Molecular docking: challenges, advances and its use in drug discovery perspective

S Saikia, M Bordoloi - Current drug targets, 2019 - ingentaconnect.com
Molecular docking is a process through which small molecules are docked into the
macromolecular structures for scoring its complementary values at the binding sites. It is a …

[HTML][HTML] Computational methods in drug discovery

SP Leelananda, S Lindert - Beilstein journal of organic …, 2016 - beilstein-journals.org
The process for drug discovery and development is challenging, time consuming and
expensive. Computer-aided drug discovery (CADD) tools can act as a virtual shortcut …

Role of computer-aided drug design in modern drug discovery

SJY Macalino, V Gosu, S Hong, S Choi - Archives of pharmacal research, 2015 - Springer
Drug discovery utilizes chemical biology and computational drug design approaches for the
efficient identification and optimization of lead compounds. Chemical biology is mostly …

Principles and overview of sampling methods for modeling macromolecular structure and dynamics

T Maximova, R Moffatt, B Ma, R Nussinov… - PLoS computational …, 2016 - journals.plos.org
Investigation of macromolecular structure and dynamics is fundamental to understanding
how macromolecules carry out their functions in the cell. Significant advances have been …

Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity

DJ Huggins, PC Biggin, MA Dämgen… - Wiley …, 2019 - Wiley Online Library
Biomolecular simulation is increasingly central to understanding and designing biological
molecules and their interactions. Detailed, physics‐based simulation methods are …

Combined strategies in structure-based virtual screening

Z Wang, H Sun, C Shen, X Hu, J Gao, D Li… - Physical Chemistry …, 2020 - pubs.rsc.org
The identification and optimization of lead compounds are inalienable components in drug
design and discovery pipelines. As a powerful computational approach for the identification …

Dynamic docking: a paradigm shift in computational drug discovery

D Gioia, M Bertazzo, M Recanatini, M Masetti, A Cavalli - Molecules, 2017 - mdpi.com
Molecular docking is the methodology of choice for studying in silico protein-ligand binding
and for prioritizing compounds to discover new lead candidates. Traditional docking …

Integrated molecular modeling and machine learning for drug design

S Xia, E Chen, Y Zhang - Journal of chemical theory and …, 2023 - ACS Publications
Modern therapeutic development often involves several stages that are interconnected, and
multiple iterations are usually required to bring a new drug to the market. Computational …

Improving structure-based virtual screening with ensemble docking and machine learning

J Ricci-Lopez, SA Aguila, MK Gilson… - Journal of chemical …, 2021 - ACS Publications
One of the main challenges of structure-based virtual screening (SBVS) is the incorporation
of the receptor's flexibility, as its explicit representation in every docking run implies a high …

Current NMR techniques for structure-based drug discovery

T Sugiki, K Furuita, T Fujiwara, C Kojima - Molecules, 2018 - mdpi.com
A variety of nuclear magnetic resonance (NMR) applications have been developed for
structure-based drug discovery (SBDD). NMR provides many advantages over other …