Linked Life Data

19462571

Source:http://linkedlifedata.com/resource/pubmed/id/19462571

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
43
pubmed:dateCreated
2009-5-25
pubmed:abstractText
We present a comparison of various computational approaches aiming at predicting the binding free energy in ligand-protein systems where the ligand is located within a highly hydrophobic cavity. The relative binding free energy between similar ligands is obtained by means of the thermodynamic integration (TI) method and compared to experimental data obtained through isothermal titration calorimetry measurements. The absolute free energy of binding prediction was obtained on a similar system (a pyrazine derivative bound to a lipocalin) by TI, potential of mean force (PMF) and also by means of the MMPBSA protocols. Although the TI protocol performs poorly either with an explicit or an implicit solvation scheme, the PMF calculation using an implicit solvation scheme leads to encouraging results, with a prediction of the binding affinity being 2 kcal mol(-1) lower than the experimental value. The use of an implicit solvation scheme appears to be well suited for the study of such hydrophobic systems, due to the lack of water molecules within the binding site.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Nov
pubmed:issn
1463-9076
pubmed:author
pubmed:issnType
Print
pubmed:day
21
pubmed:volume
9
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
5761-71
pubmed:meshHeading
pubmed:year
2007
pubmed:articleTitle
Binding free energy prediction in strongly hydrophobic biomolecular systems.
pubmed:affiliation
LCMBA, Faculté des sciences de Nice-Sophia Antipolis, Centre National de la Recherche Scientifique, UMR 6001, Universitè de Nice-Sophia-Antipolis, UFR Sciences, Parc Valrose, 28, avenue Valrose, 06108 Nice Cedex 2, France.
pubmed:publicationType
Journal Article