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Suitability of MMGBSA for the selection of correct ligand binding modes from docking results

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

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Scalable molecular dynamics with NAMD
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Fast and accurate predictions of binding free energies using MM‐PBSA and MM‐GBSA
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Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database
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Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking
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BODIL: a molecular modeling environment for structure-function analysis and drug design
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Effect of B-ring substitution pattern on binding mode of propionamide selective androgen receptor modulators
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Phosphodiesterase inhibitors. Part 1: Synthesis and structure–activity relationships of pyrazolopyridine–pyridazinone PDE inhibitors developed from ibudilast
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Discovery of oxazole-based PDE4 inhibitors with picomolar potency
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Phosphodiesterase inhibitors. Part 4: Design, synthesis and structure-activity relationships of dual PDE3/4-inhibitory fused bicyclic heteroaromatic-4,4-dimethylpyrazolones
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Phosphodiesterase inhibitors. Part 5: Hybrid PDE3/4 inhibitors as dual bronchorelaxant/anti-inflammatory agents for inhaled administration
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Identification of the 5,5-dioxo-7,8-dihydro-6H-thiopyrano[3,2-d]pyrimidine derivatives as highly selective PDE4B inhibitors
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Predicting Absolute Ligand Binding Free Energies to a Simple Model Site
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Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site
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Automatic atom type and bond type perception in molecular mechanical calculations
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Effects of protein flexibility on the site of metabolism prediction for CYP2A6 substrates
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Case-specific performance of MM-PBSA, MM-GBSA, and SIE in virtual screening
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Identification of a new androgen receptor (AR) co‐regulator BUD31 and related peptides to suppress wild‐type and mutated AR‐mediated prostate cancer growth via peptide screening and X‐ray structure analysis
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Phosphodiesterase inhibitors: A novel mechanism for receptor-independent antipsychotic medications
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Alchemical free energy methods for drug discovery: progress and challenges
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CYP2A6: a human coumarin 7-hydroxylase
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Consensus scoring for ligand/protein interactions
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Chapter 4 Alchemical Free Energy Calculations: Ready for Prime Time?
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Annual Reports in Computational Chemistry
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Knowledge-Based Methods To Train and Optimize Virtual Screening Ensembles
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Modeling Binding with Large Conformational Changes: Key Points in Ensemble-Docking Approaches
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How To Deal with Multiple Binding Poses in Alchemical Relative Protein–Ligand Binding Free Energy Calculations
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ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
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Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models
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Efficient Drug Lead Discovery and Optimization
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Efficient Virtual Screening Using Multiple Protein Conformations Described as Negative Images of the Ligand-Binding Site
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Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations
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Comparison of Virtual High-Throughput Screening Methods for the Identification of Phosphodiesterase-5 Inhibitors
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RS-Predictor Models Augmented with SMARTCyp Reactivities: Robust Metabolic Regioselectivity Predictions for Nine CYP Isozymes
inferredcites →https://doi.org/10.1021/ci4002475openalex-snapshot
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inferredcites →https://doi.org/10.1021/ci700052xopenalex-snapshot
Comparison of Topological, Shape, and Docking Methods in Virtual Screening
inferredcites →https://doi.org/10.1021/ci800298zopenalex-snapshot
Empirical Scoring Functions for Advanced Protein−Ligand Docking with PLANTS
inferredcites →https://doi.org/10.1021/ci900056copenalex-snapshot
Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy
inferredcites →https://doi.org/10.1021/ct100493vopenalex-snapshot
Improved Replica Exchange Method for Native-State Protein Sampling
inferredcites →https://doi.org/10.1021/ct300418hopenalex-snapshot
MMPBSA.py : An Efficient Program for End-State Free Energy Calculations
inferredcites →https://doi.org/10.1021/ct300896hopenalex-snapshot
w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations
inferredcites →https://doi.org/10.1021/ct400341popenalex-snapshot
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
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Binding Free Energy Calculations for Lead Optimization: Assessment of Their Accuracy in an Industrial Drug Design Context
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Coupling Accelerated Molecular Dynamics Methods with Thermodynamic Integration Simulations
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A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model
inferredcites →https://doi.org/10.1021/jm011072jopenalex-snapshot
Structural Basis for the Glucocorticoid Response in a Mutant Human Androgen Receptor (ARccr) Derived from an Androgen-Independent Prostate Cancer
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A Critical Assessment of Docking Programs and Scoring Functions
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Discovery of Potent, Orally-Active, and Muscle-Selective Androgen Receptor Modulators Based on an N-Aryl-hydroxybicyclohydantoin Scaffold
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Empirical Regioselectivity Models for Human Cytochromes P450 3A4, 2D6, and 2C9
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Unexpected Binding Orientation of Bulky-B-Ring Anti-Androgens and Implications for Future Drug Targets
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
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Replica Exchange with Solute Scaling: A More Efficient Version of Replica Exchange with Solute Tempering (REST2)
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Structures of human microsomal cytochrome P450 2A6 complexed with coumarin and methoxsalen
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Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set
inferredcites →https://doi.org/10.1039/c4cp03179bopenalex-snapshot
Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring
inferredcites →https://doi.org/10.1039/c6cp01555gopenalex-snapshot
Comprehensive evaluation of ten docking programs on a diverse set of protein–ligand complexes: the prediction accuracy of sampling power and scoring power
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Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules
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Comparison of simple potential functions for simulating liquid water
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Structural basis for antagonism and resistance of bicalutamide in prostate cancer
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Replica exchange with solute tempering: A method for sampling biological systems in explicit water
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On achieving high accuracy and reliability in the calculation of relative protein–ligand binding affinities
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Crystal Structure of the T877A Human Androgen Receptor Ligand-binding Domain Complexed to Cyproterone Acetate Provides Insight for Ligand-induced Conformational Changes and Structure-based Drug Design
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Structural Characterization of the Human Androgen Receptor Ligand-binding Domain Complexed with EM5744, a Rationally Designed Steroidal Ligand Bearing a Bulky Chain Directed toward Helix 12
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The Protein Data Bank
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Control of the negative IREStrans-acting factor KHSRP by ubiquitination
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Structure of the ligand-binding domain (LBD) of human androgen receptor in complex with a selective modulator LGD2226
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Comparison of crystal structures of human androgen receptor ligand‐binding domain complexed with various agonists reveals molecular determinants responsible for binding affinity
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The inhibition of CYP enzymes in mouse and human liver by pilocarpine
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Competitive inhibition of coumarin 7‐hydroxylation by pilocarpine and its interaction with mouse CYP 2A5 and human CYP2A6
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Structural comparison of cytochromes P450 2A6, 2A13, and 2E1 with pilocarpine
inferredcites →https://doi.org/10.1124/dmd.106.013425openalex-snapshot
Involvement of CYP2A6 in the Formation of a Novel Metabolite, 3-Hydroxypilocarpine, from Pilocarpine in Human Liver Microsomes
inferredcites →https://doi.org/10.1146/annurev.biophys.36.040306.132550openalex-snapshot
Calculation of Protein-Ligand Binding Affinities
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Androgen Receptor in Prostate Cancer
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CYP2A6: genetics, structure, regulation, and function
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The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities
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Reliability of Virtual Screening Methods in Prediction of PDE4Binhibitor Activity
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Inhibitory effects and oxidation of 6-methylcoumarin, 7-methylcoumarin and 7-formylcoumarinviahuman CYP2A6 and its mouse and pig orthologous enzymes
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Modeling of interactions between xenobiotics and cytochrome P450 (CYP) enzymes
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Improving Docking Performance Using Negative Image-Based Rescoring
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Endocrine Disruption at the Androgen Receptor: Employing Molecular Dynamics and Docking for Improved Virtual Screening and Toxicity Prediction
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Is It Reliable to Take the Molecular Docking Top Scoring Position as the Best Solution without Considering Available Structural Data?

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Building shape-focused pharmacophore models for effective docking screening
inferred← citeshttps://doi.org/10.1186/s43094-026-00963-2openalex-snapshot
Exploring the potential of SGLT2 inhibitors in Alzheimer’s disease: network pharmacology, molecular docking, and MD simulation study
inferred← citeshttps://doi.org/10.1371/journal.pone.0352147openalex-snapshot
Integrated in silico and in vivo larvicidal evaluation of compounds targeting juvenile hormone for malaria vector control
inferred← citeshttps://doi.org/10.21203/rs.3.rs-10620341/v1openalex-snapshot
A multi-layer computational framework for structural prioritization of transcriptome-derived proteins
inferred← citeshttps://doi.org/10.3390/app12010515openalex-snapshot
In Silico Studies of Tumor Targeted Peptide-Conjugated Natural Products for Targeting Over-Expressed Receptors in Breast Cancer Cells Using Molecular Docking, Molecular Dynamics and MMGBSA Calculations
inferred← citeshttps://doi.org/10.3390/ijms262412038openalex-snapshot
In Silico Lead Identification of Staphylococcus aureus LtaS Inhibitors: A High-Throughput Computational Pipeline Towards Prototype Development
inferred← citeshttps://doi.org/10.3390/metabo13101090openalex-snapshot
Marine-Derived Compounds for CDK5 Inhibition in Cancer: Integrating Multi-Stage Virtual Screening, MM/GBSA Analysis and Molecular Dynamics Investigations
inferred← citeshttps://doi.org/10.3390/molecules28145320openalex-snapshot
In Silico Discovery of Small-Molecule Inhibitors Targeting SARS-CoV-2 Main Protease
inferred← citeshttps://doi.org/10.6084/m9.figshare.13300130openalex-snapshot
Additional file 1 of KLF7: a new candidate biomarker and therapeutic target for high-grade serous ovarian cancer
inferred← citeshttps://doi.org/10.6084/m9.figshare.13300133openalex-snapshot
Additional file 2 of KLF7: a new candidate biomarker and therapeutic target for high-grade serous ovarian cancer
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