(Q87611444)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24700414%20AND%20SRC:MED&resulttype=core&format=json

12 March 2020

title

Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies (English)

1 reference

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12 March 2020

6

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12 March 2020

Ricardo A. Mata

7

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12 March 2020

Pär Söderhjelm

8

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12 March 2020

Ulf Ryde

9

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12 March 2020

author name string

Paulius Mikulskis

1

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12 March 2020

Daniela Cioloboc

2

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12 March 2020

Milica Andrejić

3

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12 March 2020

Sakshi Khare

4

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12 March 2020

Joakim Brorsson

5

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12 March 2020

publication date

4 April 2014

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Journal of Computer - Aided Molecular Design

12 March 2020

published in

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12 March 2020

volume

28

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12 March 2020

issue

4

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12 March 2020

page(s)

375-400

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Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition

12 March 2020

cites work

1 reference

12 December 2020

Paradynamics: an effective and reliable model for ab initio QM/MM free-energy calculations and related tasks

1 reference

12 December 2020

How accurate can a force field become? A polarizable multipole model combined with fragment-wise quantum-mechanical calculations

1 reference

12 December 2020

Are free energy calculations useful in practice? A comparison with rapid scoring functions for the p38 MAP kinase protein system

1 reference

12 December 2020

Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation

1 reference

12 December 2020

Guests of Differing Polarities Provide Insight into Structural Requirements for Templates of Water-Soluble Nano-Capsules

1 reference

12 December 2020

Effect of the damping function in dispersion corrected density functional theory.

1 reference

12 December 2020

The SAMPL4 host-guest blind prediction challenge: an overview.

1 reference

12 December 2020

Theory of free energy and entropy in noncovalent binding

1 reference

12 December 2020

Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations.

1 reference

12 December 2020

Development and testing of a general amber force field

1 reference

12 December 2020

Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration

1 reference

12 December 2020

Proton Transfer at Metal Sites in Proteins Studied by Quantum Mechanical Free-Energy Perturbations

1 reference

12 December 2020

Reductive half-reaction of aldehyde oxidoreductase toward acetaldehyde: Ab initio and free energy quantum mechanical/molecular mechanical calculations

1 reference

12 December 2020

An efficient method for the calculation of quantum mechanics/molecular mechanics free energies.

1 reference

12 December 2020

Improving the Efficiency of Protein-Ligand Binding Free-Energy Calculations by System Truncation.

1 reference

12 December 2020

Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations

1 reference

12 December 2020

Protein Influence on Electronic Spectra Modeled by Multipoles and Polarizabilities

1 reference

12 December 2020

How to obtain statistically converged MM/GBSA results.

1 reference

12 December 2020

Semiempirical GGA-type density functional constructed with a long-range dispersion correction.

1 reference

12 December 2020

Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors

1 reference

12 December 2020

Statistically optimal analysis of samples from multiple equilibrium states

1 reference

12 December 2020

A simple QM/MM approach for capturing polarization effects in protein-ligand binding free energy calculations.

1 reference

12 December 2020

Polarizable force fields

1 reference

12 December 2020

Efficient drug lead discovery and optimization

1 reference

12 December 2020

Quantum mechanical free energy barrier for an enzymatic reaction

1 reference

12 December 2020

The role of quantum mechanics in structure-based drug design

1 reference

12 December 2020

Density-functional approximation for the correlation energy of the inhomogeneous electron gas

1 reference

12 December 2020

A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu

1 reference

12 December 2020

Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy.

1 reference

12 December 2020

Climbing the Density Functional Ladder: Nonempirical Meta–Generalized Gradient Approximation Designed for Molecules and Solids

1 reference

12 December 2020

Do quantum mechanical energies calculated for small models of protein-active sites converge?

1 reference

12 December 2020

Estimates of ligand-binding affinities supported by quantum mechanical methods.

1 reference

12 December 2020

Blind Prediction of Binding Affinities for Charged Supramolecular Host–Guest Systems: Achievements and Shortcomings of DFT-D3

1 reference

12 December 2020

Blind prediction of host-guest binding affinities: a new SAMPL3 challenge.

1 reference

12 December 2020

Fully ab initio protein-ligand interaction energies with dispersion corrected density functional theory

1 reference

12 December 2020

Does DFT-D estimate accurate energies for the binding of ligands to metal complexes?

1 reference

12 December 2020

Corrected small basis set Hartree-Fock method for large systems

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12 December 2020

1 reference

12 December 2020

Convergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations

1 reference

12 December 2020

Well-defined, organic nanoenvironments in water: the hydrophobic effect drives a capsular assembly

1 reference

12 December 2020

Frozen Density Functional Free Energy Simulations of Redox Proteins: Computational Studies of the Reduction Potential of Plastocyanin and Rusticyanin

1 reference

12 December 2020

Density-functional exchange-energy approximation with correct asymptotic behavior

1 reference

12 December 2020

A comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations

1 reference

12 December 2020

Basic ingredients of free energy calculations: a review

1 reference

12 December 2020

Binding affinities of factor Xa inhibitors estimated by thermodynamic integration and MM/GBSA.

1 reference

12 December 2020

Binding affinities in the SAMPL3 trypsin and host–guest blind tests estimated with the MM/PBSA and LIE methods

1 reference

12 December 2020

Supramolecular binding thermodynamics by dispersion-corrected density functional theory

1 reference

12 December 2020

Non-Boltzmann sampling and Bennett's acceptance ratio method: how to profit from bending the rules.

1 reference

12 December 2020

10.1007/S10822-014-9739-X

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24700414%20AND%20SRC:MED&resulttype=core&format=json

journals/jcamd/MikulskisCAKBGMSR14

12 March 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference