CReM: chemically reasonable mutations

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15110%2F20%3A73606929" target="_blank" >RIV/61989592:15110/20:73606929 - isvavai.cz</a>

Result on the web

<a href="https://github.com/DrrDom/crem" target="_blank" >https://github.com/DrrDom/crem</a>

DOI - Digital Object Identifier

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Result language

angličtina

Original language name

CReM: chemically reasonable mutations

Original language description

CReM is an open-source Python framework to generate chemical structures using a fragment-based approach. It uses historical data about previously synthesized compounds (e.g. ChEMBL) to generate new ones. Known molecules are exhaustively fragmented by breaking acyclic single bonds and the created fragment database is used to generate new structures by replacement of one fragment with others. The major feature is to take into account local context (chemical environment) of fragments and in the course of generation we exchange only fragments occurring in the same chemical context that leads to synthetically more feasible replacements. The local context is encoded by all atoms on the specified maximum distance (radius) from attachment points of a fragment. We demonstrated on a series of ligand-based Guacamol benchmarks that this approach is highly competitive to modern generative models based on neural networks and other state-of-the-art approaches in terms of the quality of generated compounds and their synthetic feasibility. On these benchmarks we also demonstrated that synthetic accessibility of generated compounds can be improved by considering the context of a larger radius and by selection of synthetically more feasible compounds to create fragment databases.

Czech name

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Czech description

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Type

R - Software

CEP classification

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OECD FORD branch

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Project

<a href="/en/project/LTARF18013" target="_blank" >LTARF18013: Improve the output of primary screening of biologically active compounds using computational models</a><br>

Continuities

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

Publication year

2020

Confidentiality

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

Internal product ID

CReM

Technical parameters

CReM is a cross-platform framework to generate structures of chemical compounds and requires Python 3.6 and RDKit 2019.

Economical parameters

speed up and facilitate de novo design and optimization of compound properties for drug development research; can be integrated in other software as a Python module

Owner IČO

61989592

Owner name

ÚMTM