Predicting absolute ligand binding free energies to a simple model site - Test2 - elhamkhani - TriplyDB

Predicting absolute ligand binding free energies to a simple model site

Predicting absolute ligand binding free energies to a simple model site

http://www.wikidata.org/entity/Q24683618

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Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules Design of protein-ligand binding based on the molecular-mechanics energy model The free energy landscape of small molecule unbinding Rescoring Docking Hit Lists for Model Cavity Sites: Predictions and Experimental Testing Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site Blind Prediction of Charged Ligand Binding Affinities in a Model Binding Site Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock A machine learning-based method to improve docking scoring functions and its application to drug repurposing Absolute free energy of binding of avidin/biotin, revisited Calculation of the Absolute Free Energy of Binding and Related Entropies with the HSMD-TI Method: The FKBP12-L8 Complex AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening Computational fragment-based binding site identification by ligand competitive saturation Drug discovery using chemical systems biology: weak inhibition of multiple kinases may contribute to the anti-cancer effect of nelfinavir Protein-Ligand Electrostatic Binding Free Energies from Explicit and Implicit Solvation Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations Bringing Clarity to the Prediction of Protein-Ligand Binding Free Energies via "Blurring"Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics.Lead optimization mapper: automating free energy calculations for lead optimization.Alchemical prediction of hydration free energies for SAMPL.Perspective: Alchemical free energy calculations for drug discovery.Alchemical free energy methods for drug discovery: progress and challenges Docking Screens for Novel Ligands Conferring New Biology.Standard binding free energies from computer simulations: What is the best strategy?Toward a molecular understanding of the interaction of dual specificity phosphatases with substrates: insights from structure-based modeling and high throughput screening.Using free energy of binding calculations to improve the accuracy of virtual screening predictions.Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design.Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements.The Binding Energy Distribution Analysis Method (BEDAM) for the Estimation of Protein-Ligand Binding Affinities.Computing Relative Free Energies of Solvation using Single Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange Correlating protein hot spot surface analysis using ProBiS with simulated free energies of protein-protein interfacial residues Structure-based systems biology for analyzing off-target binding Effects of Biomolecular Flexibility on Alchemical Calculations of Absolute Binding Free Energies Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations Molecular insights of protein contour recognition with ligand pharmacophoric sites through combinatorial library design and MD simulation in validating HTLV-1 PR inhibitors.Improved Binding Free Energy Predictions from Single-Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange Site Identification by Ligand Competitive Saturation (SILCS) simulations for fragment-based drug design Computational investigation of glycosylation effects on a family 1 carbohydrate-binding module.DOCK 6: Impact of new features and current docking performance.Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations.Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition.

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P2860

Predicting absolute ligand binding free energies to a simple model site

http://www.wikidata.org/entity/Q24683618

description

2007 nî lūn-bûn

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2007 թուականի Օգոստոսին հրատարակուած գիտական յօդուած

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2007 թվականի օգոստոսին հրատարակված գիտական հոդված

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2007年の論文

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2007年論文

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2007年論文

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2007年論文

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2007年論文

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2007年論文

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2007年论文

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name

Predicting absolute ligand binding free energies to a simple model site

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Predicting absolute ligand binding free energies to a simple model site

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Predicting absolute ligand binding free energies to a simple model site

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Predicting absolute ligand binding free energies to a simple model site

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Predicting absolute ligand binding free energies to a simple model site

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J.JMB.2007.06.002

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Journal of Molecular Biology

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Predicting absolute ligand binding free energies to a simple model site

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Alan P Graves

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Andrea C McReynolds

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Brian K Shoichet

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John D Chodera

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Ken A Dill

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P2860

A model binding site for testing scoring functions in molecular docking

Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme: linkage of dynamics and structural plasticity

Similar hydrophobic replacements of Leu99 and Phe153 within the core of T4 lysozyme have different structural and thermodynamic consequences

Coot: model-building tools for molecular graphics

GROMACS: fast, flexible, and free

Refinement of macromolecular structures by the maximum-likelihood method

Principles of docking: An overview of search algorithms and a guide to scoring functions

Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect

Development and testing of a general amber force field

Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

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2414849

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10.1016/J.JMB.2007.06.002

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371

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David L. Mobley

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