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Docking Ligands into Flexible and Solvated Macromolecules. 5. Force-Field-Based Prediction of Binding Affinities of Ligands to Proteins
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
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Derivation of class II force fields. VIII. Derivation of a general quantum mechanical force field for organic compounds
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An all atom force field for simulations of proteins and nucleic acids
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Validation of the general purpose tripos 5.2 force field
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Principles of docking: An overview of search algorithms and a guide to scoring functions
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A statistical rescoring scheme for protein–ligand docking: Consideration of entropic effect
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A Fast Flexible Docking Method using an Incremental Construction Algorithm
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Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen
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Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities
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The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
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Virtual ligand screening: strategies, perspectives and limitations
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Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”
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LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites
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Docking Ligands into Flexible and Solvated Macromolecules. 1. Development and Validation of FITTED 1.0
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Docking Ligands into Flexible and Solvated Macromolecules. 2. Development and Application of F itted 1.5 to the Virtual Screening of Potential HCV Polymerase Inhibitors
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Docking Ligands into Flexible and Solvated Macromolecules. 3. Impact of Input Ligand Conformation, Protein Flexibility, and Water Molecules on the Accuracy of Docking Programs
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Docking Ligands into Flexible and Solvated Macromolecules. 4. Are Popular Scoring Functions Accurate for this Class of Proteins?
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Free energy calculations: Applications to chemical and biochemical phenomena
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DREIDING: a generic force field for molecular simulations
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A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
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Comparative Evaluation of 11 Scoring Functions for Molecular Docking
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A Method for Induced-Fit Docking, Scoring, and Ranking of Flexible Ligands. Application to Peptidic and Pseudopeptidic β-secretase (BACE 1) Inhibitors
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Benchmarking Sets for Molecular Docking
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The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii
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Ligand binding affinity prediction by linear interaction energy methods
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Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
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DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
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Further development and validation of empirical scoring functions for structure-based binding affinity prediction
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Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go
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A new method for predicting binding affinity in computer-aided drug design
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The Many Roles of Computation in Drug Discovery
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Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Consideration of Water and Solvation Effects in Virtual Screening
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The Challenge of Affinity Prediction: Scoring Functions for Structure‐Based Virtual Screening
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Scoring Functions for Protein–Ligand Interactions
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Do electrostatic interactions make a difference in physics‐based AutoDock4 scoring function?
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Challenges and advances in computational docking: 2009 in review
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Discovery of potent polyphosphate kinase 1 (PPK1) inhibitors using structure‐based exploration of PPK1Pharmacophoric space coupled with docking analyses
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Retrospective molecular docking study of WY-25105 ligand to β-secretase and bias of the three-dimensional structure flexibility
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Experimental versus predicted affinities for ligand binding to estrogen receptor: iterative selection and rescoring of docked poses systematically improves the correlation
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Global Free Energy Scoring Functions Based on Distance-Dependent Atom-Type Pair Descriptors
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From desktop to benchtop - Developing computational tools for organic and medicinal chemistry
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