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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
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......
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......
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
EasyDock: customizable and scalable docking tool
Springer Science and Business Media LLC - Tập 15 - Trang 1-11 - 2023
Docking of large compound collections becomes an important procedure to discover new chemical entities. Screening of large sets of compounds may also occur in de novo design projects guided by molecular docking. To facilitate these processes, there is a need for automated tools capable of efficiently docking a large number of molecules using multiple computational nodes within a reasonable timefra......
A graph-based approach to construct target-focused libraries for virtual screening
Springer Science and Business Media LLC - Tập 8 - Trang 1-16 - 2016
Due to exorbitant costs of high-throughput screening, many drug discovery projects commonly employ inexpensive virtual screening to support experimental efforts. However, the vast majority of compounds in widely used screening libraries, such as the ZINC database, will have a very low probability to exhibit the desired bioactivity for a given protein. Although combinatorial chemistry methods can b......
A CRF-based system for recognizing chemical entity mentions (CEMs) in biomedical literatureAbstract
Background
In order to improve information access on chemical compounds and drugs (chemical entities) described in text repositories, it is very crucial to be able to identify chemical entity mentions (CEMs) automatically within text. The CHEMDNER challenge in BioCreative IV was speciall... ...
Springer Science and Business Media LLC - Tập 7 Số S1 - 2015
RepTB: a gene ontology based drug repurposing approach for tuberculosis
Springer Science and Business Media LLC - Tập 10 - Trang 1-12 - 2018
Tuberculosis (TB) is the world’s leading infectious killer with 1.8 million deaths in 2015 as reported by WHO. It is therefore imperative that alternate routes of identification of novel anti-TB compounds are explored given the time and costs involved in new drug discovery process. Towards this, we have developed RepTB. This is a unique drug repurposing approach for TB that uses molecular function......
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