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Solvated Interaction Energy (SIE) for Scoring Protein−Ligand Binding Affinities. 1. Exploring the Parameter Space

https://doi.org/10.1021/ci600406v
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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/(sici)1096-987x(199810)19:13<1494::aid-jcc6>3.0.co;2-lopenalex-snapshot
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inferredcites →https://doi.org/10.1002/(sici)1096-987x(20000130)21:2<132::aid-jcc5>3.0.co;2-popenalex-snapshot
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inferredcites →https://doi.org/10.1002/0471477435openalex-snapshot
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inferredcites →https://doi.org/10.1002/1521-3773(20020802)41:15<2644::aid-anie2644>3.0.co;2-oopenalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.bpj.2008.12.3965openalex-snapshot
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In silico identification of natural products with anticancer activity using a chemo-structural database of Brazilian biodiversity
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2023.107856openalex-snapshot
Structure-based virtual screening for potent inhibitors of GH-20 β-N-acetylglucosaminidase: Classical and machine learning scoring functions, and molecular dynamics simulations
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2025.108575openalex-snapshot
Targeting the RARα–Gankyrin–PI3K axis with retinoid analogs to modulate autophagy in breast cancer cells: Computational insights and experimental validation
inferred← citeshttps://doi.org/10.1016/j.comptc.2014.07.002openalex-snapshot
Insight into the interaction mechanism of inhibitors P4 and WK23 with MDM2 based on molecular dynamics simulation and different free energy methods
inferred← citeshttps://doi.org/10.1016/j.cplett.2010.06.048openalex-snapshot
Theoretical study on the HIV-1 integrase–5CITEP complex based on polarized force fields
inferred← citeshttps://doi.org/10.1016/j.cplett.2017.10.030openalex-snapshot
Binding of anti-apoptotic Bcl-2 with different BH3 peptides: A molecular dynamics study
inferred← citeshttps://doi.org/10.1016/j.cplett.2018.06.040openalex-snapshot
Exploring drug-resistant mechanisms of I84V mutation in HIV-1 protease toward different inhibitors by thermodynamics integration and solvated interaction energy method
inferred← citeshttps://doi.org/10.1016/j.cplett.2019.05.001openalex-snapshot
Insights into the binding mechanisms of inhibitors of MDM2 based on molecular dynamics simulations and binding free energy calculations
inferred← citeshttps://doi.org/10.1016/j.csbj.2022.10.039openalex-snapshot
In silico investigation and surmounting of Lipopolysaccharide barrier in Gram-Negative Bacteria: How far has molecular dynamics Come?
inferred← citeshttps://doi.org/10.1016/j.ejmech.2011.05.020openalex-snapshot
Molecular modelling studies on Arylthioindoles as potent inhibitors of tubulin polymerization
inferred← citeshttps://doi.org/10.1016/j.ejmech.2013.12.008openalex-snapshot
1,2,3,4-Tetrahydrobenzo[h][1,6]naphthyridines as a new family of potent peripheral-to-midgorge-site inhibitors of acetylcholinesterase: Synthesis, pharmacological evaluation and mechanistic studies
inferred← citeshttps://doi.org/10.1016/j.ejmech.2014.04.044openalex-snapshot
Molecular basis of the selective binding of MDMA enantiomers to the alpha4beta2 nicotinic receptor subtype: Synthesis, pharmacological evaluation and mechanistic studies
inferred← citeshttps://doi.org/10.1016/j.ejmech.2014.07.021openalex-snapshot
Tetrahydrobenzo[h][1,6]naphthyridine-6-chlorotacrine hybrids as a new family of anti-Alzheimer agents targeting β-amyloid, tau, and cholinesterase pathologies
inferred← citeshttps://doi.org/10.1016/j.ejmech.2014.07.052openalex-snapshot
Design, synthesis, antimicrobial evaluation and molecular docking studies of some new thiophene, pyrazole and pyridone derivatives bearing sulfisoxazole moiety
inferred← citeshttps://doi.org/10.1016/j.ejmech.2014.12.037openalex-snapshot
Design, synthesis and bioevaluation of novel 6-(4-Hydroxypiperidino)naphthalen-2-ol-based potential Selective Estrogen Receptor Modulators for breast cancer
inferred← citeshttps://doi.org/10.1016/j.ejmech.2016.11.031openalex-snapshot
Biology-oriented drug synthesis (BIODS): In vitro β-glucuronidase inhibitory and in silico studies on 2-(2-methyl-5-nitro-1H-imidazol-1-yl)ethyl aryl carboxylate derivatives
inferred← citeshttps://doi.org/10.1016/j.ejmech.2017.05.033openalex-snapshot
Novel propanamides as fatty acid amide hydrolase inhibitors
inferred← citeshttps://doi.org/10.1016/j.ejmech.2018.01.044openalex-snapshot
First homology model of Plasmodium falciparum glucose-6-phosphate dehydrogenase: Discovery of selective substrate analog-based inhibitors as novel antimalarial agents
inferred← citeshttps://doi.org/10.1016/j.ejmech.2020.112696openalex-snapshot
New indolylarylsulfone non-nucleoside reverse transcriptase inhibitors show low nanomolar inhibition of single and double HIV-1 mutant strains
inferred← citeshttps://doi.org/10.1016/j.ejphar.2019.172684openalex-snapshot
Evaluation of the anticonvulsant effect of novel melatonin derivatives in the intravenous pentylenetetrazol seizure test in mice
inferred← citeshttps://doi.org/10.1016/j.emcon.2025.100543openalex-snapshot
Exploring the binding mechanism of contaminants of emerging concern in personal care products to transthyretin using molecular dynamics simulations
inferred← citeshttps://doi.org/10.1016/j.envint.2024.108926openalex-snapshot
Insight into the molecular recognition of human and polar bear pregnane X receptor by three organic pollutants using molecular docking and molecular dynamics simulations
inferred← citeshttps://doi.org/10.1016/j.exppara.2013.10.003openalex-snapshot
Activity of chalcones derived from 2,4,5-trimethoxybenzaldehyde against Meloidogyne exigua and in silico interaction of one chalcone with a putative caffeic acid 3-O-methyltransferase from Meloidogyne incognita
inferred← citeshttps://doi.org/10.1016/j.fob.2013.08.008openalex-snapshot
Interaction of Carthamus tinctorius lignan arctigenin with the binding site of tryptophan‐degrading enzyme indoleamine 2,3‐dioxygenase
inferred← citeshttps://doi.org/10.1016/j.heliyon.2025.e41894openalex-snapshot
Drug repurposing of argatroban, glimepiride and ranolazine shows anti-SARS-CoV-2 activity via diverse mechanisms
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2019.09.120openalex-snapshot
Exploring the molecular mechanism of the effect of puerarin on P2X3
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2025.140475openalex-snapshot
Allosteric site engagement and cooperativity mechanism by PHI1 for BRAFV600E kinase inhibition
inferred← citeshttps://doi.org/10.1016/j.jaim.2024.101036openalex-snapshot
Hepatoprotective effect of flavonoid rich fraction of Sesbania grandiflora: Results of In vivo, in vitro, and molecular docking studies
inferred← citeshttps://doi.org/10.1016/j.jcis.2020.07.097openalex-snapshot
Binding mechanism of a de novo coiled coil complex elucidated from surface forces measurements
inferred← citeshttps://doi.org/10.1016/j.jgar.2019.02.003openalex-snapshot
Discovery of NDM-1 inhibitors from natural products
inferred← citeshttps://doi.org/10.1016/j.jhazmat.2022.130174openalex-snapshot
Structural and energetic basis of interaction between human estrogen-related receptor γ and environmental endocrine disruptors from multiple molecular dynamics simulations and free energy predictions
inferred← citeshttps://doi.org/10.1016/j.jmb.2008.04.035openalex-snapshot
Molecular Dynamics—Solvated Interaction Energy Studies of Protein–Protein Interactions: The MP1–p14 Scaffolding Complex
inferred← citeshttps://doi.org/10.1016/j.jmb.2008.07.065openalex-snapshot
Stability and ATP Binding of the Nucleotide-binding Domain of the Wilson Disease Protein: Effect of the Common H1069Q Mutation
inferred← citeshttps://doi.org/10.1016/j.jmgm.2011.02.002openalex-snapshot
Prediction of the PPARα agonism of fibrates by combined MM–docking approaches
inferred← citeshttps://doi.org/10.1016/j.jmgm.2013.09.001openalex-snapshot
Binding of modulators to mouse and human multidrug resistance P-glycoprotein. A computational study
inferred← citeshttps://doi.org/10.1016/j.jmgm.2015.10.012openalex-snapshot
Case-specific performance of MM-PBSA, MM-GBSA, and SIE in virtual screening
inferred← citeshttps://doi.org/10.1016/j.jmgm.2016.11.011openalex-snapshot
Homology modeling and molecular dynamics simulation of the HIF2α degradation-related HIF2α-VHL complex
inferred← citeshttps://doi.org/10.1016/j.jmgm.2018.03.005openalex-snapshot
The role of ZA channel water-mediated interactions in the design of bromodomain-selective BET inhibitors
inferred← citeshttps://doi.org/10.1016/j.jmgm.2020.107735openalex-snapshot
Targeting shikimate pathway: In silico analysis of phosphoenolpyruvate derivatives as inhibitors of EPSP synthase and DAHP synthase
inferred← citeshttps://doi.org/10.1016/j.jmgm.2021.107978openalex-snapshot
A molecular model to study FosA enzyme inhibition
inferred← citeshttps://doi.org/10.1016/j.jmgm.2021.108119openalex-snapshot
Self-docking and cross-docking simulations of G protein-coupled receptor-ligand complexes: Impact of ligand type and receptor activation state
inferred← citeshttps://doi.org/10.1016/j.jsbmb.2008.04.009openalex-snapshot
An investigation into CAG repeat length variation and N/C terminal interactions in the T877A mutant androgen receptor found in prostate cancer
inferred← citeshttps://doi.org/10.1016/j.molliq.2018.10.111openalex-snapshot
Binding pattern and susceptibility of epigallocatechin gallate against envelope protein homodimer of Zika virus: A molecular dynamics study
inferred← citeshttps://doi.org/10.1016/j.molliq.2020.114999openalex-snapshot
Computational study on peptidomimetic inhibitors against SARS-CoV-2 main protease
inferred← citeshttps://doi.org/10.1016/j.molliq.2021.117501openalex-snapshot
Tricationic asymmetric monomeric monomethine cyanine dyes with chlorine and trifluoromethyl functionality – Fluorogenic nucleic acids probes
inferred← citeshttps://doi.org/10.1016/j.molliq.2022.119737openalex-snapshot
Structural dynamics and in silico design of pyrazolopyran-based inhibitors against Plasmodium serine hydroxymethyltransferases
inferred← citeshttps://doi.org/10.1016/j.molstruc.2019.126951openalex-snapshot
Zinc ternary complexes with gabapentin and neurotransmitters: Synthesis, spectral, thermal and molecular docking studies
inferred← citeshttps://doi.org/10.1016/j.neuint.2014.03.004openalex-snapshot
Puerarin alleviates aggravated sympathoexcitatory response induced by myocardial ischemia via regulating P2X3 receptor in rat superior cervical ganglia
inferred← citeshttps://doi.org/10.1016/j.taap.2017.04.011openalex-snapshot
The scaffold protein RACK1 is a target of endocrine disrupting chemicals (EDCs) with important implication in immunity
inferred← citeshttps://doi.org/10.1016/j.taap.2022.115974openalex-snapshot
The position of the nitro group affects the mutagenicity of nitroarenes
inferred← citeshttps://doi.org/10.1016/j.toxrep.2022.02.003openalex-snapshot
Radioiodination of zearalenone and determination of Lactobacillus plantarum effect of on zearalenone organ distribution: In silico study and preclinical evaluation
inferred← citeshttps://doi.org/10.1016/j.ymeth.2014.08.010openalex-snapshot
Virtual screening strategies: Recent advances in the identification and design of anti-cancer agents
inferred← citeshttps://doi.org/10.1017/cbo9780511730412.007openalex-snapshot
Free-energy calculations in structure-based drug design
inferred← citeshttps://doi.org/10.1021/acs.biochem.5b01257openalex-snapshot
Structural Studies of Trypanosoma brucei RNA Editing Ligases and Their Binding Partner Proteins
inferred← citeshttps://doi.org/10.1021/acs.chemrev.9b00055openalex-snapshot
End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00944openalex-snapshot
EViS: An Enhanced Virtual Screening Approach Based on Pocket–Ligand Similarity
inferred← citeshttps://doi.org/10.1021/acs.jcim.4c01957openalex-snapshot
Improved Structure-Based Histidine pKa Prediction for pH-Responsive Protein Design
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00278openalex-snapshot
Evaluation of the Wilma-SIE Virtual Screening Method in Community Structure–Activity Resource 2013 and 2014 Blind Challenges
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00043openalex-snapshot
Assessment of Solvated Interaction Energy Function for Ranking Antibody–Antigen Binding Affinities
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.6b00972openalex-snapshot
1,2,4-Triazolyl 5-Azaspiro[2.4]heptanes: Lead Identification and Early Lead Optimization of a New Series of Potent and Selective Dopamine D3 Receptor Antagonists
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.6b01906openalex-snapshot
Chiral Indolylarylsulfone Non-Nucleoside Reverse Transcriptase Inhibitors as New Potent and Broad Spectrum Anti-HIV-1 Agents
inferred← citeshttps://doi.org/10.1021/acs.joc.1c00314openalex-snapshot
Pillar[5]arene-Derived endo-Functionalized Molecular Tube for Mimicking Protein–Ligand Interactions
inferred← citeshttps://doi.org/10.1021/acs.jpcb.1c07060openalex-snapshot
In Silico Elucidation of Potent Inhibitors and Rational Drug Design against SARS-CoV-2 Papain-like Protease
inferred← citeshttps://doi.org/10.1021/acs.langmuir.0c02151openalex-snapshot
Multiple Molecular Dynamics Simulations of the Inhibitor GRL-02031 Complex with Wild Type and Mutant HIV-1 Protease Reveal the Binding and Drug-Resistance Mechanism
inferred← citeshttps://doi.org/10.1021/acs.langmuir.1c02348openalex-snapshot
Multiple Molecular Dynamics Simulations and Free-Energy Predictions Uncover the Susceptibility of Variants of HIV-1 Protease against Inhibitors Darunavir and KNI-1657
inferred← citeshttps://doi.org/10.1021/acschembio.6b00561openalex-snapshot
19F NMR-Guided Design of Glycomimetic Langerin Ligands
inferred← citeshttps://doi.org/10.1021/acschemneuro.9b00332openalex-snapshot
Tracing the GSAP–APP C-99 Interaction Site in the β-Amyloid Pathway Leading to Alzheimer’s Disease
inferred← citeshttps://doi.org/10.1021/acsomega.2c03951openalex-snapshot
Molecular Docking, Molecular Dynamics Simulations, and Free Energy Calculation Insights into the Binding Mechanism between VS-4718 and Focal Adhesion Kinase
inferred← citeshttps://doi.org/10.1021/acsomega.3c01309openalex-snapshot
In Silico and In Vitro Potential of FDA-Approved Drugs for Antimalarial Drug Repurposing against Plasmodium Serine Hydroxymethyltransferases
inferred← citeshttps://doi.org/10.1021/acsomega.5c05832openalex-snapshot
Unraveling the Molecular Inhibition and Conformational Changes of Hsp70 and Hsc70 Induced by VER-155008, a Competitive ATPase Inhibitor through Molecular Dynamics Simulations and Principal Component Analysis
inferred← citeshttps://doi.org/10.1021/acsomega.6c00279openalex-snapshot
Optimized Aqueous Sedimentation for Methoxyflavone Enrichment from Kaempferia parviflora and Its Mechanistic Suppression of Benign Prostatic Hyperplasia via TGF-β/SMAD/ERK Signaling
inferred← citeshttps://doi.org/10.1021/acsomega.9b02800openalex-snapshot
Insights into the Binding Recognition and Susceptibility of Tofacitinib toward Janus Kinases
inferred← citeshttps://doi.org/10.1021/acsomega.9b03157openalex-snapshot
Exploring the Potentiality of Natural Products from Essential Oils as Inhibitors of Odorant-Binding Proteins: A Structure- and Ligand-Based Virtual Screening Approach To Find Novel Mosquito Repellents
inferred← citeshttps://doi.org/10.1021/acsptsci.5c00431openalex-snapshot
3-(4-Hydroxyphenyl-1,2,3-Triazol-1-yl)Quinuclidine, a Selective α7 Nicotinic Acetylcholine Receptor Agonist, Attenuates Inflammatory Pain with a Favorable Central Nervous System Safety Profile in Mice
inferred← citeshttps://doi.org/10.1021/bi2004558openalex-snapshot
Efficient Incorporation of Protein Flexibility and Dynamics into Molecular Docking Simulations
inferred← citeshttps://doi.org/10.1021/bi201213wopenalex-snapshot
Structural Basis for NHERF1 PDZ Domain Binding
inferred← citeshttps://doi.org/10.1021/bi900235gopenalex-snapshot
Conformational Dynamics of Metal-Binding Domains in Wilson Disease Protein: Molecular Insights into Selective Copper Transfer
inferred← citeshttps://doi.org/10.1021/bk-2021-1397.ch003openalex-snapshot
Perspective on the SAMPL and D3R Blind Prediction Challenges for Physics-Based Free Energy Methods
inferred← citeshttps://doi.org/10.1021/ci100068wopenalex-snapshot
Correlation Analyses on Binding Affinity of Substituted Benzenesulfonamides with Carbonic Anhydrase Using ab Initio MO Calculations on Their Complex Structures
inferred← citeshttps://doi.org/10.1021/ci2000242openalex-snapshot
Solvated Interaction Energy (SIE) for Scoring Protein–Ligand Binding Affinities. 2. Benchmark in the CSAR-2010 Scoring Exercise
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/ci200191mopenalex-snapshot
Solvent Interaction Energy Calculations on Molecular Dynamics Trajectories: Increasing the Efficiency Using Systematic Frame Selection
inferred← citeshttps://doi.org/10.1021/ci2002395openalex-snapshot
Correlation Analyses on Binding Affinity of Sialic Acid Analogues and Anti-Influenza Drugs with Human Neuraminidase Using ab Initio MO Calculations on Their Complex Structures – LERE-QSAR Analysis (IV)
inferred← citeshttps://doi.org/10.1021/ci200269qopenalex-snapshot
CSAR Benchmark Exercise of 2010: Combined Evaluation Across All Submitted Scoring Functions
inferred← citeshttps://doi.org/10.1021/ci9002238openalex-snapshot
Predictions of Binding for Dopamine D2 Receptor Antagonists by the SIE Method
inferred← citeshttps://doi.org/10.1021/ct1002913openalex-snapshot
Binding Energy Distribution Analysis Method (BEDAM) for Estimation of Protein−Ligand Binding Affinities
inferred← citeshttps://doi.org/10.1021/ct800123copenalex-snapshot
Accurate Molecular Polarizabilities Based on Continuum Electrostatics
inferred← citeshttps://doi.org/10.1021/ja0779250openalex-snapshot
Rapid and Accurate Prediction of Binding Free Energies for Saquinavir-Bound HIV-1 Proteases
inferred← citeshttps://doi.org/10.1021/jm101334yopenalex-snapshot
Exploring the Size Limit of Templates for Inhibitors of the M2 Ion Channel of Influenza A Virus
inferred← citeshttps://doi.org/10.1021/jp1086416openalex-snapshot
Computational Determination of Binding Structures and Free Energies of Phosphodiesterase-2 with Benzo[1,4]diazepin-2-one Derivatives
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