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HierVLS Hierarchical Docking Protocol for Virtual Ligand Screening of Large-Molecule Databases
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Critical evaluation of search algorithms for automated molecular docking and database screening
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Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
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ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
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Positions of His‐64 and a bound water in human carbonic anhydrase II upon binding three structurally related inhibitors
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Satisfying Hydrogen Bonding Potential in Proteins
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A Fast Flexible Docking Method using an Incremental Construction Algorithm
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Predicting binding modes, binding affinities and ‘hot spots’ for protein-ligand complexes using a knowledge-based scoring function
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Structure-Based Ligand Design
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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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Binding site characteristics in structure-based virtual screening: evaluation of current docking tools
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A geometric approach to macromolecule-ligand interactions
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Iterative partial equalization of orbital electronegativity—a rapid access to atomic charges
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Structure-based drug design
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DREIDING: a generic force field for molecular simulations
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Use of MM-PBSA in Reproducing the Binding Free Energies to HIV-1 RT of TIBO Derivatives and Predicting the Binding Mode to HIV-1 RT of Efavirenz by Docking and MM-PBSA
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SMoG: de Novo Design Method Based on Simple, Fast, and Accurate Free Energy Estimates. 1. Methodology and Supporting Evidence
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Secondary Interactions Significantly Removed from the Sulfonamide Binding Pocket of Carbonic Anhydrase II Influence Inhibitor Binding Constants
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Protein-Based Virtual Screening of Chemical Databases. 1. Evaluation of Different Docking/Scoring Combinations
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A General and Fast Scoring Function for Protein−Ligand Interactions: A Simplified Potential Approach
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Two-Stage Method for Protein−Ligand Docking
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All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
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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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PRO_SELECT: Combining structure-based drug design and combinatorial chemistry for rapid lead discovery. 1. Technology
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Predicting binding modes, binding affinities and `hot spots' for protein-ligand complexes using a knowledge-based scoring function
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DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
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Comparative study of several algorithms for flexible ligand docking
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Substrate specificity and affinity of a protein modulated by bound water molecules
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Prediction of new serine proteinase inhibitors
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Prediction of structure and function of G protein-coupled receptors
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Identification of a functional water channel in cytochrome P450 enzymes
inferredcites →https://doi.org/10.1073/pnas.97.20.10712openalex-snapshot
Molecular mechanisms underlying differential odor responses of a mouse olfactory receptor
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Unexpected Binding Mode of the Sulfonamide Fluorophore 5-Dimethylamino-1-naphthalene Sulfonamide to Human Carbonic Anhydrase II
inferredcites →https://doi.org/10.1107/s0907444998007124openalex-snapshot
Databases for Protein–Ligand Complexes
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Structures of Two Thermolysin-Inhibitor Complexes That Differ by a Single Hydrogen Bond
inferredcites →https://doi.org/10.1126/science.3810157openalex-snapshot
Calculation of the Relative Change in Binding Free Energy of a Protein-Inhibitor Complex
inferredcites →https://doi.org/10.1126/science.51.1312.181openalex-snapshot
The California Institute of Technology
inferredcites →https://doi.org/10.1146/annurev.pharmtox.37.1.71openalex-snapshot
STRUCTURE-BASED DRUG DESIGN:Computational Advances
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Incoming claims: where this work appears in other papers’ reference lists and arguments.
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