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A new implicit solvent model for protein–ligand docking

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO)

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Ligand solvation in molecular docking

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Exhaustive docking of molecular fragments with electrostatic solvation

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Efficient electrostatic solvation model for protein-fragment docking

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Solvation energy density occlusion approximation for evaluation of desolvation penalties in biomolecular interactions

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Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal‐gas entropy correction?

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FDS: Flexible ligand and receptor docking with a continuum solvent model and soft‐core energy function

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Rapid grid‐based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects

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A critical analysis of continuum electrostatics: The screened Coulomb potential–implicit solvent model and the study of the alanine dipeptide and discrimination of misfolded structures of proteins

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What are the dielectric “constants” of proteins and how to validate electrostatic models?

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Salt Effects on Ligand-DNA Binding

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Satisfying Hydrogen Bonding Potential in Proteins

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Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4

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MOPAC: A semiempirical molecular orbital program

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Virtual Screening against Highly Charged Active Sites: Identifying Substrates of Alpha−Beta Barrel Enzymes

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Theoretical Methods for the Description of the Solvent Effect in Biomolecular Systems

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Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models

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A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

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Semianalytical treatment of solvation for molecular mechanics and dynamics

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Inclusion of Solvation in Ligand Binding Free Energy Calculations Using the Generalized-Born Model

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Ligand−Protein DataBase: Linking Protein−Ligand Complex Structures to Binding Data

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Evaluation of Docking Functions for Protein−Ligand Docking

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A Computational Model of Binding Thermodynamics: The Design of Cyclin-dependent Kinase 2 Inhibitors

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Virtual Screening with Flexible Docking and COMBINE-Based Models. Application to a Series of Factor Xa Inhibitors

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Assessing Scoring Functions for Protein−Ligand Interactions

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Validation and Use of the MM-PBSA Approach for Drug Discovery

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Hierarchical Database Screenings for HIV-1 Reverse Transcriptase Using a Pharmacophore Model, Rigid Docking, Solvation Docking, and MM−PB/SA

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Efficient Evaluation of Binding Free Energy Using Continuum Electrostatics Solvation

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Assessment of Solvation Effects on Calculated Binding Affinity Differences: Trypsin Inhibition by Flavonoids as a Model System for Congeneric Series.

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Pairwise GB/SA Scoring Function for Structure-based Drug Design

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Protein/Ligand Binding Free Energies Calculated with Quantum Mechanics/Molecular Mechanics

inferredcites →https://doi.org/10.1021/jp052883sopenalex-snapshot

Limitations of Atom-Centered Dielectric Functions in Implicit Solvent Models

inferredcites →https://doi.org/10.1021/jp060334wopenalex-snapshot

Electrostatics of Ligand Binding: Parametrization of the Generalized Born Model and Comparison with the Poisson−Boltzmann Approach

inferredcites →https://doi.org/10.1021/jp993895eopenalex-snapshot

A General Treatment of Solvent Effects Based on Screened Coulomb Potentials

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Characterization of Hydrogen Bonding in a Continuum Solvent Model

inferredcites →https://doi.org/10.1073/pnas.92.10.4691openalex-snapshot

On the magnitude of the electrostatic contribution to ligand-DNA interactions.

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Classical Electrostatics in Biology and Chemistry

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Biomolecular Simulations: Recent Developments in Force Fields, Simulations of Enzyme Catalysis, Protein-Ligand, Protein-Protein, and Protein-Nucleic Acid Noncovalent Interactions

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Generalized Born Models of Macromolecular Solvation Effects

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Virtual Ligand Screening against Escherichia coli Dihydrofolate Reductase: Improving Docking Enrichment Using Physics-Based Methods

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Docking: Successes and Challenges

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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In memoriam

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Structural Modeling in Systems Biology

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Molecular Docking: A Structure-Based Approach for Drug Repurposing

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Self-Complementarity within Proteins: Bridging the Gap between Binding and Folding

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Parameterization of the hydration free energy computations for organic solutes in the framework of the implicit solvent model with the nonuniform dielectric function

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Rapid Context-Dependent Ligand Desolvation in Molecular Docking

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Structure-Based Discovery of Novel Non-nucleosidic DNA Alkyltransferase Inhibitors: Virtual Screening and in Vitro and in Vivo Activities

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An Integrated Approach to Ligand- and Structure-Based Drug Design: Development and Application to a Series of Serine Protease Inhibitors

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MM-ISMSA: An Ultrafast and Accurate Scoring Function for Protein–Protein Docking

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Protein−Ion Binding Process on Finite Macromolecular Concentration. A Poisson−Boltzmann and Monte Carlo Study

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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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COMparative BINding Energy (COMBINE) Analysis as a Structure-Based 3D-QSAR Method

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Computational Strategies and Challenges for Targeting Protein–Protein Interactions with Small Molecules

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Identification of the naphthoquinone derivative inhibitors binding site in heat shock protein 90: an induced-fit docking, molecular dynamics and 3D-QSAR study

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Structural features of mammalian histidine decarboxylase reveal the basis for specific inhibition

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Pneumococcal phosphoglycerate kinase interacts with plasminogen and its tissue activator

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Derivation of Equations Describing Distance Solute Oscillation of Induced Solvent Polarization

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Esterase LpEst1 from Lactobacillus plantarum: A Novel and Atypical Member of the αβ Hydrolase Superfamily of Enzymes

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Theoretical and computational modeling of rna-ligand interactions

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Allosteric Inhibition of Neutral Sphingomyelinase 2 (nSMase2) by DPTIP: From Antiflaviviral Activity to Deciphering Its Binding Site through In Silico Studies and Experimental Validation

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Molecular Docking

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