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Discovery of a Novel Binding Trench in HIV Integrase
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Outgoing claims: the papers this work cites, builds on, or argues with.
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Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
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Molecular Dynamics Studies of the Wild-Type and Double Mutant HIV-1 Integrase Complexed with the 5CITEP Inhibitor: Mechanism for Inhibition and Drug Resistance
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Mapping Features of HIV-1 Integrase Near Selected Sites on Viral and Target DNA Molecules in an Active Enzyme−DNA Complex by Photo-Cross-Linking
inferredcites →https://doi.org/10.1021/ja001152xopenalex-snapshot
HIV-1 Integrase Inhibitor Interactions at the Active Site: Prediction of Binding Modes Unaffected by Crystal Packing
inferredcites →https://doi.org/10.1073/pnas.96.23.13040openalex-snapshot
Structure of the HIV-1 integrase catalytic domain complexed with an inhibitor: A platform for antiviral drug design
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Aminopyrimidine Derivatives as Multiflavivirus Antiviral Compounds Identified from a Consensus Virtual Screening Approach
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A Pipeline To Enhance Ligand Virtual Screening: Integrating Molecular Dynamics and Fingerprints for Ligand and Proteins
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c03093openalex-snapshot
Enhanced Sampling on Domain/Motif Level with Kinetic Accelerated Molecular Dynamics
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00312openalex-snapshot
Evaluation of AutoDock and AutoDock Vina on the CASF-2013 Benchmark
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.9b00346openalex-snapshot
Comparative Assessment of Seven Docking Programs on a Nonredundant Metalloprotein Subset of the PDBbind Refined
inferred← citeshttps://doi.org/10.1021/acs.jctc.0c00185openalex-snapshot
Introducing Virtual Oligomerization Inhibition to Identify Potent Inhibitors of Aβ Oligomerization
inferred← citeshttps://doi.org/10.1021/acs.jctc.0c00370openalex-snapshot
A Benzene-Mapping Approach for Uncovering Cryptic Pockets in Membrane-Bound Proteins
inferred← citeshttps://doi.org/10.1021/acs.jctc.1c01177openalex-snapshot
Accelerated Ligand-Mapping Molecular Dynamics Simulations for the Detection of Recalcitrant Cryptic Pockets and Occluded Binding Sites
inferred← citeshttps://doi.org/10.1021/acs.jctc.3c00478openalex-snapshot
Worth the Weight: Sub-Pocket EXplorer (SubPEx), a Weighted Ensemble Method to Enhance Binding-Pocket Conformational Sampling
inferred← citeshttps://doi.org/10.1021/acs.jctc.8b00687openalex-snapshot
A Multiscale Simulation Approach to Modeling Drug–Protein Binding Kinetics
inferred← citeshttps://doi.org/10.1021/ar500356nopenalex-snapshot
Investigating Drug–Target Association and Dissociation Mechanisms Using Metadynamics-Based Algorithms
inferred← citeshttps://doi.org/10.1021/bi800894uopenalex-snapshot
Simulations of a Protein Crystal: Explicit Treatment of Crystallization Conditions Links Theory and Experiment in the Streptavidin−Biotin Complex
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/ci300399wopenalex-snapshot
Consensus Docking: Improving the Reliability of Docking in a Virtual Screening Context
inferred← citeshttps://doi.org/10.1021/ci300541copenalex-snapshot
Exploring the Molecular Mechanism of Cross-Resistance to HIV-1 Integrase Strand Transfer Inhibitors by Molecular Dynamics Simulation and Residue Interaction Network Analysis
inferred← citeshttps://doi.org/10.1021/ci4000294openalex-snapshot
TRAPP: A Tool for Analysis ofTransient BindingPockets inProteins
inferred← citeshttps://doi.org/10.1021/ci400225wopenalex-snapshot
Molecular Simulations of Aromatase Reveal New Insights Into the Mechanism of Ligand Binding
inferred← citeshttps://doi.org/10.1021/ci400427aopenalex-snapshot
Assessing Molecular Docking Tools for Relative Biological Activity Prediction: A Case Study of Triazole HIV-1 NNRTIs
inferred← citeshttps://doi.org/10.1021/ci400474uopenalex-snapshot
LIBSA – A Method for the Determination of Ligand-Binding Preference to Allosteric Sites on Receptor Ensembles
inferred← citeshttps://doi.org/10.1021/ci400729jopenalex-snapshot
Ensemble-Based Docking Using Biased Molecular Dynamics
inferred← citeshttps://doi.org/10.1021/ci5003334openalex-snapshot
Exploring Protein Kinase Conformation Using Swarm-Enhanced Sampling Molecular Dynamics
inferred← citeshttps://doi.org/10.1021/ci700067fopenalex-snapshot
Docking of ATP to Ca-ATPase: Considering Protein Domain Motions
inferred← citeshttps://doi.org/10.1021/cr040426mopenalex-snapshot
Molecular Dynamics: Survey of Methods for Simulating the Activity of Proteins
inferred← citeshttps://doi.org/10.1021/ct3001377openalex-snapshot
Assessing the Performance of Metadynamics and Path Variables in Predicting the Binding Free Energies of p38 Inhibitors
inferred← citeshttps://doi.org/10.1021/ct401098bopenalex-snapshot
Efficient Characterization of Protein Cavities within Molecular Simulation Trajectories:trj_cavity
inferred← citeshttps://doi.org/10.1021/ja0723535openalex-snapshot
Remarkable Loop Flexibility in Avian Influenza N1 and Its Implications for Antiviral Drug Design
inferred← citeshttps://doi.org/10.1021/ja2005253openalex-snapshot
Direct Detection of Structurally Resolved Dynamics in a Multiconformation Receptor−Ligand Complex
inferred← citeshttps://doi.org/10.1021/jacs.6b05425openalex-snapshot
Understanding Cryptic Pocket Formation in Protein Targets by Enhanced Sampling Simulations
inferred← citeshttps://doi.org/10.1021/jm049410eopenalex-snapshot
Dynamic Receptor-Based Pharmacophore Model Development and Its Application in Designing Novel HIV-1 Integrase Inhibitors
inferred← citeshttps://doi.org/10.1021/jm049944fopenalex-snapshot
Design and Synthesis of Novel Indole β-Diketo Acid Derivatives as HIV-1 Integrase Inhibitors
inferred← citeshttps://doi.org/10.1021/jm100456aopenalex-snapshot
Computer-Aided Identification ofTrypanosoma bruceiUridine Diphosphate Galactose 4′-Epimerase Inhibitors: Toward the Development of Novel Therapies for African Sleeping Sickness
inferred← citeshttps://doi.org/10.1021/jm8001197openalex-snapshot
Ensemble-Based Virtual Screening Reveals Potential Novel Antiviral Compounds for Avian Influenza Neuraminidase
inferred← citeshttps://doi.org/10.1021/jm800562dopenalex-snapshot
Target Flexibility: An Emerging Consideration in Drug Discovery and Design
inferred← citeshttps://doi.org/10.1021/jp2015275openalex-snapshot
Modulation of Prototropic Activity and Rotational Relaxation Dynamics of a Cationic Biological Photosensitizer within the Motionally Constrained Bio-environment of a Protein
inferred← citeshttps://doi.org/10.1021/jp311851ropenalex-snapshot
Derivation of Fixed Partial Charges for Amino Acids Accommodating a Specific Water Model and Implicit Polarization
inferred← citeshttps://doi.org/10.1021/jp9010372openalex-snapshot
Dynamics of the Streptavidin−Biotin Complex in Solution and in Its Crystal Lattice: Distinct Behavior Revealed by Molecular Simulations
inferred← citeshttps://doi.org/10.1021/jp911689ropenalex-snapshot
Free-Energy-Based Methods for Binding Profile Determination in a Congeneric Series of CDK2 Inhibitors
inferred← citeshttps://doi.org/10.1021/jp912120nopenalex-snapshot
Insights into the Mechanism of Binding of Arachidonic Acid to Mammalian 15-Lipoxygenases
inferred← citeshttps://doi.org/10.1021/mp2002208openalex-snapshot
Effects of Solution Concentration on the Physicochemical Properties of a Polymeric Anticancer Therapeutic
inferred← citeshttps://doi.org/10.1038/nchem.1821openalex-snapshot
Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways
inferred← citeshttps://doi.org/10.1038/s41467-023-36699-3openalex-snapshot
Predicting locations of cryptic pockets from single protein structures using the PocketMiner graph neural network
inferred← citeshttps://doi.org/10.1038/s41598-021-86471-0openalex-snapshot
Molecular dynamics and in silico mutagenesis on the reversible inhibitor-bound SARS-CoV-2 main protease complexes reveal the role of lateral pocket in enhancing the ligand affinity
inferred← citeshttps://doi.org/10.1038/s44386-024-00001-2openalex-snapshot
Structure and dynamics in drug discovery
inferred← citeshttps://doi.org/10.1038/srep18555openalex-snapshot
HIV-1 Protease Dimerization Dynamics Reveals a Transient Druggable Binding Pocket at the Interface
inferred← citeshttps://doi.org/10.1038/srep22878openalex-snapshot
Structure-Based Virtual Ligand Screening on the XRCC4/DNA Ligase IV Interface
inferred← citeshttps://doi.org/10.1039/9781849735056-00281openalex-snapshot
Molecular Simulation in Computer-aided Drug Design: Algorithms and Applications
inferred← citeshttps://doi.org/10.1039/9781849735056-00316openalex-snapshot
Computer-aided Drug Discovery: Two Antiviral Drugs for HIV/AIDS
inferred← citeshttps://doi.org/10.1039/9781849735377-00171openalex-snapshot
Docking and Virtual Screening
inferred← citeshttps://doi.org/10.1039/9781849735377-00360openalex-snapshot
Using Molecular Simulations and Metadynamics to Predict Binding Free Energies and Kinetics: the Case of Cox and Cdk2
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