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Multi-PLI: interpretable multi‐task deep learning model for unifying protein–ligand interaction datasets
Springer Science and Business Media LLC - Tập 13 - Trang 1-14 - 2021
Fan Hu, Jiaxin Jiang, Dongqi Wang, Muchun Zhu, Peng Yin
The assessment of protein–ligand interactions is critical at early stage of drug discovery. Computational approaches for efficiently predicting such interactions facilitate drug development. Recently, methods based on deep learning, including structure- and sequence-based models, have achieved impressive performance on several different datasets. However, their application still suffers from a gen...... hiện toàn bộ
The influence of training actives/inactives ratio on machine learning performance
Springer Science and Business Media LLC - Tập 5 - Trang 1-1 - 2013
Rafał Kurczab, Sabina Smusz, Andrzej J Bojarski
Taking the PubChem web sketcher to the next level
Springer Science and Business Media LLC - Tập 5 Số S1 - 2013
Wolf‐Dietrich Ihlenfeldt
InChI - the worldwide chemical structure standard
Springer Science and Business Media LLC - Tập 5 Số S1 - 2013
Stephen R. Heller
Searching substructures in fragment spaces
Springer Science and Business Media LLC - - 2011
Hans‐Christian Ehrlich, Matthias Rarey
Pocket Crafter: a 3D generative modeling based workflow for the rapid generation of hit molecules in drug discovery
Springer Science and Business Media LLC - - 2024
Lingling Shen, Jian Fang, Lulu Liu, Fei Yang, Jeremy L. Jenkins, Peter S. Kutchukian, He Wang
We present a user-friendly molecular generative pipeline called Pocket Crafter, specifically designed to facilitate hit finding activity in the drug discovery process. This workflow utilized a three-dimensional (3D) generative modeling method Pocket2Mol, for the de novo design of molecules in spatial perspective for the targeted protein structures, followed by filters for chemical-physical propert...... hiện toàn bộ
Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted contact map
Springer Science and Business Media LLC - Tập 13 - Trang 1-10 - 2021
Jianwen Chen, Shuangjia Zheng, Huiying Zhao, Yuedong Yang
Protein solubility is significant in producing new soluble proteins that can reduce the cost of biocatalysts or therapeutic agents. Therefore, a computational model is highly desired to accurately predict protein solubility from the amino acid sequence. Many methods have been developed, but they are mostly based on the one-dimensional embedding of amino acids that is limited to catch spatially str...... hiện toàn bộ
Towards automated metabolome assembly: application of text mining to correlate small molecules, targets and tissues
Springer Science and Business Media LLC - Tập 3 - Trang 1-1 - 2011
P Moreno, KV Jayaseelan, C Steinbeck
Computational modeling, docking and molecular dynamics of the transcriptional activator ComA bound to a newly-identified functional DNA binding site
Springer Science and Business Media LLC - Tập 6 - Trang 1-1 - 2014
Juan C Mobarec, Diana Wolf, Ilka B Bischofs, Peter Kolb
DrugEx v2: de novo design of drug molecules by Pareto-based multi-objective reinforcement learning in polypharmacology
Springer Science and Business Media LLC - Tập 13 - Trang 1-15 - 2021
Xuhan Liu, Kai Ye, Herman W. T. van Vlijmen, Michael T. M. Emmerich, Adriaan P. IJzerman, Gerard J. P. van Westen
In polypharmacology drugs are required to bind to multiple specific targets, for example to enhance efficacy or to reduce resistance formation. Although deep learning has achieved a breakthrough in de novo design in drug discovery, most of its applications only focus on a single drug target to generate drug-like active molecules. However, in reality drug molecules often interact with more than one...... hiện toàn bộ
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