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Application of a Molecular Dynamics Simulation Method with a Generalized Effective Potential to the Flexible Molecular Docking Problems
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Docking by Monte Carlo minimization with a solvation correction: Application to an FKBP?substrate complex
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Critical evaluation of search algorithms for automated molecular docking and database screening
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Docking small ligands in flexible binding sites
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Assessing energy functions for flexible docking
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Assessing search strategies for flexible docking
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Flexible docking allowing induced fit in proteins: Insights from an open to closed conformational isomers
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CHARMM : A program for macromolecular energy, minimization, and dynamics calculations
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Automated docking of substrates to proteins by simulated annealing
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Molecular dynamics simulation of the docking of substrates to proteins
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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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Flexible ligand docking using a genetic algorithm
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Possible generalization of Boltzmann-Gibbs statistics
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Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
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Crystal structure of the Cys2 activator-binding domain of protein kinase Cδ in complex with phorbol ester
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Flexible docking of a ligand peptide to a receptor protein by multicanonical molecular dynamics simulation
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Complexes of HIV-1 Reverse Transcriptase with Inhibitors of the HEPT Series Reveal Conformational Changes Relevant to the Design of Potent Non-Nucleoside Inhibitors
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All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
inferredcites →https://doi.org/10.1023/a:1008005918983openalex-snapshot
MCDOCK: A Monte Carlo simulation approach to the molecular docking problem
inferredcites →https://doi.org/10.1063/1.448118openalex-snapshot
Molecular dynamics with coupling to an external bath
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Method for accelerating chain folding and mixing
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On Monte Carlo and molecular dynamics methods inspired by Tsallis statistics: Methodology, optimization, and application to atomic clusters
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Folding of a 16-residue helical peptide using molecular dynamics simulation with Tsallis effective potential
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Quaternary ligand binding to aromatic residues in the active-site gorge of acetylcholinesterase.
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Generalized statistical mechanics: connection with thermodynamics
inferredcites →https://doi.org/10.1103/physreve.53.r3055openalex-snapshot
Generalized simulated annealing algorithms using Tsallis statistics: Application to conformational optimization of a tetrapeptide
inferredcites →https://doi.org/10.1126/science.2911722openalex-snapshot
Structural Origins of High-Affinity Biotin Binding to Streptavidin
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Principles of flexible protein–protein docking
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Generalized Ensemble Molecular Dynamics Methods
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Protein Ligand Docking in Drug Discovery
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Accounting for global protein deformability during protein–protein and protein–ligand docking
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Spirohydantoin derivatives of thiopyrano[2,3-b]pyridin-4(4H)-one as potent in vitro and in vivo aldose reductase inhibitors
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Molecular Dynamics: Survey of Methods for Simulating the Activity of Proteins
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Molecular Docking at a Glance
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