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Hands-off Linear Interaction Energy Approach to Binding Mode and Affinity Estimation of Estrogens
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Outgoing claims: the papers this work cites, builds on, or argues with.
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Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94
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LINCS: A linear constraint solver for molecular simulations
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Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
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Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method
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Hybrid Monte Carlo simulations theory and initial comparison with molecular dynamics
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Fast, efficient generation of high‐quality atomic charges. AM1‐BCC model: II. Parameterization and validation
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Development and testing of a general amber force field
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Comparison of multiple Amber force fields and development of improved protein backbone parameters
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A Fast Flexible Docking Method using an Incremental Construction Algorithm
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Numerical Simulation in Molecular Dynamics: Numerics, Algorithms, Parallelization, Applications
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How to simulate affinities for host–guest systems lacking binding mode information: application to the liquid chromatographic separation of hexabromocyclododecane stereoisomers
inferredcites →https://doi.org/10.1007/s10822-006-9060-4openalex-snapshot
Development and validation of a modular, extensible docking program: DOCK 5
inferredcites →https://doi.org/10.1007/s10822-007-9104-4openalex-snapshot
Improved estimation of ligand–macromolecule binding affinities by linear response approach using a combination of multi-mode MD simulation and QM/MM methods
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Prediction of protein–ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations
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GROMACS: A message-passing parallel molecular dynamics implementation
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A geometric approach to macromolecule-ligand interactions
inferredcites →https://doi.org/10.1016/0272-0590(84)90089-7openalex-snapshot
Diethylstilbestrol and other estrogens in the environment*1
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Automatic atom type and bond type perception in molecular mechanical calculations
inferredcites →https://doi.org/10.1021/ci000066dopenalex-snapshot
QSAR Models Using a Large Diverse Set of Estrogens
inferredcites →https://doi.org/10.1021/ci0601214openalex-snapshot
Are Automated Molecular Dynamics Simulations and Binding Free Energy Calculations Realistic Tools in Lead Optimization? An Evaluation of the Linear Interaction Energy (LIE) Method
inferredcites →https://doi.org/10.1021/ci200411sopenalex-snapshot
A 3D-QSAR-Driven Approach to Binding Mode and Affinity Prediction
inferredcites →https://doi.org/10.1021/cr00023a004openalex-snapshot
Free energy calculations: Applications to chemical and biochemical phenomena
inferredcites →https://doi.org/10.1021/ct700301qopenalex-snapshot
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
inferredcites →https://doi.org/10.1021/ja00074a030openalex-snapshot
Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation
inferredcites →https://doi.org/10.1021/jm0003992openalex-snapshot
Detailed Analysis of Scoring Functions for Virtual Screening
inferredcites →https://doi.org/10.1021/jm0309607openalex-snapshot
Prediction of Ligand Binding Affinity and Orientation of Xenoestrogens to the Estrogen Receptor by Molecular Dynamics Simulations and the Linear Interaction Energy Method
inferredcites →https://doi.org/10.1021/jm050362nopenalex-snapshot
A Critical Assessment of Docking Programs and Scoring Functions
inferredcites →https://doi.org/10.1021/jm701218jopenalex-snapshot
Predicting Binding Modes from Free Energy Calculations
inferredcites →https://doi.org/10.1063/1.1740409openalex-snapshot
High-Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases
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Statistical Mechanics of Fluid Mixtures
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Canonical sampling through velocity rescaling
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Comparison of simple potential functions for simulating liquid water
inferredcites →https://doi.org/10.1063/1.448118openalex-snapshot
Molecular dynamics with coupling to an external bath
inferredcites →https://doi.org/10.1074/jbc.m200764200openalex-snapshot
Interaction of Transcriptional Intermediary Factor 2 Nuclear Receptor Box Peptides with the Coactivator Binding Site of Estrogen Receptor α
inferredcites →https://doi.org/10.1080/08927020802208968openalex-snapshot
Classical hybrid Monte-Carlo simulation of the interconversion of hexabromocyclododecane stereoisomers
inferredcites →https://doi.org/10.1093/comjnl/7.2.149openalex-snapshot
Function minimization by conjugate gradients
inferredcites →https://doi.org/10.1093/protein/7.3.385openalex-snapshot
A new method for predicting binding affinity in computer-aided drug design
inferredcites →https://doi.org/10.1093/toxsci/54.1.138openalex-snapshot
The Estrogen Receptor Relative Binding Affinities of 188 Natural and Xenochemicals: Structural Diversity of Ligands
inferredcites →https://doi.org/10.1124/dmd.110.032946openalex-snapshot
Computational Prediction of Binding Affinity for CYP1A2-Ligand Complexes Using Empirical Free Energy Calculations
inferredcites →https://doi.org/10.1146/annurev.bb.18.060189.002243openalex-snapshot
Free Energy Via Molecular Simulation: Applications to Chemical and Biomolecular Systems
inferredcites →https://doi.org/10.1210/endo.138.3.4979openalex-snapshot
Comparison of the Ligand Binding Specificity and Transcript Tissue Distribution of Estrogen Receptors α and β
inferredcites →https://doi.org/10.1214/ss/1177011136openalex-snapshot
Inference from Iterative Simulation Using Multiple Sequences
inferredcites →https://doi.org/10.1529/biophysj.104.051938openalex-snapshot
Exploring the Helix-Coil Transition via All-Atom Equilibrium Ensemble Simulations
inferredcites →https://doi.org/10.2174/092986706779026165openalex-snapshot
Towards Predictive Ligand Design With Free-Energy Based Computational Methods?
inferredcites →https://doi.org/10.2174/138920306778559395openalex-snapshot
Scoring Functions for Protein-Ligand Docking
inferredcites →https://doi.org/10.3390/ijms11093434openalex-snapshot
In Silico Prediction of Estrogen Receptor Subtype Binding Affinity and Selectivity Using Statistical Methods and Molecular Docking with 2-Arylnaphthalenes and 2-Arylquinolines
inferredcites →https://doi.org/10.6028/jres.049.044openalex-snapshot
Methods of conjugate gradients for solving linear systems
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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High Affinity Fluorescent Ligands for the Estrogen Receptor
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The strategy for estrogen receptor mediated-risk assessment in environmental water: A combination of species sensitivity distributions and in silico approaches
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Effects of carbamazepine and two of its metabolites on the non-biting midge Chironomus riparius in a sediment full life cycle toxicity test
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Comprehensive and Automated Linear Interaction Energy Based Binding-Affinity Prediction for Multifarious Cytochrome P450 Aromatase Inhibitors
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Structural bioinformatics analysis of SARS-CoV-2 variants reveals higher hACE2 receptor binding affinity for Omicron B.1.1.529 spike RBD compared to wild type reference
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Adequate prediction for inhibitor affinity of Aβ 40 protofibril using the linear interaction energy method
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Effective estimation of the inhibitor affinity of HIV-1 protease via a modified LIE approach
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Running Simulations in HPC and Cloud Resources by Implementing Enhanced TOSCA Workflows
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A nontoxic pain killer designed by modeling of pathological receptor conformations
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Arctigenin inhibits STAT3 and exhibits anticancer potential in human triple-negative breast cancer therapy
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Environmental chemical exposures and breast cancer
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Free Energy Simulations of Cargo-Carrier Interactions for Core-Multishell Nanotransporters
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