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CheML.io: an online database of ML-generated molecules.

ABSTRACT: Several recent ML algorithms for de novo molecule generation have been utilized to create an open-access database of virtual molecules. The algorithms were trained on samples from ZINC, a free database of commercially available compounds. Generated molecules, stemming from 10 different ML frameworks, along with their calculated properties were merged into a database and coupled to a web interface, which allows users to browse the data in a user friendly and convenient manner. ML-generated molecules with desired structures and properties can be retrieved with the help of a drawing widget. For the case of a specific search leading to insufficient results, users are able to create new molecules on demand. These newly created molecules will be added to the existing database and as a result, the content as well as the diversity of the database keeps growing in line with the user's requirements.

SUBMITTER: Zhumagambetov R

PROVIDER: S-EPMC9058596 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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cheML.io: an online database of ML-generated molecules.

Zhumagambetov Rustam R Kazbek Daniyar D Shakipov Mansur M Maksut Daulet D Peshkov Vsevolod A VA Fazli Siamac S

RSC advances 20201222 73

Several recent ML algorithms for <i>de novo</i> molecule generation have been utilized to create an open-access database of virtual molecules. The algorithms were trained on samples from ZINC, a free database of commercially available compounds. Generated molecules, stemming from 10 different ML frameworks, along with their calculated properties were merged into a database and coupled to a web interface, which allows users to browse the data in a user friendly and convenient manner. ML-generated ...[more]

PMID: 35516285

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Project description:BackgroundInteractions between ions and proteins have been extensively studied, yet most of the studies focus on the ion binding site. The binding mechanism for many ion binding sites can be clearly described from high resolution structures. Although knowledge accumulated on a case-by-case basis is valuable, it is also important to study the ion-protein interaction statistically. From experimentally determined structures, it is possible to examine the ion distribution around each amino acid. Such distributions can reveal relation between ions and amino acids, so it is desirable to carry out a systematic survey of 'ion-amino acid' pairing interaction and share the information with a publicly available database.ResultsThe survey in the Protein Data Bank (PDB) revealed that approximately 40% of molecules records contain at least one ion. To reduce the bias resulted from protein redundancy, the statistics were extracted from a non-redundant dataset by excluding the proteins with similar sequences. Based on the structures of protein molecules and the location of ions, the statistical distributions of ions around each proteinogenic amino acid type were investigated and further summarized in a database. To systematically quantify the interactions between ions and each amino acid, the positions of ions were mapped to the coordinate system centered at each neighboring amino acid. It was found that the distribution of ions follows the expected rules governed by the physicochemical interactions in general. Large variations were observed, reflecting the preference in 'ion-amino acid' interactions. The analysis program is written in the Python programming language. The statistical results and program are available from the online database: ion distribution in protein molecules (IDPM) at http://liulab.csrc.ac.cn/idpm/ .ConclusionThe spatial distribution of ions around amino acids is documented and analyzed. The statistics can be useful for identifying ion types for a given site in biomolecules, and can be potentially used in ion position prediction for given structures.

Dataset Information

CheML.io: an online database of ML-generated molecules.

Publications

cheML.io: an online database of ML-generated molecules.

Similar Datasets

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