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

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What this work says

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

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Critical evaluation of search algorithms for automated molecular docking and database screening

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Docking small ligands in flexible binding sites

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

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Predicting structural effects in HIV-1 protease mutant complexes with flexible ligand docking and protein side-chain optimization

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Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation

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The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme

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An iterative knowledge‐based scoring function to predict protein–ligand interactions: I. Derivation of interaction potentials

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An iterative knowledge‐based scoring function to predict protein–ligand interactions: II. Validation of the scoring function

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Automated docking with grid‐based energy evaluation

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ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation

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Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock

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Principles of docking: An overview of search algorithms and a guide to scoring functions

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Modeling correlated main‐chain motions in proteins for flexible molecular recognition

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Comparing protein–ligand docking programs is difficult

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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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A geometric approach to macromolecule-ligand interactions

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“Soft docking”: Matching of molecular surface cubes

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Protein Flexibility in Ligand Docking and Virtual Screening to Protein Kinases

inferredcites →https://doi.org/10.1016/j.jmb.2004.02.015openalex-snapshot

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

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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

inferredcites →https://doi.org/10.1016/s1093-3263(00)00036-xopenalex-snapshot

A method for including protein flexibility in protein-ligand docking: improving tools for database mining and virtual screening

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Using CONCORD to construct a large database of three-dimensional coordinates from connection tables

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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/ja0469378openalex-snapshot

Incorporating Protein Flexibility in Structure-Based Drug Discovery: Using HIV-1 Protease as a Test Case

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

Lessons in Molecular Recognition: The Effects of Ligand and Protein Flexibility on Molecular Docking Accuracy

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Unveiling the Full Potential of Flexible Receptor Docking Using Multiple Crystallographic Structures

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/jm990073xopenalex-snapshot

Evaluation of PMF Scoring in Docking Weak Ligands to the FK506 Binding Protein

inferredcites →https://doi.org/10.1021/jm990322hopenalex-snapshot

Developing a Dynamic Pharmacophore Model for HIV-1 Integrase

inferredcites →https://doi.org/10.1021/jm990352kopenalex-snapshot

Consensus Scoring: A Method for Obtaining Improved Hit Rates from Docking Databases of Three-Dimensional Structures into Proteins

inferredcites →https://doi.org/10.1023/a:1008015827877openalex-snapshot

The sensitivity of the results of molecular docking to induced fit effects: Application to thrombin, thermolysin and neuraminidase

inferredcites →https://doi.org/10.1023/a:1011115820450openalex-snapshot

DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases

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

Implications of protein flexibility for drug discovery

inferredcites →https://doi.org/10.1089/cmb.1998.5.631openalex-snapshot

A Method for Biomolecular Structural Recognition and Docking Allowing Conformational Flexibility

inferredcites →https://doi.org/10.1093/comjnl/7.4.308openalex-snapshot

A Simplex Method for Function Minimization

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The Protein Data Bank

inferredcites →https://doi.org/10.1096/fasebj.11.2.9039959openalex-snapshot

Computation of the binding of fully flexible peptides to proteins with flexible side chains

inferredcites →https://doi.org/10.1107/s0567739477000862openalex-snapshot

A different best rigid-body molecular fit routine

inferredcites →https://doi.org/10.1146/annurev.biophys.32.110601.142532openalex-snapshot

Molecular Recognition and Docking Algorithms

inferredcites →https://doi.org/10.2174/1381612023394232openalex-snapshot

Protein Flexibility is an Important Component of Structure-Based Drug Discovery

inferredcites →https://doi.org/10.2174/1381612033454595openalex-snapshot

Conformational Flexibility Models for the Receptor in Structure Based Drug Design

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

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Managing protein flexibility in docking and its applications

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Search strategies and evaluation in protein–protein docking: principles, advances and challenges

inferred← citeshttps://doi.org/10.1016/j.ejmech.2012.09.029openalex-snapshot

Exploring the PDE5 H-pocket by ensemble docking and structure-based design and synthesis of novel β-carboline derivatives

inferred← citeshttps://doi.org/10.1016/j.ejmech.2012.10.024openalex-snapshot

Application of a post-docking procedure based on MM-PBSA and MM-GBSA on single and multiple protein conformations

inferred← citeshttps://doi.org/10.1016/j.eswa.2014.05.038openalex-snapshot

A strategic solution to optimize molecular docking simulations using Fully-Flexible Receptor models

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From prediction to validation: Critical assessment of computational plastizyme discovery pipelines for plastic biodegradation

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Computational Analysis of Antimicrobial Peptides Targeting Agglutinin-Like Protein 3 (Als3) and β-Glucan Synthase in Denture-Associated Candidiasis

inferred← citeshttps://doi.org/10.1016/j.jmb.2017.06.013openalex-snapshot

3D-NuS: A Web Server for Automated Modeling and Visualization of Non-Canonical 3-D imensional Nu cleic Acid S tructures

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Binding and Transport of Carboxylated Drugs by the Multidrug Transporter AcrB

inferred← citeshttps://doi.org/10.1016/j.jmgm.2008.12.005openalex-snapshot

Molecular modeling of the heterodimer of human CFTR’s nucleotide-binding domains using a protein–protein docking approach

inferred← citeshttps://doi.org/10.1016/j.jmgm.2010.11.004openalex-snapshot

2,4-Diamino-5-(2′-arylpropargyl)pyrimidine derivatives as new nonclassical antifolates for human dihydrofolate reductase inhibition

inferred← citeshttps://doi.org/10.1016/j.jmgm.2011.01.002openalex-snapshot

An inverse docking approach for identifying new potential anti-cancer targets

inferred← citeshttps://doi.org/10.1016/j.jmgm.2011.09.006openalex-snapshot

Binding of GSH conjugates to π-GST: A cross-docking approach

inferred← citeshttps://doi.org/10.1016/j.jmgm.2016.05.001openalex-snapshot

Visualizing ensembles in structural biology

inferred← citeshttps://doi.org/10.1016/j.jmgm.2019.06.011openalex-snapshot

On the relationship between docking scores and protein conformational changes in HIV-1 protease

inferred← citeshttps://doi.org/10.1016/j.jpha.2026.101681openalex-snapshot

AI for TCM: From target identification to drug design

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Multi-target QSAR modelling of chemo-genomic data analysis based on Extreme Learning Machine

inferred← citeshttps://doi.org/10.1016/j.mex.2022.101788openalex-snapshot

Consensus combining outcomes of multiple ensemble dockings: examples using dDAT crystalized complexes

inferred← citeshttps://doi.org/10.1016/j.molstruc.2014.05.073openalex-snapshot

Supramolecular complex formed by DNA oligonucleotide and thiacalix[4]arene. NMR-spectroscopy and molecular docking

inferred← citeshttps://doi.org/10.1016/j.molstruc.2015.05.007openalex-snapshot

Protein flexibility oriented virtual screening strategy for JAK2 inhibitors

inferred← citeshttps://doi.org/10.1016/j.molstruc.2024.141068openalex-snapshot

Synthesis, evaluation of α-glucosidase inhibitory and antimicrobial activities of novel N-(5-arylidene-4-oxo-2-thioxothiazolidin-3-yl)-2-(naphthalen-1-yl)acetamide derivatives

inferred← citeshttps://doi.org/10.1016/j.sbi.2008.01.004openalex-snapshot

Flexible ligand docking to multiple receptor conformations: a practical alternative

inferred← citeshttps://doi.org/10.1016/j.sbi.2011.04.001openalex-snapshot

Constructing ensembles for intrinsically disordered proteins

inferred← citeshttps://doi.org/10.1016/j.semcancer.2014.03.002openalex-snapshot

Atomic basis of CRM1-cargo recognition, release and inhibition

inferred← citeshttps://doi.org/10.1016/j.virusres.2022.198769openalex-snapshot

Anurans against SARS-CoV-2: A review of the potential antiviral action of anurans cutaneous peptides

inferred← citeshttps://doi.org/10.1016/s1574-1400(10)06014-7openalex-snapshot

Mean-Force Scoring Functions for Protein–Ligand Binding

inferred← citeshttps://doi.org/10.1017/qrd.2022.20openalex-snapshot

Computational drug discovery under RNA times

inferred← citeshttps://doi.org/10.1017/qrd.2022.20.pr1openalex-snapshot

Review: Computational drug discovery under RNA times — R0/PR1

inferred← citeshttps://doi.org/10.1017/qrd.2022.20.pr2openalex-snapshot

Review: Computational drug discovery under RNA times — R0/PR2

inferred← citeshttps://doi.org/10.1017/qrd.2022.20.pr3openalex-snapshot

Decision: Computational drug discovery under RNA times — R0/PR3

inferred← citeshttps://doi.org/10.1017/qrd.2022.20.pr4openalex-snapshot

Decision: Computational drug discovery under RNA times — R1/PR4

inferred← citeshttps://doi.org/10.1017/qrd.2022.20.pr5openalex-snapshot

Decision: Computational drug discovery under RNA times — R2/PR5

inferred← citeshttps://doi.org/10.1017/s0033583512000066openalex-snapshot

Protein flexibility in docking and surface mapping

inferred← citeshttps://doi.org/10.1021/acs.biochem.3c00562openalex-snapshot

Antimicrobial Peptide Recognition Motif of the Substrate Binding Protein SapA from Nontypeable Haemophilus influenzae

inferred← citeshttps://doi.org/10.1021/acs.chemrev.5b00562openalex-snapshot

Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell

inferred← citeshttps://doi.org/10.1021/acs.jafc.4c03761openalex-snapshot

QPH-FR: A Novel Quinoa Peptide Enhances Chemosensitivity by Targeting Leucine-Rich Repeat-Containing G Protein-Coupled Receptor 5 in Colorectal Cancer

inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00411openalex-snapshot

Three-Dimensional Convolutional Neural Networks and a Cross-Docked Data Set for Structure-Based Drug Design

inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00341openalex-snapshot

NLDock: a Fast Nucleic Acid–Ligand Docking Algorithm for Modeling RNA/DNA–Ligand Complexes

inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00511openalex-snapshot

Improving Structure-Based Virtual Screening with Ensemble Docking and Machine Learning

inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00924openalex-snapshot

Cosolvent and Dynamic Effects in Binding Pocket Search by Docking Simulations

inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00895openalex-snapshot

Holo Protein Conformation Generation from Apo Structures by Ligand Binding Site Refinement

inferred← citeshttps://doi.org/10.1021/acs.jcim.4c01810openalex-snapshot

Toward the Prediction of Binding Events in Very Flexible, Allosteric, Multidomain Proteins

inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00169openalex-snapshot

A Pipeline To Enhance Ligand Virtual Screening: Integrating Molecular Dynamics and Fingerprints for Ligand and Proteins

inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00210openalex-snapshot

ASCONA: Rapid Detection and Alignment of Protein Binding Site Conformations

inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00275openalex-snapshot

HybridDock: A Hybrid Protein–Ligand Docking Protocol Integrating Protein- and Ligand-Based Approaches

inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00299openalex-snapshot

Inexpensive Method for Selecting Receptor Structures for Virtual Screening

inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00344openalex-snapshot

Protein Flexibility in Docking-Based Virtual Screening: Discovery of Novel Lymphoid-Specific Tyrosine Phosphatase Inhibitors Using Multiple Crystal Structures

inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00387openalex-snapshot

CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge

inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00484openalex-snapshot

Ensemble-Based Virtual Screening Led to the Discovery of New Classes of Potent Tyrosinase Inhibitors

inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00504openalex-snapshot

Iterative Knowledge-Based Scoring Functions Derived from Rigid and Flexible Decoy Structures: Evaluation with the 2013 and 2014 CSAR Benchmarks

inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00523openalex-snapshot

CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma

inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00572openalex-snapshot

Ultra-High-Throughput Structure-Based Virtual Screening for Small-Molecule Inhibitors of Protein–Protein Interactions

inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00587openalex-snapshot

Adaptive BP-Dock: An Induced Fit Docking Approach for Full Receptor Flexibility

inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00598openalex-snapshot

Structure-Based Consensus Scoring Scheme for Selecting Class A Aminergic GPCR Fragments

inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00684openalex-snapshot

Knowledge-Based Methods To Train and Optimize Virtual Screening Ensembles

inferred← citeshttps://doi.org/10.1021/acs.jcim.5c00427openalex-snapshot

Improved Prediction of Drug–Protein Interactions through Physics-Based Few-Shot Learning

inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00064openalex-snapshot

Protease Inhibitors in View of Peptide Substrate Databases

inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00163openalex-snapshot

PL-PatchSurfer2: Improved Local Surface Matching-Based Virtual Screening Method That Is Tolerant to Target and Ligand Structure Variation

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.6c00077openalex-snapshot

Absolute Binding Free Energy Calculations between the SARS-CoV-2 Main Protease and 130 Drug Leads Using Implicit Ligand Theory

inferred← citeshttps://doi.org/10.1021/acs.jcim.6c00967openalex-snapshot

A Reproducible Hierarchical Virtual Screening Framework Integrating Scaffold-Aware Machine Learning, Ensemble Docking, and Molecular Dynamics: Application to IDO1

inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00277openalex-snapshot

ProSelection: A Novel Algorithm to Select Proper Protein Structure Subsets for in Silico Target Identification and Drug Discovery Research

inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00564openalex-snapshot

Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations

inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00142openalex-snapshot

Hierarchical Flexible Peptide Docking by Conformer Generation and Ensemble Docking of Peptides

inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00730openalex-snapshot

Holo-like and Druggable Protein Conformations from Enhanced Sampling of Binding Pocket Volume and Shape

inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00963openalex-snapshot

Applications of Ensemble Docking in Potential Inhibitor Screening for Mycobacterium tuberculosis Isocitrate Lyase Using a Local Plant Database

inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00686openalex-snapshot

CANDOCK: Chemical Atomic Network-Based Hierarchical Flexible Docking Algorithm Using Generalized Statistical Potentials

inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00905openalex-snapshot

Highly Flexible Ligand Docking: Benchmarking of the DockThor Program on the LEADS-PEP Protein–Peptide Data Set

inferred← citeshttps://doi.org/10.1021/acs.jctc.7b00500openalex-snapshot

POVME 3.0: Software for Mapping Binding Pocket Flexibility

inferred← citeshttps://doi.org/10.1021/acs.jmedchem.0c01316openalex-snapshot

Discovery of Small-Molecule Inhibitors of Receptor Activator of Nuclear Factor-κB Ligand with a Superior Therapeutic Index

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.1c00016openalex-snapshot

Rapid Identification of Inhibitors and Prediction of Ligand Selectivity for Multiple Proteins: Application to Protein Kinases

inferred← citeshttps://doi.org/10.1021/acs.jpcb.1c01826openalex-snapshot

Introduction of a Glycine Linker Connecting the Heavy and Light Chains in Synthetic Cardosin B-Derived Rennet Changes the Specificity of Subpocket S3′

inferred← citeshttps://doi.org/10.1021/acs.jpcb.3c04421openalex-snapshot

Iterative Knowledge-Based Scoring Function for Protein–Ligand Interactions by Considering Binding Affinity Information

inferred← citeshttps://doi.org/10.1021/acs.jpcb.4c02047openalex-snapshot

PepBinding: A Workflow for Predicting Peptide Binding Structures by Combining Peptide Docking and Peptide Gaussian Accelerated Molecular Dynamics Simulations

inferred← citeshttps://doi.org/10.1021/acsinfecdis.5c00329openalex-snapshot

Chemical and Genetic Validation of an Essential Calcium Entry Channel of Trypanosoma brucei as a Therapeutic Target

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

RosettaLigandEnsemble: A Small-Molecule Ensemble-Driven Docking Approach

inferred← citeshttps://doi.org/10.1021/ci100101wopenalex-snapshot

HIV-1 TAR RNA Spontaneously Undergoes Relevant Apo-to-Holo Conformational Transitions in Molecular Dynamics and Constrained Geometrical Simulations

inferred← citeshttps://doi.org/10.1021/ci100340wopenalex-snapshot

Sequence, Structure, and Active Site Analyses of p38 MAP Kinase: Exploiting DFG-out Conformation as a Strategy to Design New Type II Leads

inferred← citeshttps://doi.org/10.1021/ci2000727openalex-snapshot

Scoring and Lessons Learned with the CSAR Benchmark Using an Improved Iterative Knowledge-Based Scoring Function

inferred← citeshttps://doi.org/10.1021/ci200080gopenalex-snapshot

Construction and Test of Ligand Decoy Sets Using MDock: Community Structure–Activity Resource Benchmarks for Binding Mode Prediction

inferred← citeshttps://doi.org/10.1021/ci200117nopenalex-snapshot

Predictive Power of Molecular Dynamics Receptor Structures in Virtual Screening

inferred← citeshttps://doi.org/10.1021/ci200168bopenalex-snapshot

Pocket-Space Maps To Identify Novel Binding-Site Conformations in Proteins

inferred← citeshttps://doi.org/10.1021/ci2002796openalex-snapshot

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

inferred← citeshttps://doi.org/10.1021/ci2005934openalex-snapshot

Potential and Limitations of Ensemble Docking

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/ci300342zopenalex-snapshot

GalaxyDock: Protein–Ligand Docking with Flexible Protein Side-chains

inferred← citeshttps://doi.org/10.1021/ci300432wopenalex-snapshot

Cyclophilin A Inhibition: Targeting Transition-State-Bound Enzyme Conformations for Structure-Based Drug Design

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/ci300478yopenalex-snapshot

Incorporating Backbone Flexibility in MedusaDock Improves Ligand-Binding Pose Prediction in the CSAR2011 Docking Benchmark

inferred← citeshttps://doi.org/10.1021/ci400040dopenalex-snapshot

Docking Challenge: Protein Sampling and Molecular Docking Performance

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