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Learning protein-ligand binding affinity with atomic environment vectors
Springer Science and Business Media LLC - - 2021
Rocco Meli, Andrew Anighoro, Michael J. Bodkin, Garrett M. Morris, Philip C. Biggin
AbstractScoring functions for the prediction of protein-ligand binding affinity have seen renewed interest in recent years when novel machine learning and deep learning methods started to consistently outperform classical scoring functions. Here we explore the use of atomic environment vectors (AEVs) and feed-forward neural networks, the building blocks of several ...... hiện toàn bộ
CardioTox net: một công cụ dự đoán chắc chắn cho việc chặn kênh hERG dựa trên các tổ hợp meta-feature học sâu Dịch bởi AI
Springer Science and Business Media LLC - Tập 13 - Trang 1-13 - 2021
Abdul Karim, Matthew Lee, Thomas Balle, Abdul Sattar
Việc chặn kênh gene liên quan đến ether-a-go-go (hERG) bằng các phân tử nhỏ là một mối quan tâm lớn trong quá trình phát triển thuốc trong ngành dược phẩm. Việc chặn các kênh hERG có thể gây ra khoảng QT kéo dài, điều này có thể dẫn đến độc tính tim mạch. Nhiều kỹ thuật in-silico, bao gồm các mô hình học sâu, được sử dụng rộng rãi để sàng lọc các phân tử nhỏ có độc tính liên quan đến hERG tiềm năn...... hiện toàn bộ
#hERG #độc tính tim mạch #chặn kênh ion #mô hình học sâu #sàng lọc thuốc #thông tin hóa học
InChI in the wild: an assessment of InChIKey searching in Google
Springer Science and Business Media LLC - Tập 5 - Trang 1-10 - 2013
Christopher Southan
While chemical databases can be queried using the InChI string and InChIKey (IK) the latter was designed for open-web searching. It is becoming increasingly effective for this since more sources enhance crawling of their websites by the Googlebot and consequent IK indexing. Searchers who use Google as an adjunct to database access may be less familiar with the advantages of using the IK as explore...... hiện toàn bộ
Virtual screening of bioassay data
Springer Science and Business Media LLC - Tập 1 - Trang 1-12 - 2009
Amanda C Schierz
There are three main problems associated with the virtual screening of bioassay data. The first is access to freely-available curated data, the second is the number of false positives that occur in the physical primary screening process, and finally the data is highly-imbalanced with a low ratio of Active compounds to Inactive compounds. This paper first discusses these three problems and then a s...... hiện toàn bộ
Comparative analysis of chemical similarity methods for modular natural products with a hypothetical structure enumeration algorithm
Springer Science and Business Media LLC - - 2017
Michael A. Skinnider, Chris A. Dejong, Brian C. Franczak, Paul D. McNicholas, Nathan A. Magarvey
Natural products represent a prominent source of pharmaceutically and industrially important agents. Calculating the chemical similarity of two molecules is a central task in cheminformatics, with applications at multiple stages of the drug discovery pipeline. Quantifying the similarity of natural products is a particularly important problem, as the biological activities of these molecules have be...... hiện toàn bộ
Comparison and improvement of the predictability and interpretability with ensemble learning models in QSPR applications
Springer Science and Business Media LLC - Tập 12 - Trang 1-16 - 2020
Chia-Hsiu Chen, Kenichi Tanaka, Masaaki Kotera, Kimito Funatsu
Ensemble learning helps improve machine learning results by combining several models and allows the production of better predictive performance compared to a single model. It also benefits and accelerates the researches in quantitative structure–activity relationship (QSAR) and quantitative structure–property relationship (QSPR). With the growing number of ensemble learning models such as random f...... hiện toàn bộ
A comparison of conditional random fields and structured support vector machines for chemical entity recognition in biomedical literature
Springer Science and Business Media LLC - - 2015
Buzhou Tang, Ying Feng, Xiaolong Wang, Yonghui Wu, Yaoyun Zhang, Min Jiang, Jingqi Wang, Hua Xu
Abstract Background Chemical compounds and drugs (together called chemical entities) embedded in scientific articles are crucial for many information extraction tasks in the biomedical domain. However, only a very limited number of chemical entity recognition systems are publically available, pro...... hiện toàn bộ
Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm
Springer Science and Business Media LLC - Tập 11 - Trang 1-16 - 2019
Martin Pérez-Pérez, Gael Pérez-Rodríguez, Aitor Blanco-Míguez, Florentino Fdez-Riverola, Alfonso Valencia, Martin Krallinger, Anália Lourenço
Shared tasks and community challenges represent key instruments to promote research, collaboration and determine the state of the art of biomedical and chemical text mining technologies. Traditionally, such tasks relied on the comparison of automatically generated results against a so-called Gold Standard dataset of manually labelled textual data, regardless of efficiency and robustness of the und...... hiện toàn bộ
MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics
Springer Science and Business Media LLC - Tập 7 - Trang 1-8 - 2015
James G Jeffryes, Ricardo L Colastani, Mona Elbadawi-Sidhu, Tobias Kind, Thomas D Niehaus, Linda J Broadbelt, Andrew D Hanson, Oliver Fiehn, Keith E J Tyo, Christopher S Henry
In spite of its great promise, metabolomics has proven difficult to execute in an untargeted and generalizable manner. Liquid chromatography–mass spectrometry (LC–MS) has made it possible to gather data on thousands of cellular metabolites. However, matching metabolites to their spectral features continues to be a bottleneck, meaning that much of the collected information remains uninterpreted and...... hiện toàn bộ
Efficient enumeration of monocyclic chemical graphs with given path frequencies
Springer Science and Business Media LLC - - 2014
Masaki Suzuki, Hiroshi Nagamochi, Tatsuya Akutsu
The enumeration of chemical graphs (molecular graphs) satisfying given constraints is one of the fundamental problems in chemoinformatics and bioinformatics because it leads to a variety of useful applications including structure determination and development of novel chemical compounds. We consider the problem of enumerating chemical graphs with monocyclic structure (a graph structure that contai...... hiện toàn bộ
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