A multivariate approach to investigate docking parameters' effects on docking performance

↓ Direkt till sidans innehåll
↓ Direkt till sidans sekundära innehåll (sidomenyn)

Sökning: WFRF:(Linusson Anna 1970 ) > A multivariate appr...

Andersson, David C.,1978-Umeå universitet,Kemiska institutionen (författare)

A multivariate approach to investigate docking parameters' effects on docking performance

Artikel/kapitelEngelska2007

Förlag, utgivningsår, omfång ...

2007-06-09
American Chemical Society Publications,2007
printrdacarrier

Nummerbeteckningar

LIBRIS-ID:oai:DiVA.org:umu-16146
https://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-16146URI
https://doi.org/10.1021/ci6005596DOI

Kompletterande språkuppgifter

Språk:engelska
Sammanfattning på:engelska

Ingår i deldatabas

SwePubSwePub

Klassifikation

Ämneskategori:ref swepub-contenttype
Ämneskategori:art swepub-publicationtype

Anmärkningar

Increasingly powerful docking programs for analyzing and estimating the strength of protein-ligand interactions have been developed in recent decades, and they are now valuable tools in drug discovery. Software used to perform dockings relies on a number of parameters that affect various steps in the docking procedure. However, identifying the best choices of the settings for these parameters is often challenging. Therefore, the settings of the parameters are quite often left at their default values, even though scientists with long experience with a specific docking tool know that modifying certain parameters can improve the results. In the study presented here, we have used statistical experimental design and subsequent regression based on root-mean-square deviation values using partial least-square projections to latent structures (PLS) to scrutinize the effects of different parameters on the docking performance of two software packages: FRED and GOLD. Protein-ligand complexes with a high level of ligand diversity were selected from the PDBbind database for the study, using principal component analysis based on 1D and 2D descriptors, and space-filling design. The PLS models showed quantitative relationships between the docking parameters and the ability of the programs to reproduce the ligand crystallographic conformation. The PLS models also revealed which of the parameters and what parameter settings were important for the docking performance of the two programs. Furthermore, the variation in docking results obtained with specific parameter settings for different protein-ligand complexes in the diverse set examined indicates that there is great potential for optimizing the parameter settings for selected sets of proteins.

Biuppslag (personer, institutioner, konferenser, titlar ...)

Thysell, ElinUmeå universitet,Kemiska institutionen(Swepub:umu)elnsjn00 (författare)
Lindström, AntonUmeå universitet,Kemiska institutionen(Swepub:umu)anli0018 (författare)
Bylesjö, MaxUmeå universitet,Kemiska institutionen(Swepub:umu)byomax01 (författare)
Raubacher, Florian (författare)
Linusson Jonsson, Anna,1970-Umeå universitet,Kemiska institutionen(Swepub:umu)analin99 (författare)
Umeå universitetKemiska institutionen (creator_code:org_t)

Sammanhörande titlar

Ingår i:Journal of chemical information and modeling: American Chemical Society Publications47:4, s. 1673-16871549-95961549-960X

Internetlänk

Hitta via bibliotek

Journal of chemical information and modeling (Sök värdpublikationen i LIBRIS)

Till lärosätets databas

Hitta mer i SwePub

Av författaren/redakt...: Andersson, David ...; Thysell, Elin; Lindström, Anton; Bylesjö, Max; Raubacher, Flori ...; Linusson Jonsson ...

Artiklar i publikationen: Journal of chemi ...

Av lärosätet: Umeå universitet

Sök utanför SwePub

Sök vidare i:: Google; Google Book Search; Google Scholar

Kungliga biblioteket hanterar dina personuppgifter i enlighet med EU:s dataskyddsförordning (2018), GDPR. Läs mer om hur det funkar här.
Så här hanterar KB dina uppgifter vid användning av denna tjänst.

LIBRIS.kb.se