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Prediction of Potency of Protease Inhibitors Using Free Energy Simulations with Polarizable Quantum Mechanics-Based Ligand Charges and a Hybrid Water Model

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What this work says

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

inferredcites →https://doi.org/10.1002/jcc.20222openalex-snapshot
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Overcoming HIV drug resistance through rational drug design based on molecular, biochemical, and structural profiles of HIV resistance
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Binding free energy calculations of N-sulphonyl-glutamic acid inhibitors of MurD ligase
inferredcites →https://doi.org/10.1016/j.bmcl.2006.01.035openalex-snapshot
Ultra-potent P1 modified arylsulfonamide HIV protease inhibitors: The discovery of GW0385
inferredcites →https://doi.org/10.1016/j.drudis.2006.05.014openalex-snapshot
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inferredcites →https://doi.org/10.1016/j.jmb.2007.04.081openalex-snapshot
Computational Characterization of Structural Role of the Non-active Site Mutation M36I of Human Immunodeficiency Virus Type 1 Protease
inferredcites →https://doi.org/10.1016/j.jmb.2007.09.083openalex-snapshot
Molecular Analysis of the HIV-1 Resistance Development: Enzymatic Activities, Crystal Structures, and Thermodynamics of Nelfinavir-resistant HIV Protease Mutants
inferredcites →https://doi.org/10.1016/s0968-0896(02)00051-2openalex-snapshot
X-ray crystallographic structure of ABT-378 (Lopinavir) bound to HIV-1 protease
inferredcites →https://doi.org/10.1021/bi049459mopenalex-snapshot
Comparing the Accumulation of Active- and Nonactive-Site Mutations in the HIV-1 Protease
inferredcites →https://doi.org/10.1021/bi051886sopenalex-snapshot
Analysis of HIV-1 CRF_01 A/E Protease Inhibitor Resistance: Structural Determinants for Maintaining Sensitivity and Developing Resistance to Atazanavir
inferredcites →https://doi.org/10.1021/ci6003527openalex-snapshot
Analysis of Ligand-Bound Water Molecules in High-Resolution Crystal Structures of Protein−Ligand Complexes
inferredcites →https://doi.org/10.1021/ja00108a056openalex-snapshot
Crystal structure of HIV-1 protease in complex with VX-478, a potent and orally bioavailable inhibitor of the enzyme
inferredcites →https://doi.org/10.1021/ja060682bopenalex-snapshot
Computational Simulations of HIV-1 ProteasesMulti-drug Resistance Due to Nonactive Site Mutation L90M
inferredcites →https://doi.org/10.1021/jm00115a028openalex-snapshot
Novel binding mode of highly potent HIV-proteinase inhibitors incorporating the (R)-hydroxyethylamine isostere
inferredcites →https://doi.org/10.1021/jm010533yopenalex-snapshot
A Common Mechanism Underlying Promiscuous Inhibitors from Virtual and High-Throughput Screening
inferredcites →https://doi.org/10.1021/jm030596bopenalex-snapshot
Simple, Intuitive Calculations of Free Energy of Binding for Protein−Ligand Complexes. 3. The Free Energy Contribution of Structural Water Molecules in HIV-1 Protease Complexes
inferredcites →https://doi.org/10.1021/jm0306430openalex-snapshot
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
inferredcites →https://doi.org/10.1021/jm050943copenalex-snapshot
Effectiveness of Nonpeptide Clinical Inhibitor TMC-114 on HIV-1 Protease with Highly Drug Resistant Mutations D30N, I50V, and L90M
inferredcites →https://doi.org/10.1021/jm051256oopenalex-snapshot
Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein−Ligand Complexes
inferredcites →https://doi.org/10.1021/jm060522aopenalex-snapshot
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inferredcites →https://doi.org/10.1021/jm060561mopenalex-snapshot
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inferredcites →https://doi.org/10.1021/jm060999mopenalex-snapshot
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inferredcites →https://doi.org/10.1021/jm061158iopenalex-snapshot
Mechanism of Drug Resistance Due to N88S in CRF01_AE HIV-1 Protease, Analyzed by Molecular Dynamics Simulations
inferredcites →https://doi.org/10.1021/jm070482qopenalex-snapshot
Potent New Antiviral Compound Shows Similar Inhibition and Structural Interactions with Drug Resistant Mutants and Wild Type HIV-1 Protease
inferredcites →https://doi.org/10.1021/jm8006239openalex-snapshot
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inferredcites →https://doi.org/10.1021/jm960541sopenalex-snapshot
Structure-Based Design of HIV Protease Inhibitors: Sulfonamide-Containing 5,6-Dihydro-4-hydroxy-2-pyrones as Non-Peptidic Inhibitors
inferredcites →https://doi.org/10.1021/jm9704098openalex-snapshot
Viracept (Nelfinavir Mesylate, AG1343): A Potent, Orally Bioavailable Inhibitor of HIV-1 Protease
inferredcites →https://doi.org/10.1021/jm9802158openalex-snapshot
Tipranavir (PNU-140690): A Potent, Orally Bioavailable Nonpeptidic HIV Protease Inhibitor of the 5,6-Dihydro-4-hydroxy-2-pyrone Sulfonamide Class
inferredcites →https://doi.org/10.1021/jo049156yopenalex-snapshot
Stereoselective Photochemical 1,3-Dioxolane Addition to 5-Alkoxymethyl-2(5H)-furanone: Synthesis of Bis-tetrahydrofuranyl Ligand for HIV Protease Inhibitor UIC-94017 (TMC-114)
inferredcites →https://doi.org/10.1021/jp060292bopenalex-snapshot
Free Energy Simulations of Uncatalyzed DNA Replication Fidelity: Structure and Stability of T·G and dTTP·G Terminal DNA Mismatches Flanked by a Single Dangling Nucleotide
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inferredcites →https://doi.org/10.1038/nsb0395-244openalex-snapshot
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inferredcites →https://doi.org/10.1073/pnas.96.15.8675openalex-snapshot
JE-2147: A dipeptide protease inhibitor (PI) that potently inhibits multi-PI-resistant HIV-1
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inferredcites →https://doi.org/10.1110/ps.9.10.1898openalex-snapshot
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inferredcites →https://doi.org/10.1111/j.1432-1033.2004.04060.xopenalex-snapshot
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inferredcites →https://doi.org/10.1128/aac.00689-08openalex-snapshot
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inferredcites →https://doi.org/10.1128/aac.01413-06openalex-snapshot
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inferredcites →https://doi.org/10.1128/aac.47.10.3123-3129.2003openalex-snapshot
Novel bis -Tetrahydrofuranylurethane-Containing Nonpeptidic Protease Inhibitor (PI) UIC-94017 (TMC114) with Potent Activity against Multi-PI-Resistant Human Immunodeficiency Virus In Vitro
inferredcites →https://doi.org/10.1128/jvi.02706-06openalex-snapshot
Unique Thermodynamic Response of Tipranavir to Human Immunodeficiency Virus Type 1 Protease Drug Resistance Mutations
inferredcites →https://doi.org/10.1146/annurev.bi.62.070193.002551openalex-snapshot
STRUCTURE-BASED INHIBITORS OF HIV-1 PROTEASE
inferredcites →https://doi.org/10.1146/annurev.biophys.27.1.249openalex-snapshot
INHIBITORS OF HIV-1 PROTEASE: A Major Success of Structure-Assisted Drug Design
inferredcites →https://doi.org/10.1146/annurev.pc.43.100192.002203openalex-snapshot
Computational Alchemy
inferredcites →https://doi.org/10.1517/17460441.3.8.841openalex-snapshot
What has virtual screening ever done for drug discovery?

What points at this work

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

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ChemInform Abstract: Prediction of Potency of Protease Inhibitors Using Free Energy Simulations with Polarizable Quantum Mechanics‐Based Ligand Charges and a Hybrid Water Model.
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Additional file 1 of Antioxidant evaluation and computational prediction of prospective drug-like compounds from polyphenolic-rich extract of Hibiscus cannabinus L. seed as antidiabetic and neuroprotective targets: assessment through in vitro and in silico studies
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Navigating Molecular Complexity : a Comprehensive Molecular Modeling Study on Neonicotinoids, Sulfoxaflor, and Flupyradifurone Interacting with the Human α7 Nicotinic Acetylcholine Receptor
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