Machine learning–assisted molecular design and efficiency prediction for high-performance organic photovoltaic materials

W Sun, Y Zheng, K Yang, Q Zhang, AA Shah, Z Wu… - Science …, 2019 - science.org
In the process of finding high-performance materials for organic photovoltaics (OPVs), it is
meaningful if one can establish the relationship between chemical structures and …

Computer-aided drug design methods

W Yu, AD MacKerell - Antibiotics: methods and protocols, 2017 - Springer
Computational approaches are useful tools to interpret and guide experiments to expedite
the antibiotic drug design process. Structure-based drug design (SBDD) and ligand-based …

BATMAN-TCM: a bioinformatics analysis tool for molecular mechANism of traditional Chinese medicine

Z Liu, F Guo, Y Wang, C Li, X Zhang, H Li, L Diao… - Scientific reports, 2016 - nature.com
Abstract Traditional Chinese Medicine (TCM), with a history of thousands of years of clinical
practice, is gaining more and more attention and application worldwide. And TCM-based …

DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism

EW Bell, Y Zhang - Journal of cheminformatics, 2019 - Springer
Abstract Comparison of ligand poses generated by protein–ligand docking programs has
often been carried out with the assumption of direct atomic correspondence between ligand …

Evaluation of AutoDock and AutoDock Vina on the CASF-2013 benchmark

T Gaillard - Journal of chemical information and modeling, 2018 - ACS Publications
Computer-aided protein–ligand binding predictions are a valuable help in drug discovery.
Protein–ligand docking programs generally consist of two main components: a scoring …

Identification of potent inhibitors of NEK7 protein using a comprehensive computational approach

M Aziz, SA Ejaz, N Tamam, F Siddique, N Riaz… - Scientific reports, 2022 - nature.com
NIMA related Kinases (NEK7) plays an important role in spindle assembly and mitotic
division of the cell. Over expression of NEK7 leads to the progression of different cancers …

Improving protein-ligand docking results with high-throughput molecular dynamics simulations

H Guterres, W Im - Journal of chemical information and modeling, 2020 - ACS Publications
Structure-based virtual screening relies on classical scoring functions that often fail to
reliably discriminate binders from nonbinders. In this work, we present a high-throughput …

Proteome-wide covalent ligand discovery in native biological systems

KM Backus, BE Correia, KM Lum, S Forli, BD Horning… - Nature, 2016 - nature.com
Small molecules are powerful tools for investigating protein function and can serve as leads
for new therapeutics. Most human proteins, however, lack small-molecule ligands, and …

Searching molecular structure databases with tandem mass spectra using CSI: FingerID

K Dührkop, H Shen, M Meusel… - Proceedings of the …, 2015 - National Acad Sciences
Metabolites provide a direct functional signature of cellular state. Untargeted metabolomics
experiments usually rely on tandem MS to identify the thousands of compounds in a …

Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

Y Shao, Z Gan, E Epifanovsky, ATB Gilbert… - Molecular …, 2015 - Taylor & Francis
A summary of the technical advances that are incorporated in the fourth major release of the
q-Chem quantum chemistry program is provided, covering approximately the last seven …