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A Reliable Docking/Scoring Scheme Based on the Semiempirical Quantum Mechanical PM6-DH2 Method Accurately Covering Dispersion and H-Bonding: HIV-1 Protease with 22 Ligands

https://doi.org/10.1021/jp1032965
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities
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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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Assessment of Semiempirical Quantum Mechanical Methods for the Evaluation of Protein Structures
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Semiempirical Quantum Chemical PM6 Method Augmented by Dispersion and H-Bonding Correction Terms Reliably Describes Various Types of Noncovalent Complexes
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A Transferable H-Bonding Correction for Semiempirical Quantum-Chemical Methods
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Crystal structure of HIV-1 protease in complex with VX-478, a potent and orally bioavailable inhibitor of the enzyme
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inferredcites →https://doi.org/10.1021/jm0203783openalex-snapshot
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inferredcites →https://doi.org/10.1021/jm048973nopenalex-snapshot
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Structure-based discovery of β 2 -adrenergic receptor ligands
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The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding
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ABT-538 is a potent inhibitor of human immunodeficiency virus protease and has high oral bioavailability in humans.
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A new method for predicting binding affinity in computer-aided drug design
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Rapid X-ray diffraction analysis of HIV-1 protease–inhibitor complexes: inhibitor exchange in single crystals of the bound enzyme
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Configurations of Diastereomeric Hydroxyethylene Isosteres Strongly Affect Biological Activities of a Series of Specific Inhibitors of Human‐Immunodeficiency‐Virus Proteinase
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Role of hydroxyl group and R/S configuration of isostere in binding properties of HIV‐1 protease inhibitors
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Rational Approach to AIDS Drug Design Through Structural Biology
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Current and Novel Inhibitors of HIV Protease

What points at this work

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

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Modulation of Aldose Reductase Inhibition by Halogen Bond Tuning
inferred← citeshttps://doi.org/10.1021/ct200751eopenalex-snapshot
Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods
inferred← citeshttps://doi.org/10.1021/ct3002738openalex-snapshot
Calculation of Host–Guest Binding Affinities Using a Quantum-Mechanical Energy Model
inferred← citeshttps://doi.org/10.1021/ct400995copenalex-snapshot
Bringing Clarity to the Prediction of Protein–Ligand Binding Free Energies via “Blurring”
inferred← citeshttps://doi.org/10.1021/ct401111copenalex-snapshot
Quantum Mechanical Calculation of Noncovalent Interactions: A Large-Scale Evaluation of PMx, DFT, and SAPT Approaches
inferred← citeshttps://doi.org/10.1021/jm500497vopenalex-snapshot
Structural Basis for Inhibition of Mycobacterial and Human Adenosine Kinase by 7‑Substituted 7‑(Het)aryl-7-deazaadenine Ribonucleosides
inferred← citeshttps://doi.org/10.1021/jp200565wopenalex-snapshot
Understanding the HIV-1 Protease Reactivity with DFT: What Do We Gain from Recent Functionals?
inferred← citeshttps://doi.org/10.1021/jp2010265openalex-snapshot
Ligand Conformational and Solvation/Desolvation Free Energy in Protein−Ligand Complex Formation
inferred← citeshttps://doi.org/10.1021/jp202149zopenalex-snapshot
Semiempirical Quantum Mechanical Method PM6-DH2X Describes the Geometry and Energetics of CK2-Inhibitor Complexes Involving Halogen Bonds Well, While the Empirical Potential Fails
inferred← citeshttps://doi.org/10.1021/jp203885nopenalex-snapshot
Hydration Free Energies Using Semiempirical Quantum Mechanical Hamiltonians and a Continuum Solvent Model with Multiple Atomic-Type Parameters
inferred← citeshttps://doi.org/10.1021/jp203963fopenalex-snapshot
Protein–Ligand Interaction Energies with Dispersion Corrected Density Functional Theory and High-Level Wave Function Based Methods
inferred← citeshttps://doi.org/10.1021/jp205442popenalex-snapshot
Interaction of Metal Ions with Biomolecular Ligands: How Accurate Are Calculated Free Energies Associated with Metal Ion Complexation?
inferred← citeshttps://doi.org/10.1021/jp402117copenalex-snapshot
Assessing the Accuracy and Performance of Implicit Solvent Models for Drug Molecules: Conformational Ensemble Approaches
inferred← citeshttps://doi.org/10.1021/jp409604nopenalex-snapshot
Quantum Mechanics-Based Scoring Rationalizes the Irreversible Inactivation of ParasiticSchistosoma mansoniCysteine Peptidase by Vinyl Sulfone Inhibitors
inferred← citeshttps://doi.org/10.1038/s41598-018-33963-1openalex-snapshot
Molecular mechanism of substrate selectivity of the arginine-agmatine Antiporter AdiC
inferred← citeshttps://doi.org/10.1039/9781788010016-00067openalex-snapshot
Molecular Mechanisms of Drug Action: X-ray Crystallography at the Basis of Structure-based and Ligand-based Drug Design
inferred← citeshttps://doi.org/10.1039/9781788010139-00145openalex-snapshot
Computational Chemistry Tools in Glycobiology: Modelling of Carbohydrate–Protein Interactions
inferred← citeshttps://doi.org/10.1039/9781849735377-00001openalex-snapshot
Recognition of Ligands by Macromolecular Targets
inferred← citeshttps://doi.org/10.1039/c1cp21944hopenalex-snapshot
Accounting for non-optimal interactions in molecular recognition: a study of ion–π complexes using a QM/MM model with a dipole-polarisable MM region
inferred← citeshttps://doi.org/10.1039/c5cc09499bopenalex-snapshot
The SQM/COSMO filter: reliable native pose identification based on the quantum-mechanical description of protein–ligand interactions and implicit COSMO solvation
inferred← citeshttps://doi.org/10.1039/c5ra20185copenalex-snapshot
Calculation of protein–ligand binding affinities based on a fragment quantum mechanical method
inferred← citeshttps://doi.org/10.1039/c7cp02160gopenalex-snapshot
Approximate quantum chemical methods for modelling carbohydrate conformation and aromatic interactions: β-cyclodextrin and its adsorption on a single-layer graphene sheet
inferred← citeshttps://doi.org/10.1039/d2cp04673copenalex-snapshot
B–H⋯π and C–H⋯π interactions in protein–ligand complexes: carbonic anhydrase II inhibition by carborane sulfonamides
inferred← citeshttps://doi.org/10.1039/d3cp04483aopenalex-snapshot
Target–ligand binding affinity from single point enthalpy calculation and elemental composition
inferred← citeshttps://doi.org/10.1039/d5qi01546dopenalex-snapshot
Fat or flat? The impact of dipole moment vectors on non-covalent interactions between aromatic tags and macromolecules
inferred← citeshttps://doi.org/10.1063/1.4886655openalex-snapshot
Water interactions with hydrophobic groups: Assessment and recalibration of semiempirical molecular orbital methods
inferred← citeshttps://doi.org/10.1063/5.0068862openalex-snapshot
NENCI-2021. I. A large benchmark database of non-equilibrium non-covalent interactions emphasizing close intermolecular contacts
inferred← citeshttps://doi.org/10.1080/17460441.2025.2497912openalex-snapshot
Water in drug design: pitfalls and good practices
inferred← citeshttps://doi.org/10.1135/cccc2011035openalex-snapshot
On the reliability of the corrected semiempirical quantum chemical method (PM6-DH2) for assigning the protonation states in HIV-1 protease/inhibitor complexes
inferred← citeshttps://doi.org/10.12691/ajmo-4-3-2openalex-snapshot
Docking and Ligand Binding Affinity: Uses and Pitfalls
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/10.1515/chem-2025-0212openalex-snapshot
Molecular insights and biological evaluation of compounds isolated from Ferula oopoda against diabetes, advanced glycation end products and inflammation in diabetics
inferred← citeshttps://doi.org/10.1515/psr-2020-0034openalex-snapshot
Computational methods for calculation of protein-ligand binding affinities in structure-based drug design
inferred← citeshttps://doi.org/10.1517/17460441.2013.752812openalex-snapshot
The application of quantum mechanics in structure-based drug design
inferred← citeshttps://doi.org/10.18388/abp.2011_2274openalex-snapshot
Computational study of binding of epothilone A to β-tubulin.
inferred← citeshttps://doi.org/10.18388/abp.2012_2106openalex-snapshot
Assessment of the free binding energy of 1,25-dihydroxyvitamin D3 and its analogs with the human VDR receptor model.
inferred← citeshttps://doi.org/10.2174/0929867325666180904115000openalex-snapshot
Advances in Docking
inferred← citeshttps://doi.org/10.2174/1568026620666201207095626openalex-snapshot
Docking Paradigm in Drug Design
inferred← citeshttps://doi.org/10.2210/pdb5nxg/pdbopenalex-snapshot
Carbonic Anhydrase II Inhibitor RA1
inferred← citeshttps://doi.org/10.2298/jsc250607059mopenalex-snapshot
A computational study to identify the metabolites in Lippia alba capable of inhibiting gastric cancer through BCL-2 protein inhibition
inferred← citeshttps://doi.org/10.26434/chemrxiv-2022-68n6hopenalex-snapshot
Enhancing Semiempirical Quantum Mechanical Scoring with Machine Learning: a new scoring function that accounts for both the enthalpic and entropic contributions to the ligand binding free energy
inferred← citeshttps://doi.org/10.26434/chemrxiv-2022-68n6h-v2openalex-snapshot
Enhancing Semiempirical Quantum Mechanical Scoring with Machine Learning: a new scoring function that accounts for both the enthalpic and entropic contributions to the ligand binding free energy
inferred← citeshttps://doi.org/10.3389/fchem.2020.595097openalex-snapshot
In Silico Study of Coumarins and Quinolines Derivatives as Potent Inhibitors of SARS-CoV-2 Main Protease
inferred← citeshttps://doi.org/10.3390/books978-3-03897-615-8openalex-snapshot
Molecular Modeling in Drug Design
inferred← citeshttps://doi.org/10.3390/ijms17050742openalex-snapshot
Recent Progress in Treating Protein–Ligand Interactions with Quantum-Mechanical Methods
inferred← citeshttps://doi.org/10.3390/ijms21030847openalex-snapshot
Integrated Computational Approaches and Tools for Allosteric Drug Discovery
inferred← citeshttps://doi.org/10.3390/ijms241411784openalex-snapshot
The Advances and Limitations of the Determination and Applications of Water Structure in Molecular Engineering
inferred← citeshttps://doi.org/10.3390/molecules22091397openalex-snapshot
Looking Back, Looking Forward at Halogen Bonding in Drug Discovery
inferred← citeshttps://doi.org/10.3390/molecules23071641openalex-snapshot
Targeting Dynamical Binding Processes in the Design of Non-Antibiotic Anti-Adhesives by Molecular Simulation—The Example of FimH
inferred← citeshttps://doi.org/10.3390/molecules26041007openalex-snapshot
Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase
inferred← citeshttps://doi.org/10.3390/pr9050817openalex-snapshot
New Perspectives of CYP1B1 Inhibitors in the Light of Molecular Studies
inferred← citeshttps://doi.org/10.4155/fmc.11.30openalex-snapshot
Physics-Based Scoring of Protein–Ligand Interactions: Explicit Polarizability, Quantum Mechanics and Free Energies
inferred← citeshttps://doi.org/10.5772/19447openalex-snapshot
Thermodynamics of Ligand-Protein Interactions: Implications for Molecular Design
inferred← citeshttps://doi.org/10.70675/e1440166z54e6z4925za4d6z41afe0b0dc93openalex-snapshot
New computational approaches for investigating the impact of mutations on the transglucosylation activity of sucrose phosphorylase enzyme
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