ClassyFire: automated chemical classification with a comprehensive, computable taxonomy Tập 8 Số 1 - 2016
Yannick Djoumbou-Feunang, Roman Eisner, Craig Knox, Leonid Chepelev, Janna Hastings, Gareth Owen, Eoin Fahy, Christoph Steinbeck, Shankar Subramanian, Evan Bolton, Russell Greiner, David S. Wishart
COCONUT online: Collection of Open Natural Products database - 2021
Maria Sorokina, Peter Merseburger, Kohulan Rajan, Mehmet Aziz Yirik, Christoph Steinbeck
AbstractNatural products (NPs) are small molecules produced by living organisms
with potential applications in pharmacology and other industries as many of them
are bioactive. This potential raised great interest in NP research around the
world and in different application fields, therefore, over the years a
multiplication of generalistic and thematic NP databases has been observed.
However, there... hiện toàn bộ
Towards a Universal SMILES representation - A standard method to generate canonical SMILES based on the InChI - 2012
Noel M. O’Boyle
Abstract Background There are two line notations of chemical structures that
have established themselves in the field: the SMILES string and the InChI
string. The InChI aims to provide a unique, or canonical, identifier for
chemical structures, while SMILES strings are widely used for storage and
interchange of chemical structures, but no standard exists to generate a
canonical SMILES string. Resu... hiện toàn bộ
Transformer-CNN: Swiss knife for QSAR modeling and interpretation - 2020
Pavel Karpov, Guillaume Godin, Igor V. Tetko
AbstractWe present SMILES-embeddings derived from the internal encoder state of
a Transformer [1] model trained to canonize SMILES as a Seq2Seq problem. Using a
CharNN [2] architecture upon the embeddings results in higher quality
interpretable QSAR/QSPR models on diverse benchmark datasets including
regression and classification tasks. The proposed Transformer-CNN method uses
SMILES augmentation ... hiện toàn bộ
Data governance in predictive toxicology: A review Tập 3 - Trang 1-16 - 2011
Xin Fu, Anna Wojak, Daniel Neagu, Mick Ridley, Kim Travis
Due to recent advances in data storage and sharing for further data processing
in predictive toxicology, there is an increasing need for flexible data
representations, secure and consistent data curation and automated data quality
checking. Toxicity prediction involves multidisciplinary data. There are
hundreds of collections of chemical, biological and toxicological data that are
widely dispersed... hiện toàn bộ
Towards reproducible computational drug discovery - 2020
Nalini Schaduangrat, Samuel Lampa, Saw Simeon, M. Paul Gleeson, Ola Spjuth, Chanin Nantasenamat
AbstractThe reproducibility of experiments has been a long standing impediment
for further scientific progress. Computational methods have been instrumental in
drug discovery efforts owing to its multifaceted utilization for data
collection, pre-processing, analysis and inference. This article provides an
in-depth coverage on the reproducibility of computational drug discovery. This
review explore... hiện toàn bộ