Benchmarking Platform for Ligand-Based Virtual Screening

Result code in 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>

Result on the web

<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>

Result language

angličtina

Original language name

Benchmarking Platform for Ligand-Based Virtual Screening

Original language description

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.

Czech name

—

Czech description

—

Type

D - Article in proceedings

CEP classification

IN - Informatics

OECD FORD branch

—

Project

<a href="/en/project/GP14-29032P" target="_blank" >GP14-29032P: Efficient chemical space exploration using multi-objective optimization</a><br>

Continuities

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

Publication year

2016

Confidentiality

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

Article name in the collection

2016 IEEE International Conference on Bioinformatics and Biomedicine

ISBN

978-1-5090-1611-2

ISSN

—

e-ISSN

—

Number of pages

8

Pages from-to

1225-1232

Publisher name

IEEE (The Institute of Electrical and Electronics Engineers)

Place of publication

Neuveden.

Event location

Shenzhen

Event date

Dec 15, 2016

Type of event by nationality

WRD - Celosvětová akce

UT code for WoS article

—