Ualign: pushing the limit of template-free retrosynthesis prediction with unsupervised SMILES alignment
BMC | Journal of Cheminformatics
by Kaipeng Zeng, Bo Yang, Xin Zhao, Yu Zhang, Fan Nie, Xiaokang Yang, Yaohui Jin and Yanyan Xu
2d ago
Retrosynthesis planning poses a formidable challenge in the organic chemical industry, particularly in pharmaceuticals. Single-step retrosynthesis prediction, a crucial step in the planning process, has witnes ..read more
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LVPocket: integrated 3D global-local information to protein binding pockets prediction with transfer learning of protein structure classification
BMC | Journal of Cheminformatics
by Ruifeng Zhou, Jing Fan, Sishu Li, Wenjie Zeng, Yilun Chen, Xiaoshan Zheng, Hongyang Chen and Jun Liao
2d ago
Previous deep learning methods for predicting protein binding pockets mainly employed 3D convolution, yet an abundance of convolution operations may lead the model to excessively prioritize local information ..read more
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Advancements in hand-drawn chemical structure recognition through an enhanced DECIMER architecture
BMC | Journal of Cheminformatics
by Kohulan Rajan, Henning Otto Brinkhaus, Achim Zielesny and Christoph Steinbeck
1w ago
Accurate recognition of hand-drawn chemical structures is crucial for digitising hand-written chemical information in traditional laboratory notebooks or facilitating stylus-based structure entry on tablets or ..read more
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PromptSMILES: prompting for scaffold decoration and fragment linking in chemical language models
BMC | Journal of Cheminformatics
by Morgan Thomas, Mazen Ahmad, Gary Tresadern and Gianni de Fabritiis
1w ago
SMILES-based generative models are amongst the most robust and successful recent methods used to augment drug design. They are typically used for complete de novo generation, however, scaffold decoration and f ..read more
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AutoTemplate: enhancing chemical reaction datasets for machine learning applications in organic chemistry
BMC | Journal of Cheminformatics
by Lung-Yi Chen and Yi-Pei Li
3w ago
This paper presents AutoTemplate, an innovative data preprocessing protocol, addressing the crucial need for high-quality chemical reaction datasets in the realm of machine learning applications in organic che ..read more
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Physicochemical modelling of the retention mechanism of temperature-responsive polymeric columns for HPLC through machine learning algorithms
BMC | Journal of Cheminformatics
by Elena Bandini, Rodrigo Castellano Ontiveros, Ardiana Kajtazi, Hamed Eghbali and Frédéric Lynen
3w ago
Temperature-responsive liquid chromatography (TRLC) offers a promising alternative to reversed-phase liquid chromatography (RPLC) for environmentally friendly analytical techniques by utilizing pure water as a ..read more
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A BERT-based pretraining model for extracting molecular structural information from a SMILES sequence
BMC | Journal of Cheminformatics
by Xiaofan Zheng and Yoichi Tomiura
3w ago
Among the various molecular properties and their combinations, it is a costly process to obtain the desired molecular properties through theory or experiment. Using machine learning to analyze molecular struct ..read more
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Stereochemically-aware bioactivity descriptors for uncharacterized chemical compounds
BMC | Journal of Cheminformatics
by Arnau Comajuncosa-Creus, Aksel Lenes, Miguel Sánchez-Palomino, Dylan Dalton and Patrick Aloy
1M ago
Stereochemistry plays a fundamental role in pharmacology. Here, we systematically investigate the relationship between stereoisomerism and bioactivity on over 1 M compounds, finding that a very significant fra ..read more
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PubChem synonym filtering process using crowdsourcing
BMC | Journal of Cheminformatics
by Sunghwan Kim, Bo Yu, Qingliang Li and Evan E. Bolton
1M ago
PubChem (https://pubchem.ncbi.nlm.nih.gov) is a public chemical information resource containing more than 100 million unique chemical structures. One of the most r ..read more
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Correction: QuanDB: a quantum chemical property database towards enhancing 3D molecular representation learning
BMC | Journal of Cheminformatics
by Zhijiang Yang, Tengxin Huang, Li Pan, Jingjing Wang, Liangliang Wang, Junjie Ding and Junhua Xiao
1M ago
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