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eSOL specifications

Information


Unique identifier OMICS_05294
Name eSOL
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Taxon


  • Bacteria
    • Escherichia coli

Publication for eSOL

eSOL citations

 (6)
library_books

Protein docking refinement by convex underestimation in the low dimensional subspace of encounter complexes

2018
Sci Rep
PMCID: 5955889
PMID: 29650980
DOI: 10.1038/s41598-018-23982-3

[…] our earlier work,, we consider the following energy terms to find the interaction free energy value:E=wVDWEVDW+wSOLESOL+wCOULECOUL+wHBEHB+wDARSEDARS+wRPERP,where EVDW is the Lennard-Jones potential, ESOL is an implicit solvation term, ECOUL is the Coulomb potential, EHB is a knowledge-based hydrogen bonding term, and EDARS is a structure-based intermolecular potential that is derived from the non […]

library_books

SwissADME: a free web tool to evaluate pharmacokinetics, drug likeness and medicinal chemistry friendliness of small molecules

2017
Sci Rep
PMCID: 5335600
PMID: 28256516
DOI: 10.1038/srep42717

[…] antity of active ingredient in the small volume of such pharmaceutical dosage. Two topological methods to predict Water Solubility are included in SwissADME. The first one is an implementation of the ESOL model and the second one is adapted from Ali et al.. Both differ from the seminal general solubility equation since they avoid the melting point parameter; the latter being challenging to predict […]

library_books

A review of machine learning methods to predict the solubility of overexpressed recombinant proteins in Escherichia coli

2014
BMC Bioinformatics
PMCID: 4098780
PMID: 24885721
DOI: 10.1186/1471-2105-15-134

[…] fterwards, the best models based on the obtained accuracies are introduced. Then, the most convenient to use models are mentioned. Lastly, some data-related challenges are discussed.In terms of data, eSol is the most widely used dataset in the field. Considering input features, the following features are the most common ones computed from the protein sequence: aliphatic index, amino acid sequence […]

library_books

The Molecular Basis of Conformational Instability of the Ecdysone Receptor DNA Binding Domain Studied by In Silico and In Vitro Experiments

2014
PLoS One
PMCID: 3900457
PMID: 24465866
DOI: 10.1371/journal.pone.0086052

[…] approach, an energy-based criterion was assumed as follows: if the sum of the Lennard-Jones attractive energy (Eatr), Lennard-Jones repulsive energy (Erep) and the Lazaridis-Karplus solvation energy (Esol) terms of a given residue is less than or equal to −1.9, the residue will be classified as the hydrophobic core of the domain . In the same manner, the calculations were performed for the UspDBD […]

library_books

Peptide binding to HLA DP proteins at pH 5.0 and pH 7.0: a quantitative molecular docking study

2012
BMC Struct Biol
PMCID: 3508589
PMID: 22862845
DOI: 10.1186/1472-6807-12-20

[…] inding interface. Several energy terms are generated: Etot is the sum of all energies between the pair residues; Eatr and Erep are the Lennard – Jones attractive and repulsive energies, respectively; Esol is the solvation energy according to the Lazaridis–Karplus solvation model [], which penalizes buried polar groups; Ehbnd is the hydrogen bonding energy per residue; Epair is a statistically-bas […]

library_books

Protonate3D: Assignment of ionization states and hydrogen coordinates to macromolecular structures

2008
Proteins
PMCID: 3056144
PMID: 18814299
DOI: 10.1002/prot.22234

[…] T (log 10) (pH−pKa), where k is Boltzmann's constant and T is the temperature of the system. Because the (vertical) reaction equation H2 + PAH → PH + HAH is balanced and, by construction, E = ECOUL + ESOL is the free energy of charging and solvating the system, we may simply writeThe case of a noncovalently bound group AH near a macromolecule P is simpler in that the H2 molecule is not required to […]

Citations

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eSOL institution(s)
Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan; Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan; Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
eSOL funding source(s)
Supported in part by Grants-in-Aid for Scientific Research on Priority Area 17049009, 19037007, and 19058002 from the Ministry of Education, Culture, Sports, Science and Technology, Japan.

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