An improved method to predict the entropy term with the MM/PBSA approach. (Q46378945)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18781280%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

title

An improved method to predict the entropy term with the MM/PBSA approach (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18781280%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18781280%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

Ulf Ryde

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18781280%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

author name string

Ulf Ryde

series ordinal

2

1 reference

21 December 2017

http://europepmc.org/abstract/MED/18781280

publication date

10 September 2008

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18781280%20AND%20SRC:MED&resulttype=core&format=json

Journal of Computer - Aided Molecular Design

14 January 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18781280%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

volume

23

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18781280%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

issue

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18781280%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

page(s)

63-71

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18781280%20AND%20SRC:MED&resulttype=core&format=json

Novel scoring functions comprising QXP, SASA, and protein side-chain entropy terms.

14 January 2020

cites work

1 reference

Crossref

https://api.crossref.org/works/10.1007%2FS10822-008-9238-Z

Loss of translational entropy in binding, folding, and catalysis

21 January 2018

1 reference

12 December 2020

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

1 reference

12 December 2020

Validation and use of the MM-PBSA approach for drug discovery

1 reference

12 December 2020

Ligand binding affinity prediction by linear interaction energy methods

1 reference

12 December 2020

Development and testing of a general amber force field

1 reference

12 December 2020

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.

1 reference

12 December 2020

A quantum mechanics-based scoring function: study of zinc ion-mediated ligand binding.

1 reference

12 December 2020

Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: insight into structure-based ligand design

1 reference

12 December 2020

Evaluating the molecular mechanics poisson-boltzmann surface area free energy method using a congeneric series of ligands to p38 MAP kinase

1 reference

12 December 2020

The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure

1 reference

12 December 2020

Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf.

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

Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis

1 reference

12 December 2020

Novel mechanism of interaction of p85 subunit of phosphatidylinositol 3-kinase and ErbB3 receptor-derived phosphotyrosyl peptides.

1 reference

12 December 2020

Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy

1 reference

12 December 2020

Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches

1 reference

12 December 2020

Conformational dependence of charges in protein simulations.

1 reference

12 December 2020

Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models

1 reference

12 December 2020

Design and quantitative structure-activity relationship of 3-amidinobenzyl-1H-indole-2-carboxamides as potent, nonchiral, and selective inhibitors of blood coagulation factor Xa

1 reference

12 December 2020

Ligand affinities predicted with the MM/PBSA method: dependence on the simulation method and the force field.

1 reference

12 December 2020

Transition-metal systems in biochemistry studied by high-accuracy quantum chemical methods

1 reference

12 December 2020

The statistical-thermodynamic basis for computation of binding affinities: a critical review

1 reference

12 December 2020

High-throughput calculation of protein-ligand binding affinities: modification and adaptation of the MM-PBSA protocol to enterprise grid computing.

1 reference

12 December 2020

Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

1 reference

12 December 2020

Very fast empirical prediction and rationalization of protein pKa values

1 reference

12 December 2020

Exploring protein native states and large-scale conformational changes with a modified generalized born model

1 reference

12 December 2020

Transition-State Docking of Flunitrazepam and Progesterone in Cytochrome P450.

1 reference

12 December 2020

Contributions to the binding free energy of ligands to avidin and streptavidin.

1 reference

12 December 2020

Free energy via molecular simulation: applications to chemical and biomolecular systems

1 reference

12 December 2020

10.1007/S10822-008-9238-Z

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18781280%20AND%20SRC:MED&resulttype=core&format=json

journals/jcamd/KongstedR09

14 January 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

release_k6nee4wchrgbvb6xehowtgefli

28 January 2021

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/k6nee4wchrgbvb6xehowtgefli

24 November 2022

mapped directly with Wikidata item

1 reference