IMPSCORE

Introducing stacking and halogen bonding effects into ligand-target interaction energy calculations

Coordinatore	STICHTING VU-VUMC    more  Organization address address: DE BOELELAAN 1105 city: AMSTERDAM postcode: 1081 HV contact info Titolo: Dr. Nome: Yvonne Cognome: Kops Email: send email Telefono: +31 205987500 Fax: +31 206462457
Nazionalità Coordinatore	Netherlands [NL]
Totale costo	183˙469 €
EC contributo	183˙469 €
Programma	FP7-PEOPLE Specific programme "People" implementing the Seventh Framework Programme of the European Community for research, technological development and demonstration activities (2007 to 2013)
Code Call	FP7-PEOPLE-2012-IEF
Funding Scheme	MC-IEF
Anno di inizio	2013
Periodo (anno-mese-giorno)	2013-05-15   -   2015-11-14

 Partecipanti

#	participant	country	role	EC contrib. [€]
1	STICHTING VU-VUMC  Organization address address: DE BOELELAAN 1105 city: AMSTERDAM postcode: 1081 HV contact info Titolo: Dr. Nome: Yvonne Cognome: Kops Email: send email Telefono: +31 205987500 Fax: +31 206462457	NL (AMSTERDAM)	coordinator	183˙469.80

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 Obiettivo del progetto (Objective)

'The subject of the present proposal is computational chemistry with specific aim to incorporate certain interactions into docking calculations. The docking technique helps the design and synthesis of efficient pharmaceuticals that act via ligand–receptor interactions. In the frame of the project, new scoring function (SF) term(s) will be introduced for selected interactions (π – π stacking and halogen bonds) using experimental enthalpic data and combined quantum-mechanical/molecular-mechanical calculations. Scoring functions play a central role in the quality and the speed of docking calculation In popular scoring functions (e.g. in the Autodock) enthalpic (ΔH) and entropic terms can be distinguished and the sum of these terms are correlated to experimental binding free energy (ΔG) values. Previous SF developments are principally based on this correlation, however, isothermal titration calorimetric (ITC) measurements afford the possibility of developing separately the two principal components. Introducing new terms for the description of the chosen special interactions, enthalpic part of the chosen SF (from the Autodock or Autodock-Vina program) will be improved with the help of fragment based ligand set augmented with experimental ΔH data. In addition to introducing new SF terms, the application of fragment based test library in SF development is also an important novelty. It has several advantages as, for instance, screening with a fragment trained SF function on the fragment universe one can capture a more diverse hit space than with the usual high throughput screening on the chemical universe. Furthermore, in case of a fragment-size ligand the investigated special interactions can be more obviously separated from other effects in the binding analysis. Finally, larger QM environment can be taken into account for a fragment-size ligand than for peptide substrates providing more accurate theoretical results.'