple Crystallographic Structures
inferredcites →https://doi.org/10.1021/jm049133bopenalex-snapshot
Virtual Screening for β-Secretase (BACE1) Inhibitors Reveals the Importance of Protonation States at Asp32 and Asp228
inferredcites →https://doi.org/10.1021/jm049756popenalex-snapshot
Soft Docking and Multiple Receptor Conformations in Virtual Screening
inferredcites →https://doi.org/10.1021/jm050540copenalex-snapshot
Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects
inferredcites →https://doi.org/10.1021/jm0602864openalex-snapshot
Naphthyl and Coumarinyl Biarylpiperazine Derivatives as Highly Potent Human β-Secretase Inhibitors. Design, Synthesis, and Enzymatic BACE-1 and Cell Assays
inferredcites →https://doi.org/10.1021/jm0607451openalex-snapshot
Acylguanidines as Small-Molecule β-Secretase Inhibitors
inferredcites →https://doi.org/10.1021/jm0608356openalex-snapshot
Benchmarking Sets for Molecular Docking
inferredcites →https://doi.org/10.1021/jm060999mopenalex-snapshot
Prediction of Protein−Ligand Interactions. Docking and Scoring: Successes and Gaps
inferredcites →https://doi.org/10.1021/jm061046ropenalex-snapshot
Discovery of Oxadiazoyl Tertiary Carbinamine Inhibitors of β-Secretase (BACE-1)
inferredcites →https://doi.org/10.1021/jm061242yopenalex-snapshot
Design, Synthesis, and Crystal Structure of Hydroxyethyl Secondary Amine-Based Peptidomimetic Inhibitors of Human β-Secretase
inferredcites →https://doi.org/10.1021/jm8001197openalex-snapshot
Ensemble-Based Virtual Screening Reveals Potential Novel Antiviral Compounds for Avian Influenza Neuraminidase
inferredcites →https://doi.org/10.1021/jm800562dopenalex-snapshot
Target Flexibility: An Emerging Consideration in Drug Discovery and Design
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Four-Dimensional Docking: A Fast and Accurate Account of Discrete Receptor Flexibility in Ligand Docking
inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot
The Protein Data Bank
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BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities
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The meaning and use of the area under a receiver operating characteristic (ROC) curve.
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On the Characterization of Protein Native State Ensembles
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Conformational Flexibility Models for the Receptor in Structure Based Drug Design

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Integrated Virtual Screening of Anthraquinone Derivatives for Anticancer Drug Discovery
inferred← citeshttps://doi.org/10.1186/1748-7188-8-19openalex-snapshot
MORPH-PRO: a novel algorithm and web server for protein morphing
inferred← citeshttps://doi.org/10.1371/journal.pone.0018845openalex-snapshot
Systematic Exploitation of Multiple Receptor Conformations for Virtual Ligand Screening
inferred← citeshttps://doi.org/10.1371/journal.pone.0048008openalex-snapshot
ReFlexIn: A Flexible Receptor Protein-Ligand Docking Scheme Evaluated on HIV-1 Protease
inferred← citeshttps://doi.org/10.1371/journal.pone.0132072openalex-snapshot
In Silico Identification and In Vitro and In Vivo Validation of Anti-Psychotic Drug Fluspirilene as a Potential CDK2 Inhibitor and a Candidate Anti-Cancer Drug
inferred← citeshttps://doi.org/10.1517/17460441.2015.1094458openalex-snapshot
Understanding the challenges of protein flexibility in drug design
inferred← citeshttps://doi.org/10.18632/oncotarget.25966openalex-snapshot
Online structure-based screening of purchasable approved drugs and natural compounds: retrospective examples of drug repositioning on cancer targets
inferred← citeshttps://doi.org/10.21203/rs.3.rs-138297/v1openalex-snapshot
Enrichments of Ensemble Docking Strategy Based on the Bayesian Model
inferred← citeshttps://doi.org/10.21203/rs.3.rs-352349/v1openalex-snapshot
Improving Reliability of the Virtual Screening Process for Human Dihydroorotate Dehydrogenase Enzyme by Combination of the Ensemble and Consensus Docking Approaches
inferred← citeshttps://doi.org/10.2174/0115734072327345241121185704openalex-snapshot
A Comprehensive Review on Integrated Approach for Discovery and Development of Novel Bioactive Compounds: From Natural Resources to Targeted Therapeutics
inferred← citeshttps://doi.org/10.2174/156802611794863571openalex-snapshot
Protein Flexibility and Ligand Recognition: Challenges for Molecular Modeling
inferred← citeshttps://doi.org/10.2174/1568026614666140929124445openalex-snapshot
Structure-Based Virtual Screening for Drug Discovery: Principles, Applications and Recent Advances
inferred← citeshttps://doi.org/10.2174/1574893615666191219094216openalex-snapshot
Relevance of Molecular Docking Studies in Drug Designing
inferred← citeshttps://doi.org/10.22159/ijpps.2021v13i8.41956openalex-snapshot
DATABASE ENRICHMENTS OF MAO-B THROUGH ENSEMBLE DOCKING
inferred← citeshttps://doi.org/10.22201/fesz.23958723e.2018.0.143openalex-snapshot
Acoplamiento Molecular: Avances Recientes y Retos
inferred← citeshttps://doi.org/10.26434/chemrxiv-2022-g7srcopenalex-snapshot
FLEXIBLE TOPOLOGY: A NEW METHOD FOR DYNAMIC DRUG DESIGN
inferred← citeshttps://doi.org/10.26434/chemrxiv-2024-h23vmopenalex-snapshot
Chasing new targets to fight antimicrobial resistance: identification of small molecules affecting the interaction of human hemoglobin with the IsdB hemophore of Staphylococcus aureus
inferred← citeshttps://doi.org/10.26481/dis.20141008jdopenalex-snapshot
Application of in-silico approaches to cardiovascular disease
inferred← citeshttps://doi.org/10.26512/2014.11.d.16078openalex-snapshot
Expressão e caracterização enzimática da Tioredoxina redutase (Trr1) e do seu substrato Tioredoxina (Trx1) e identificação de novas drogas por modelagem molecular do alvo Trr1 do fungo patogênico Cryptococcus neoformans
inferred← citeshttps://doi.org/10.3390/ijms22062846openalex-snapshot
Predicting Potential Endocrine Disrupting Chemicals Binding to Estrogen Receptor α (ERα) Using a Pipeline Combining Structure-Based and Ligand-Based in Silico Methods
inferred← citeshttps://doi.org/10.3390/ijms232213946openalex-snapshot
Identification of Active Compounds against Melanoma Growth by Virtual Screening for Non-Classical Human DHFR Inhibitors
inferred← citeshttps://doi.org/10.3390/ijms24098161openalex-snapshot
Identification of Catechins’ Binding Sites in Monomeric Aβ42 through Ensemble Docking and MD Simulations
inferred← citeshttps://doi.org/10.3390/life10050057openalex-snapshot
Targeting the C-Terminal Domain Small Phosphatase 1
inferred← citeshttps://doi.org/10.3390/molecules200915842openalex-snapshot
p38α MAPK and Type I Inhibitors: Binding Site Analysis and Use of Target Ensembles in Virtual Screening
inferred← citeshttps://doi.org/10.3390/molecules201018732openalex-snapshot
Charting a Path to Success in Virtual Screening
inferred← citeshttps://doi.org/10.3390/molecules22112029openalex-snapshot
Dynamic Docking: A Paradigm Shift in Computational Drug Discovery
inferred← citeshttps://doi.org/10.3390/molecules24152690openalex-snapshot
Comparison of Data Fusion Methods as Consensus Scores for Ensemble Docking
inferred← citeshttps://doi.org/10.3390/molecules25143165openalex-snapshot
Design, Synthesis and Biological Evaluation of Novel Triazole N-acylhydrazone Hybrids for Alzheimer’s Disease
inferred← citeshttps://doi.org/10.3390/ph4050758openalex-snapshot
Prediction of Positions of Active Compounds Makes It Possible To Increase Activity in Fragment-Based Drug Development
inferred← citeshttps://doi.org/10.4018/978-1-5225-0115-2.ch011openalex-snapshot
Recent Advancements in Docking Methodologies
inferred← citeshttps://doi.org/10.4018/978-1-5225-0549-5.ch033openalex-snapshot
Recent Advancements in Docking Methodologies
inferred← citeshttps://doi.org/10.4155/fmc-2019-0022openalex-snapshot
Ensemble Docking-Based Virtual Screening Toward Identifying Inhibitors against Wee1 Kinase
inferred← citeshttps://doi.org/10.57709/5135066openalex-snapshot
Using Molecular Dynamics to Elucidate the Mechanism of Cyclophilin
inferred← citeshttps://doi.org/10.6092/unibo/amsdottorato/6330openalex-snapshot
Computational strategies to include protein flexibility in Ligand Docking and Virtual Screening
inferred← citeshttps://doi.org/10.6092/unibo/amsdottorato/8624openalex-snapshot
Fully Flexible Binding of Taxane-Site Ligands to Tubulin via Enhanced Sampling MD Simulations
inferred← citeshttps://doi.org/10.70675/de51bc89z33fez456fz9467z959329cc603bopenalex-snapshot
Optimisation de méthodes de criblage virtuel et synthèse de molécules à visée thérapeutique pour le traitement des maladies auto-immunes.
inferred← citeshttps://doi.org/10.7476/9786580216123openalex-snapshot
Aplicações de química teórica no estudo de materiais: métodos in silico para nanomateriais
inferred← citeshttps://doi.org/10.7476/9786580216123.0008openalex-snapshot
Simulação por dinâmica molecular da enzima cruzaína do trypanosoma cruzi
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