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Multiscale Generalized Born Modeling of Ligand Binding Energies for Virtual Database Screening

https://doi.org/10.1021/jp901212t
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What this work says

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

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Comment on the validation of continuum electrostatics models
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Rapid boundary element solvation electrostatics calculations in folding simulations: Successful folding of a 23-residue peptide
inferredcites →https://doi.org/10.1002/jcc.10126openalex-snapshot
Effective Born radii in the generalized Born approximation: The importance of being perfect
inferredcites →https://doi.org/10.1002/jcc.10261openalex-snapshot
On the transferability of hydration‐parametrized continuum electrostatics models to solvated binding calculations
inferredcites →https://doi.org/10.1002/jcc.10272openalex-snapshot
New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations
inferredcites →https://doi.org/10.1002/jcc.1032openalex-snapshot
A smooth permittivity function for Poisson–Boltzmann solvation methods
inferredcites →https://doi.org/10.1002/jcc.10321openalex-snapshot
Generalized born model with a simple smoothing function
inferredcites →https://doi.org/10.1002/jcc.10378openalex-snapshot
Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures
inferredcites →https://doi.org/10.1002/jcc.1161openalex-snapshot
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
inferredcites →https://doi.org/10.1002/jcc.20821openalex-snapshot
Accurate prediction of protonation state as a prerequisite for reliable MM‐PB(GB)SA binding free energy calculations of HIV‐1 protease inhibitors
inferredcites →https://doi.org/10.1016/0009-2614(95)01082-kopenalex-snapshot
Pairwise solute descreening of solute charges from a dielectric medium
inferredcites →https://doi.org/10.1016/j.sbi.2008.01.003openalex-snapshot
Recent advances in implicit solvent-based methods for biomolecular simulations
inferredcites →https://doi.org/10.1016/s1367-5931(02)00339-3openalex-snapshot
Lead discovery using molecular docking
inferredcites →https://doi.org/10.1021/cr040426mopenalex-snapshot
Molecular Dynamics: Survey of Methods for Simulating the Activity of Proteins
inferredcites →https://doi.org/10.1021/ja00124a002openalex-snapshot
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
inferredcites →https://doi.org/10.1021/ja00172a038openalex-snapshot
Semianalytical treatment of solvation for molecular mechanics and dynamics
inferredcites →https://doi.org/10.1021/ja984102popenalex-snapshot
Inclusion of Solvation in Ligand Binding Free Energy Calculations Using the Generalized-Born Model
inferredcites →https://doi.org/10.1021/jp0312518openalex-snapshot
Pairwise GB/SA Scoring Function for Structure-based Drug Design
inferredcites →https://doi.org/10.1021/jp046307sopenalex-snapshot
Comparative Study of Generalized Born Models: Born Radii and Peptide Folding
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/jp066284copenalex-snapshot
GBr 6 : A Parameterization-Free, Accurate, Analytical Generalized Born Method
inferredcites →https://doi.org/10.1021/jp961710nopenalex-snapshot
Parametrized Models of Aqueous Free Energies of Solvation Based on Pairwise Descreening of Solute Atomic Charges from a Dielectric Medium
inferredcites →https://doi.org/10.1021/jp961992ropenalex-snapshot
The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii
inferredcites →https://doi.org/10.1021/jp9714227openalex-snapshot
Continuum Electrostatic Energies of Macromolecules in Aqueous Solutions
inferredcites →https://doi.org/10.1021/jp982533oopenalex-snapshot
Generalized Born Model Based on a Surface Integral Formulation
inferredcites →https://doi.org/10.1021/jp984440copenalex-snapshot
Development of a Generalized Born Model Parametrization for Proteins and Nucleic Acids
inferredcites →https://doi.org/10.1021/jp994072sopenalex-snapshot
Modification of the Generalized Born Model Suitable for Macromolecules
inferredcites →https://doi.org/10.1063/1.1480013openalex-snapshot
Novel generalized Born methods
inferredcites →https://doi.org/10.1063/1.1595641openalex-snapshot
Deficiency of the Coulomb-field approximation in the generalized Born model: An improved formula for Born radii evaluation
inferredcites →https://doi.org/10.1063/1.2735322openalex-snapshot
G Br 6 NL : A generalized Born method for accurately reproducing solvation energy of the nonlinear Poisson-Boltzmann equation
inferredcites →https://doi.org/10.1063/1.2783847openalex-snapshot
Analysis of integral expressions for effective Born radii
inferredcites →https://doi.org/10.1063/1.476697openalex-snapshot
A modification of the generalized Born theory for improved estimates of solvation energies and pK shifts
inferredcites →https://doi.org/10.1073/pnas.181342398openalex-snapshot
Electrostatics of nanosystems: Application to microtubules and the ribosome
inferredcites →https://doi.org/10.1073/pnas.251265598openalex-snapshot
Computational study of protein specificity: The molecular basis of HIV-1 protease drug resistance
inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot
The Protein Data Bank
inferredcites →https://doi.org/10.1146/annurev.biophys.32.110601.142532openalex-snapshot
Molecular Recognition and Docking Algorithms
inferredcites →https://doi.org/10.1146/annurev.biophys.36.040306.132550openalex-snapshot
Calculation of Protein-Ligand Binding Affinities
inferredcites →https://doi.org/10.1146/annurev.physchem.51.1.129openalex-snapshot
Generalized Born Models of Macromolecular Solvation Effects

What points at this work

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

inferred← citeshttps://doi.org/10.1007/s00894-015-2716-zopenalex-snapshot
Computationally unraveling how ceritinib overcomes drug-resistance mutations in ALK-rearranged lung cancer
inferred← citeshttps://doi.org/10.1016/j.cpc.2011.02.013openalex-snapshot
Biomolecular electrostatics using a fast multipole BEM on up to 512 gpus and a billion unknowns
inferred← citeshttps://doi.org/10.1016/s1574-1400(10)06014-7openalex-snapshot
Mean-Force Scoring Functions for Protein–Ligand Binding
inferred← citeshttps://doi.org/10.1021/acs.jctc.6c00299openalex-snapshot
Monte Carlo-Based Prediction of Residual Dipolar Couplings in Weakly Aligned Molecules
inferred← citeshttps://doi.org/10.1021/acs.jpcb.4c08592openalex-snapshot
An Implicit Solvation Model for Binding Free Energy Estimation in Nonaqueous Solution
inferred← citeshttps://doi.org/10.1021/ci2000727openalex-snapshot
Scoring and Lessons Learned with the CSAR Benchmark Using an Improved Iterative Knowledge-Based Scoring Function
inferred← citeshttps://doi.org/10.1021/jp101461sopenalex-snapshot
An MM/3D-RISM Approach for Ligand Binding Affinities
inferred← citeshttps://doi.org/10.1039/c0cp00151aopenalex-snapshot
Scoring functions and their evaluation methods for protein–ligand docking: recent advances and future directions
inferred← citeshttps://doi.org/10.1063/1.3641485openalex-snapshot
Mathematical analysis of the boundary-integral based electrostatics estimation approximation for molecular solvation: Exact results for spherical inclusions
inferred← citeshttps://doi.org/10.1063/1674-0068/cjcp2505069openalex-snapshot
Integrating multiple time step method and implicit solvent model for molecular dynamics simulations of proteins
inferred← citeshttps://doi.org/10.1088/1478-3975/8/3/035001openalex-snapshot
On the role of electrostatics in protein–protein interactions
inferred← citeshttps://doi.org/10.1088/1478-3975/aa5ee7openalex-snapshot
Insights into the ion-coupling mechanism in the MATE transporter NorM-VC
inferred← citeshttps://doi.org/10.2174/1389450119666181022153016openalex-snapshot
Molecular Docking: Challenges, Advances and its Use in Drug Discovery Perspective
inferred← citeshttps://doi.org/10.3390/ijms11083016openalex-snapshot
Advances and Challenges in Protein-Ligand Docking
inferred← citeshttps://doi.org/10.3390/molecules190710150openalex-snapshot
Challenges, Applications, and Recent Advances of Protein-Ligand Docking in Structure-Based Drug Design
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