Benchmarking Platform for Ligand-Based Virtual Screening

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216208%3A11320%2F16%3A10331213" target="_blank" >RIV/00216208:11320/16:10331213 - isvavai.cz</a>

Výsledek na webu

<a href="https://doi.org/10.1109/BIBM.2016.7822693" target="_blank" >https://doi.org/10.1109/BIBM.2016.7822693</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1109/BIBM.2016.7822693" target="_blank" >10.1109/BIBM.2016.7822693</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Benchmarking Platform for Ligand-Based Virtual Screening

Popis výsledku v původním jazyce

Virtual screening (VS) of databases of chemical compounds has become a common step in the drug discovery process. Ligand-based virtual screening is a variant of VS where similarity to known active compounds is utilized in the discovery of new bioactive molecules. The cornerstone, which determines success of virtual screening, is the used molecular similarity measure. Currently, there is no superior approach to modeling molecular similarity and design of new similarity approaches is an active research field in cheminformatics. Therefore, proper benchmarking is of utter importance. In this paper, we describe common pitfalls of current approach to benchmarking of new methods. We focus on the importance of reproducibility and design of benchmarking datasets. Moreover, we identify the dataset difficulty as an important, yet not wildly utilized, property of the benchmarking data. To solve the identified issues we present a new benchmarking platform. The platform implements most commonly used molecular representations and includes datasets of varying difficulty levels as well as scripts which make the platform easy to use and extend. The existing representations are benchmarked using the proposed platform and results are presented. The benchmarking platform is available at https:// github.com/skodapetr/ lbvs-environment.

Název v anglickém jazyce

Benchmarking Platform for Ligand-Based Virtual Screening

Popis výsledku anglicky

Virtual screening (VS) of databases of chemical compounds has become a common step in the drug discovery process. Ligand-based virtual screening is a variant of VS where similarity to known active compounds is utilized in the discovery of new bioactive molecules. The cornerstone, which determines success of virtual screening, is the used molecular similarity measure. Currently, there is no superior approach to modeling molecular similarity and design of new similarity approaches is an active research field in cheminformatics. Therefore, proper benchmarking is of utter importance. In this paper, we describe common pitfalls of current approach to benchmarking of new methods. We focus on the importance of reproducibility and design of benchmarking datasets. Moreover, we identify the dataset difficulty as an important, yet not wildly utilized, property of the benchmarking data. To solve the identified issues we present a new benchmarking platform. The platform implements most commonly used molecular representations and includes datasets of varying difficulty levels as well as scripts which make the platform easy to use and extend. The existing representations are benchmarked using the proposed platform and results are presented. The benchmarking platform is available at https:// github.com/skodapetr/ lbvs-environment.

Druh

D - Stať ve sborníku

CEP obor

IN - Informatika

OECD FORD obor

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Projekt

<a href="/cs/project/GP14-29032P" target="_blank" >GP14-29032P: Efektivní explorace chemického prostoru s využitím vícekriteriální optimalizace</a><br>

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2016

Kód důvěrnosti údajů

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

Název statě ve sborníku

2016 IEEE International Conference on Bioinformatics and Biomedicine

ISBN

978-1-5090-1611-2

ISSN

—

e-ISSN

—

Počet stran výsledku

8

Strana od-do

1225-1232

Název nakladatele

IEEE (The Institute of Electrical and Electronics Engineers)

Místo vydání

Neuveden.

Místo konání akce

Shenzhen

Datum konání akce

15. 12. 2016

Typ akce podle státní příslušnosti

WRD - Celosvětová akce

Kód UT WoS článku

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