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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
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...
Analysis of metabolites in human gut: illuminating the design of gut-targeted drugs
Springer Science and Business Media LLC - Tập 15 Số 1
AbstractGut-targeted drugs provide a new drug modality besides that of oral,
systemic molecules, that could tap into the growing knowledge of gut metabolites
of bacterial or host origin and their involvement in biological processes and
health through their interaction with gut targets (bacterial or host, too).
Understanding the properties of gut metabolites can provide guidance for the
design of g...
Taking the PubChem web sketcher to the next level
Springer Science and Business Media LLC - Tập 5 Số S1 - 2013
InChI - the worldwide chemical structure standard
Springer Science and Business Media LLC - Tập 5 Số S1 - 2013
In-silico predictive mutagenicity model generation using supervised learning approaches
Springer Science and Business Media LLC - Tập 4 - Trang 1-11 - 2012
Experimental screening of chemical compounds for biological activity is a time
consuming and expensive practice. In silico predictive models permit
inexpensive, rapid “virtual screening” to prioritize selection of compounds for
experimental testing. Both experimental and in silico screening can be used to
test compounds for desirable or undesirable properties. Prior work on prediction
of mutagenic...
Comparing structural fingerprints using a literature-based similarity benchmark
Springer Science and Business Media LLC - Tập 8 - Trang 1-14 - 2016
The concept of molecular similarity is one of the central ideas in
cheminformatics, despite the fact that it is ill-defined and rather difficult to
assess objectively. Here we propose a practical definition of molecular
similarity in the context of drug discovery: molecules A and B are similar if a
medicinal chemist would be likely to synthesise and test them around the same
time as part of the sa...
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
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...
Correction: DecoyFinder, a tool for finding decoy molecules
Springer Science and Business Media LLC - - 2024
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
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...
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