Parallel flexible molecular docking in computational chemistry on high performance computing clusters

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00179906%3A_____%2F15%3A10319566" target="_blank" >RIV/00179906:_____/15:10319566 - isvavai.cz</a>

Výsledek na webu

<a href="http://dx.doi.org/10.1007/978-3-319-24306-1_41" target="_blank" >http://dx.doi.org/10.1007/978-3-319-24306-1_41</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1007/978-3-319-24306-1_41" target="_blank" >10.1007/978-3-319-24306-1_41</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Parallel flexible molecular docking in computational chemistry on high performance computing clusters

Popis výsledku v původním jazyce

The main objective in pharmaceutical research is development of novel drugs with improved biological effect in specifically afflicted organisms. A common practice in drug design focuses on systematic organic derivatization of chemical structures exhibiting certain biological activity and subsequent biological in vitro evaluation of the resulted benefits. However, this classical approach can be more or less classified as a chance drug discovery, being very arduous, expensive and time consuming. Nowadays, a lot of enthusiasm is given to rationally oriented drug research techniques like computer-aided drug design, virtual screening, bioinformatics, chemometrics, quantitative structure-activity relationships, etc. In the present article, we deal with designing a high performance computing (HPC) support for flexible molecular docking (FMD) which can be beneficially utilized in structure-based virtual screening (SBVS). The principles of FMD are briefly introduced and a solution combining mes-sage passing interface (MPI) with multithreading is proposed. The merits (e.g. availability, scalability, performance) of MPI-HPC enhanced SBVS/FMD are compared with other HPC techniques utilized for novel lead structures discov-ery in medicinal chemistry.

Název v anglickém jazyce

Parallel flexible molecular docking in computational chemistry on high performance computing clusters

Popis výsledku anglicky

The main objective in pharmaceutical research is development of novel drugs with improved biological effect in specifically afflicted organisms. A common practice in drug design focuses on systematic organic derivatization of chemical structures exhibiting certain biological activity and subsequent biological in vitro evaluation of the resulted benefits. However, this classical approach can be more or less classified as a chance drug discovery, being very arduous, expensive and time consuming. Nowadays, a lot of enthusiasm is given to rationally oriented drug research techniques like computer-aided drug design, virtual screening, bioinformatics, chemometrics, quantitative structure-activity relationships, etc. In the present article, we deal with designing a high performance computing (HPC) support for flexible molecular docking (FMD) which can be beneficially utilized in structure-based virtual screening (SBVS). The principles of FMD are briefly introduced and a solution combining mes-sage passing interface (MPI) with multithreading is proposed. The merits (e.g. availability, scalability, performance) of MPI-HPC enhanced SBVS/FMD are compared with other HPC techniques utilized for novel lead structures discov-ery in medicinal chemistry.

Druh

D - Stať ve sborníku

CEP obor

IN - Informatika

OECD FORD obor

—

Projekt

—

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2015

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název statě ve sborníku

Computational Collective Intelligence (ICCCI 2015), PT II

ISBN

978-3-319-24305-4

ISSN

0302-9743

e-ISSN

—

Počet stran výsledku

10

Strana od-do

418-427

Název nakladatele

Springer

Místo vydání

Berlin

Místo konání akce

Madrid

Datum konání akce

21. 9. 2015

Typ akce podle státní příslušnosti

WRD - Celosvětová akce

Kód UT WoS článku

000366123600041