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BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark [email protected] QxPR methods in biomedicine – effect of geometry optimization Åsmund Rinnan

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Page 1: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine

BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan

Royal Veterinary and Agricultural UniversityDenmark

[email protected]

QxPR methods in biomedicine – effect of geometry optimization

Åsmund Rinnan

Page 2: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine

BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan

Royal Veterinary and Agricultural UniversityDenmark

[email protected]

QSxR?! QSAR?? QSPR!?

• Quantitative• Structure• Activity or

Property• Relationship

Estrogen -receptor

Page 3: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine

BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan

Royal Veterinary and Agricultural UniversityDenmark

[email protected]

Basics of QSxR

2D 3D

O

OHO

OH

Page 4: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine

BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan

Royal Veterinary and Agricultural UniversityDenmark

[email protected]

Basic of QSxR3D Descriptors

MW: 270.241Dipole: 3.44SASA: 470.87FISA: 182.33PISA: 288.54Volume: 795.13DonorHB: 2AccptHB: 3.75Dip^2/V: 0.0149Ac*DN^.5/SA: 0.0113

Page 5: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine

BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan

Royal Veterinary and Agricultural UniversityDenmark

[email protected]

Basic of QSxR3D Descriptors

MW: 270.241Dipole: 3.44SASA: 470.87FISA: 182.33PISA: 288.54Volume: 795.13DonorHB: 2AccptHB: 3.75Dip^2/V: 0.0149Ac*DN^.5/SA: 0.0113

Page 6: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine

BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan

Royal Veterinary and Agricultural UniversityDenmark

[email protected]

Basics of QSxRDescriptors PLS

B

And the rest is chemometrics…

Attributeof interest

Page 7: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine

BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan

Royal Veterinary and Agricultural UniversityDenmark

[email protected]

Geometry optimizationBasics

O

OHO

OH

days

sec

min

h

Page 8: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine

BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan

Royal Veterinary and Agricultural UniversityDenmark

[email protected]

Accuracy vs. Time

UFF

AM1

PM3 HF

B3LYP

Mechanical Semi-empiricalDensity

FunctionalTheorem

Time consumption

Seconds Days

Theoretical level

IntroductionQuestionStudyResultsSummary

MM3*

Page 9: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine

BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan

Royal Veterinary and Agricultural UniversityDenmark

[email protected]

Accuracy vs. Time

UFF

AM1

PM3 HF

B3LYP

Mechanical Semi-empiricalDensity

FunctionalTheorem

Time consumption

Seconds Days

Theoretical level

IntroductionQuestionStudyResultsSummary

MM3*

1 80Dielectric constant

Page 10: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine

BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan

Royal Veterinary and Agricultural UniversityDenmark

[email protected]

Accuracy vs. Time

UFF

AM1

PM3 HF

Mechanical Semi-empiricalDensity

FunctionalTheorem

Time consumption

Seconds Days

Theoretical level

IntroductionQuestionStudyResultsSummary

MM3*

6-31g(d,p)

Basis setsSTO-3g

6-31gB3LYP

Page 11: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine

BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan

Royal Veterinary and Agricultural UniversityDenmark

[email protected]

DataDatasets

O

OHO

OH

IsoflavonoidsOH

Aglycons

Estrogen like

compounds

Page 12: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine

BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan

Royal Veterinary and Agricultural UniversityDenmark

[email protected]

O

O

OH

Isoflavonoids

Estrogen like

compounds

DataProperties

Melting point

Page 13: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine

BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan

Royal Veterinary and Agricultural UniversityDenmark

[email protected]

DataProperties

OHAglycons

log P

Page 14: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine

BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan

Royal Veterinary and Agricultural UniversityDenmark

[email protected]

DataOverview

UFF

AM1

PM3

HF

B3LYP

MM3*

Meltin

g p

oin

tlo

g P

x 2

x 3

x 3

Page 15: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine

BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan

Royal Veterinary and Agricultural UniversityDenmark

[email protected]

DataDescriptors

Page 16: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine

BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan

Royal Veterinary and Agricultural UniversityDenmark

[email protected]

MethodsValidation

Leave-one out cross-validation

Page 17: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine

BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan

Royal Veterinary and Agricultural UniversityDenmark

[email protected]

MethodsVariable selection

Variable selection:• Jack-knifing• Principal variables

Page 18: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine

BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan

Royal Veterinary and Agricultural UniversityDenmark

[email protected]

ResultsDescriptor package

Page 19: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine

BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan

Royal Veterinary and Agricultural UniversityDenmark

[email protected]

ResultsDistance to optimal

Aglycons

Estrogen-like Isoflavonoids

Page 20: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine

BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan

Royal Veterinary and Agricultural UniversityDenmark

[email protected]

ResultsPrediction qualityAglycons

Estrogen-like Isoflavonoids

Page 21: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine

BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan

Royal Veterinary and Agricultural UniversityDenmark

[email protected]

Conclusion

UFF

AM1

PM3 HF

B3LYP

Mechanical Semi-empiricalDensity

FunctionalTheorem

Time consumption

Seconds Days

Theoretical level

MM3*


First tuesday bergen 04.09.2012 rune rinnan

Removal of the 1st order Rayleigh scatter effect Åsmund Rinnan

ResearchArticle 2D-QSAR and 3D-QSAR Analyses for EGFR ...downloads.hindawi.com/journals/bmri/2017/4649191.pdfResearchArticle 2D-QSAR and 3D-QSAR Analyses for EGFR Inhibitors ManmanZhao,1

QSAR Assign

Quantitative Structure Activity Relationships QSAR and 3D-QSAR Chapter 18

Brian Steffenson,UM Åsmund Bjørnstad NLH

DISEÑO DE FÁRMACOS - doctoradoquimed.es · 3 SARMC Diseño de Fármacos. QSAR y QSAR-3D. QSAR y QSAR-3D I- Introducción. II- Caracterización de receptores. Mapeo del receptor

Åsmund Skjæveland Magnetic Distortion of HPD Images

Qsar Lecture

Riley Rinnan Architecture Portfolio

3D- QSAR. QSAR A QSAR is a mathematical relationship between a biological activity of a molecular system and its physicochemical parameters. QSAR attempts

QSAR Design of Discovery Libraries for Solids Based on QSAR Models 2005 QSAR and rial Science

Åsmund B. Nilsen

The effect of ozone on VOC- emission from peatland Åsmund Rinnan Quality & Technology Department of Food Science Faculty of Life Sciences University of

Åsmund Møll Frengstad

Getting rid of Rayleigh Åsmund Rinnan. Introduction Fluorescence Light source Sample Detector Excites sample Emitted from sample

QSAR (Summary)

Åsmund Birkeland Vessels and Blood Flow from Ultrasound

HWILUM IC ME RESTE; HE SCEAL RINNAN FORÐ: DOS …

PÅL HERMANSEN Seeds for the Worldpalhermansen.com/wp-content/uploads/2014/02/engel... · Åsmund Asdal, Norwegian centre for genetic resources, Åsmund Bjørnstad and Even Bratberg,

Rune Rinnan 2 November First Tuesday

NIR Åsmund Rinnan, KU-LIFE, Denmark, [email protected] Pre-processing of NIR Åsmund Rinnan

QSAR Webinar

Quantitative Structure Activity Relationships QSAR and 3D-QSAR

NIR Preprocessing With focus on NIR Åsmund Rinnan, Frans van den Berg, Rasmus Bro, Søren Balling Engelsen, Lars Nørgaard, Jonas Thygesen

metodologie qsar

Daniel og Åsmund Holten - Brosjyre 2014

(Rinnan, in prep.). (Schneider 2001) (Schneider 2009)

Sensors Rinnan

Introduction What is QSAR? - Anil Mishra · QSAR Notes of Dr. Anil Mishra at 1 QSAR 1 Introduction QSAR Quantitative Structure-Activity Relationships

Ofte stilte spørsmål hos meglerbordet - Åsmund Sveen, Megler

Riley Rinnan Design Portfolio II

Qsar Sabah

Rinnan papillaariset tuumorit

“Quantitative Structure Activity Relationship (QSAR) …qualitynano.eu/.../7.QSARs-Lecture_CeydaOksel.pdfQSAR (Quantitative Structure‐Activity Relationship) nano‐QSAR QSAR models