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Potential and Limitations of Ensemble Docking

https://doi.org/10.1021/ci2005934

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

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Flexible docking allowing induced fit in proteins: Insights from an open to closed conformational isomers

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Side-chain flexibility in proteins upon ligand binding

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In Pursuit of Fully Flexible Protein‐Ligand Docking: Modeling the Bilateral Mechanism of Binding

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Improved protein–ligand docking using GOLD

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General and targeted statistical potentials for protein–ligand interactions

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Molecular docking of balanol to dynamics snapshots of protein kinase A

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Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking

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In pursuit of virtual lead optimization: The role of the receptor structure and ensembles in accurate docking

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Docking and scoring with alternative side‐chain conformations

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In pursuit of virtual lead optimization: Pruning ensembles of receptor structures for increased efficiency and accuracy during 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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Receiver Operating Characteristic

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Protein–ligand docking with multiple flexible side chains

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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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Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation

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Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles

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Testing a Flexible-receptor Docking Algorithm in a Model Binding Site

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Conformational Changes Observed in Enzyme Crystal Structures upon Substrate Binding

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How Different are Structurally Flexible and Rigid Binding Sites? Sequence and Structural Features Discriminating Proteins that Do and Do not Undergo Conformational Change upon Ligand Binding

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Ligand-Induced Conformational Changes: Improved Predictions of Ligand Binding Conformations and Affinities

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Ligand docking to proteins with discrete side-chain flexibility

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Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation

inferredcites →https://doi.org/10.1021/ci0341619openalex-snapshot

Identification of a Minimal Subset of Receptor Conformations for Improved Multiple Conformation Docking and Two-Step Scoring

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Extended-Connectivity Fingerprints

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Protein Kinases: Docking and Homology Modeling Reliability

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The Ensemble Performance Index: An Improved Measure for Assessing Ensemble Pose Prediction Performance

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inferredcites →https://doi.org/10.1021/ci800081sopenalex-snapshot

Fully Automated Molecular Mechanics Based Induced Fit Protein−Ligand Docking Method

inferredcites →https://doi.org/10.1021/ci8002254openalex-snapshot

Protein−Ligand Docking against Non-Native Protein Conformers

inferredcites →https://doi.org/10.1021/ci800298zopenalex-snapshot

Empirical Scoring Functions for Advanced Protein−Ligand Docking with PLANTS

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Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes

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Better than Random? The Chemotype Enrichment Problem

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Scoring Ensembles of Docked Protein:Ligand Interactions for Virtual Lead Optimization

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Recipes for the Selection of Experimental Protein Conformations for Virtual Screening

inferredcites →https://doi.org/10.1021/ci900407copenalex-snapshot

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

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From atoms and bonds to three-dimensional atomic coordinates: automatic model builders

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Ensemble Docking from Homology Models

inferredcites →https://doi.org/10.1021/ja0260162openalex-snapshot

Computational Drug Design Accommodating Receptor Flexibility: The Relaxed Complex Scheme

inferredcites →https://doi.org/10.1021/ja042260copenalex-snapshot

Representing Receptor Flexibility in Ligand Docking through Relevant Normal Modes

inferredcites →https://doi.org/10.1021/ja0709728openalex-snapshot

Exploring Experimental Sources of Multiple Protein Conformations in Structure-Based Drug Design

inferredcites →https://doi.org/10.1021/jm0300330openalex-snapshot

Information Decay in Molecular Docking Screens against Holo, Apo, and Modeled Conformations of Enzymes

inferredcites →https://doi.org/10.1021/jm030209yopenalex-snapshot

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inferredcites →https://doi.org/10.1021/jm048972vopenalex-snapshot

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inferredcites →https://doi.org/10.1021/jm049092jopenalex-snapshot

Virtual Screening Workflow Development Guided by the “Receiver Operating Characteristic” Curve Approach. Application to High-Throughput Docking on Metabotropic Glutamate Receptor Subtype 4

inferredcites →https://doi.org/10.1021/jm049756popenalex-snapshot

Soft Docking and Multiple Receptor Conformations in Virtual Screening

inferredcites →https://doi.org/10.1021/jm050196jopenalex-snapshot

Receptor Flexibility in de Novo Ligand Design and Docking

inferredcites →https://doi.org/10.1021/jm050540copenalex-snapshot

Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects

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

Benchmarking Sets for Molecular Docking

inferredcites →https://doi.org/10.1021/jm061277yopenalex-snapshot

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inferredcites →https://doi.org/10.1021/jm070593popenalex-snapshot

A Flexible Approach to Induced Fit Docking

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/jm800217kopenalex-snapshot

Flexible Side Chain Models Improve Enrichment Rates in In Silico Screening

inferredcites →https://doi.org/10.1021/jm800562dopenalex-snapshot

Target Flexibility: An Emerging Consideration in Drug Discovery and Design

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/jm801005mopenalex-snapshot

Impact of Plasticity and Flexibility on Docking Results for Cytochrome P450 2D6: A Combined Approach of Molecular Dynamics and Ligand Docking

inferredcites →https://doi.org/10.1021/jp911085dopenalex-snapshot

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inferredcites →https://doi.org/10.1023/a:1007996124545openalex-snapshot

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inferredcites →https://doi.org/10.1023/a:1023844626572openalex-snapshot

Sensitivity of molecular docking to induced fit effects in influenza virus neuraminidase

inferredcites →https://doi.org/10.1038/nrd1129openalex-snapshot

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inferred← citeshttps://doi.org/10.1021/acs.jctc.2c00381openalex-snapshot

SILCS-RNA: Toward a Structure-Based Drug Design Approach for Targeting RNAs with Small Molecules

inferred← citeshttps://doi.org/10.1021/acs.jctc.3c00870openalex-snapshot

PopShift: A Thermodynamically Sound Approach to Estimate Binding Free Energies by Accounting for Ligand-Induced Population Shifts from a Ligand-Free Markov State Model

inferred← citeshttps://doi.org/10.1021/acs.jmedchem.5b00150openalex-snapshot

DARC: Mapping Surface Topography by Ray-Casting for Effective Virtual Screening at Protein Interaction Sites

inferred← citeshttps://doi.org/10.1021/acs.jpcb.8b02756openalex-snapshot

ColDock: Concentrated Ligand Docking with All-Atom Molecular Dynamics Simulation

inferred← citeshttps://doi.org/10.1021/acsomega.0c00522openalex-snapshot

Protein Binding Pocket Optimization for Virtual High-Throughput Screening (vHTS) Drug Discovery

inferred← citeshttps://doi.org/10.1021/acsomega.7b02059openalex-snapshot

RosettaLigandEnsemble: A Small-Molecule Ensemble-Driven Docking Approach

inferred← citeshttps://doi.org/10.1021/bi401119mopenalex-snapshot

Toward an Understanding of Agonist Binding to Human Orexin-1 and Orexin-2 Receptors with G-Protein-Coupled Receptor Modeling and Site-Directed Mutagenesis

inferred← citeshttps://doi.org/10.1021/ci3001088openalex-snapshot

ALiBERO: Evolving a Team of Complementary Pocket Conformations Rather than a Single Leader

inferred← citeshttps://doi.org/10.1021/ci300320topenalex-snapshot

Novel Insights of Structure-Based Modeling for RNA-Targeted Drug Discovery

inferred← citeshttps://doi.org/10.1021/ci3004557openalex-snapshot

Multiple Structures for Virtual Ligand Screening: Defining Binding Site Properties-Based Criteria to Optimize the Selection of the Query

inferred← citeshttps://doi.org/10.1021/ci400087bopenalex-snapshot

The Impact of Molecular Dynamics Sampling on the Performance of Virtual Screening against GPCRs

inferred← citeshttps://doi.org/10.1021/ci400098yopenalex-snapshot

DOLINA – Docking Based on a Local Induced-Fit Algorithm: Application toward Small-Molecule Binding to Nuclear Receptors

inferred← citeshttps://doi.org/10.1021/ci4004927openalex-snapshot

BP-Dock: A Flexible Docking Scheme for Exploring Protein–Ligand Interactions Based on Unbound Structures

inferred← citeshttps://doi.org/10.1021/ci5003735openalex-snapshot

Improving Docking Results via Reranking of Ensembles of Ligand Poses in Multiple X-ray Protein Conformations with MM-GBSA

inferred← citeshttps://doi.org/10.1021/ci500742bopenalex-snapshot

Structure-Based Predictions of Activity Cliffs

inferred← citeshttps://doi.org/10.1038/s41594-018-0062-4openalex-snapshot

High-performance virtual screening by targeting a high-resolution RNA dynamic ensemble

inferred← citeshttps://doi.org/10.1038/s41598-021-04448-5openalex-snapshot

Ensemble learning from ensemble docking: revisiting the optimum ensemble size problem

inferred← citeshttps://doi.org/10.1038/s41598-021-82521-9openalex-snapshot

Reaction mechanism of the farnesyl pyrophosphate C-methyltransferase towards the biosynthesis of pre-sodorifen pyrophosphate by Serratia plymuthica 4Rx13

inferred← citeshttps://doi.org/10.1038/s41598-024-66348-8openalex-snapshot

In silico studies of the open form of human tissue transglutaminase

inferred← citeshttps://doi.org/10.1039/c4ob01874eopenalex-snapshot

Approaches to design non-covalent inhibitors for human granzyme B (hGrB)

inferred← citeshttps://doi.org/10.1039/c7cp08241jopenalex-snapshot

Importance of protein flexibility in molecular recognition: a case study on Type-I1/2 inhibitors of ALK

inferred← citeshttps://doi.org/10.1039/c7ob00910kopenalex-snapshot

New active leads for tuberculosis booster drugs by structure-based drug discovery

inferred← citeshttps://doi.org/10.1039/d1nj02031eopenalex-snapshot

Proposing high-affinity inhibitors from Glycyrrhiza glabra L. against SARS-CoV-2 infection: virtual screening and computational analysis

inferred← citeshttps://doi.org/10.1080/07391102.2020.1814868openalex-snapshot

Deciphering inhibitory activity of flavonoids against tau protein kinases: a coupled molecular docking and quantum chemical study

inferred← citeshttps://doi.org/10.1080/07391102.2023.2291541openalex-snapshot

Identification of potential drug molecules against fibroblast growth factor receptor 3 (FGFR3) by multi-stage computational-biophysics correlate

inferred← citeshttps://doi.org/10.1080/17460441.2019.1604677openalex-snapshot

The compromise of virtual screening and its impact on drug discovery

inferred← citeshttps://doi.org/10.1088/0953-8984/26/50/503103openalex-snapshot

Slow internal protein dynamics in solution

inferred← citeshttps://doi.org/10.1101/039446openalex-snapshot

Best Practices in Docking and Activity Prediction

inferred← citeshttps://doi.org/10.1101/2023.08.09.552513openalex-snapshot

Shifting KRAS hotspot mutations inhibition paradigm in colorectal cancer

inferred← citeshttps://doi.org/10.1142/s0219633619200013openalex-snapshot

Improving ensemble docking for drug discovery by machine learning

inferred← citeshttps://doi.org/10.11606/t.60.2014.tde-31102014-103834openalex-snapshot

Caseína quinase 1 como alvo para o planejamento de fármacos em mal de Alzheimer

inferred← citeshttps://doi.org/10.1186/s12859-016-0941-9openalex-snapshot

Drug repurposing to target Ebola virus replication and virulence using structural systems pharmacology

inferred← citeshttps://doi.org/10.1186/s12859-016-1342-9openalex-snapshot

GPCRs from fusarium graminearum detection, modeling and virtual screening - the search for new routes to control head blight disease

inferred← citeshttps://doi.org/10.1210/en.2019-00382openalex-snapshot

In Silico Predictions of Endocrine Disruptors Properties

inferred← citeshttps://doi.org/10.12955/pmp.v2.179openalex-snapshot

OPTIMIZING MOLECULAR DOCKING PROTOCOLS OF PYRROLE CONTAINING MAO-B INHIBITORS THROUGH CORRELATION COEFFICIENTS

inferred← citeshttps://doi.org/10.12955/pmp.v2.181openalex-snapshot

ANALYSIS OF DIFFERENT PREVENTIVE MEASURES TO IMPROVE HOME OFFICE ERGONOMICS – RESULTS FROM A STUDY ON THE FIRST WAVE OF THE COVID-19 PANDEMIC IN LATVIA

inferred← citeshttps://doi.org/10.13140/2.1.4664.6407openalex-snapshot

IMPROVED INITIAL VALUE PREDICTION FOR GLOBAL MOTION ESTIMATION

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1004619openalex-snapshot

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics

inferred← citeshttps://doi.org/10.1371/journal.pone.0072402openalex-snapshot

New Binding Site Conformations of the Dengue Virus NS3 Protease Accessed by Molecular Dynamics Simulation

inferred← citeshttps://doi.org/10.1371/journal.pone.0099408openalex-snapshot

Ensemble Generation and the Influence of Protein Flexibility on Geometric Tunnel Prediction in Cytochrome P450 Enzymes

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/10.1371/journal.pone.0142926openalex-snapshot

Identification of New Antifungal Compounds Targeting Thioredoxin Reductase of Paracoccidioides Genus

inferred← citeshttps://doi.org/10.1371/journal.pone.0215694openalex-snapshot

Middle-way flexible docking: Pose prediction using mixed-resolution Monte Carlo in estrogen receptor α

inferred← citeshttps://doi.org/10.1371/journal.pone.0319865openalex-snapshot

Novel target identification towards drug repurposing based on biological activity profiles

inferred← citeshttps://doi.org/10.1517/17460441.2015.1094458openalex-snapshot

Understanding the challenges of protein flexibility in drug design

inferred← citeshttps://doi.org/10.21203/rs.3.rs-3937740/v1openalex-snapshot

In silico studies of the open form of human tissue transglutaminase

inferred← citeshttps://doi.org/10.21203/rs.3.rs-9251932/v1openalex-snapshot

Structure-Based Drug Repurposing Reveals State-Independent Binding of MCC950 to the NLRP3 Inflammasome: Implications for Alzheimer’s Disease

inferred← citeshttps://doi.org/10.2174/0109298673374736250527040516openalex-snapshot

Discovery of Putative GyrB Inhibitors against Mycobacterium tuberculosis: A Combined Virtual Screening and Experimental Study

inferred← citeshttps://doi.org/10.2174/0929867324666171107101035openalex-snapshot

The In Silico Drug Discovery Toolbox: Applications in Lead Discovery and Optimization

inferred← citeshttps://doi.org/10.2174/1381612825666190903153043openalex-snapshot

Use of Molecular Dynamics Simulations in Structure-Based Drug Discovery

inferred← citeshttps://doi.org/10.2174/1389450119666181022153016openalex-snapshot

Molecular Docking: Challenges, Advances and its Use in Drug Discovery Perspective

inferred← citeshttps://doi.org/10.2174/156802612804910313openalex-snapshot

Rational Prediction with Molecular Dynamics for Hit Identification

inferred← citeshttps://doi.org/10.2174/1568026614666140929124445openalex-snapshot

Structure-Based Virtual Screening for Drug Discovery: Principles, Applications and Recent Advances

inferred← citeshttps://doi.org/10.2174/1568026622666220701091339openalex-snapshot

Machine Learning and Artificial Intelligence: A Paradigm Shift in Big Data-Driven Drug Design and Discovery

inferred← citeshttps://doi.org/10.2174/1570159x15666171016163510openalex-snapshot

Computer Aided Drug Design and its Application to the Development of Potential Drugs for Neurodegenerative Disorders

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/10.3389/fmolb.2023.1113762openalex-snapshot

Perspective: Structure determination of protein-ligand complexes at room temperature using X-ray diffraction approaches

inferred← citeshttps://doi.org/10.3389/fphar.2018.01089openalex-snapshot

Empirical Scoring Functions for Structure-Based Virtual Screening: Applications, Critical Aspects, and Challenges

inferred← citeshttps://doi.org/10.3390/biology12111442openalex-snapshot

Novel Covalent Modifier-Induced Local Conformational Changes within the Intrinsically Disordered Region of the Androgen Receptor

inferred← citeshttps://doi.org/10.3390/biom8030061openalex-snapshot

Flavonoids as Putative Epi-Modulators: Insight into Their Binding Mode with BRD4 Bromodomains Using Molecular Docking and Dynamics

inferred← citeshttps://doi.org/10.3390/biomedinformatics3040070openalex-snapshot

Transforming Drug Design: Innovations in Computer-Aided Discovery for Biosimilar Agents

inferred← citeshttps://doi.org/10.3390/books978-3-03921-105-0openalex-snapshot

New Approaches for the Discovery of Pharmacologically-Active Natural Compounds

inferred← citeshttps://doi.org/10.3390/ijms19061784openalex-snapshot

Endocrine Disruption at the Androgen Receptor: Employing Molecular Dynamics and Docking for Improved Virtual Screening and Toxicity Prediction

inferred← citeshttps://doi.org/10.3390/ijms20184574openalex-snapshot

Key Topics in Molecular Docking for Drug Design

inferred← citeshttps://doi.org/10.3390/ijms21010005openalex-snapshot

Tetrahydroquinoline-Isoxazole/Isoxazoline Hybrid Compounds as Potential Cholinesterases Inhibitors: Synthesis, Enzyme Inhibition Assays, and Molecular Modeling Studies

inferred← citeshttps://doi.org/10.3390/ijms22094688openalex-snapshot

Advances in Applying Computer-Aided Drug Design for Neurodegenerative Diseases

inferred← citeshttps://doi.org/10.3390/ijms24054401openalex-snapshot

Lessons Learnt from COVID-19: Computational Strategies for Facing Present and Future Pandemics

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/molecules24152690openalex-snapshot

Comparison of Data Fusion Methods as Consensus Scores for Ensemble Docking

inferred← citeshttps://doi.org/10.3390/molecules24203798openalex-snapshot

A Chemosensory GPCR as a Potential Target to Control the Root-Knot Nematode Meloidogyne incognita Parasitism in Plants

inferred← citeshttps://doi.org/10.3390/molecules26175335openalex-snapshot

Structural Insights and Docking Analysis of Adamantane-Linked 1,2,4-Triazole Derivatives as Potential 11β-HSD1 Inhibitors

inferred← citeshttps://doi.org/10.3390/molecules27144568openalex-snapshot

Protein–Ligand Docking in the Machine-Learning Era

inferred← citeshttps://doi.org/10.3390/molecules28010175openalex-snapshot

Comprehensive Survey of Consensus Docking for High-Throughput Virtual Screening

inferred← citeshttps://doi.org/10.3390/ph19070985openalex-snapshot

Evaluation of the Anti-Cancer Effects of KMU-11342 in In Vitro and Ex Vivo Models of Colorectal Cancer

inferred← citeshttps://doi.org/10.4155/fmc.15.150openalex-snapshot

Sampling of Conformational Ensemble for Virtual Screening Using Molecular Dynamics Simulations and Normal Mode Analysis

inferred← citeshttps://doi.org/10.4236/aim.2016.611079openalex-snapshot

Searching for Novel Targets to Control Wheat Head Blight Disease—I-Protein Identification, 3D Modeling and Virtual Screening

inferred← citeshttps://doi.org/10.48175/ijarsct-2581openalex-snapshot

Computer Aided Drug Design

inferred← citeshttps://doi.org/10.48550/arxiv.1811.09366openalex-snapshot

Prediction of Cytochrome P450-Mediated Metabolism Using a Combination of QSAR Derived Reactivity and Induced Fit Docking

inferred← citeshttps://doi.org/10.58920/sciphy01010042openalex-snapshot

Challenges and Opportunities in the Management of Cardiovascular Diseases

inferred← citeshttps://doi.org/10.70675/434de13dz7ff8z46beza24ezfaf0740f7deaopenalex-snapshot

Structure-based design of antiviral drugs against respiratory viruses using in silico approaches

inferred← citeshttps://doi.org/10.70675/9ec10756ze898z4558z9e97zba079af2b3b0openalex-snapshot

Innovative inhibition strategy against functional structural transitions of essential pathogenic factors : Computational applications to Malarial and Neurotransmitter targets

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.

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