AI in drug discovery and its clinical relevance

R Qureshi, M Irfan, TM Gondal, S Khan, J Wu, MU Hadi… - Heliyon, 2023 - cell.com
The COVID-19 pandemic has emphasized the need for novel drug discovery process.
However, the journey from conceptualizing a drug to its eventual implementation in clinical …

Progress in molecular docking

J Fan, A Fu, L Zhang - Quantitative Biology, 2019 - Springer
Background In recent years, since the molecular docking technique can greatly improve the
efficiency and reduce the research cost, it has become a key tool in computer-assisted drug …

Recent advances in molecular docking for the research and discovery of potential marine drugs

G Chen, AJ Seukep, M Guo - Marine drugs, 2020 - mdpi.com
Marine drugs have long been used and exhibit unique advantages in clinical practices.
Among the marine drugs that have been approved by the Food and Drug Administration …

X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in …

CD Putnam, M Hammel, GL Hura… - Quarterly reviews of …, 2007 - cambridge.org
Crystallography supplies unparalleled detail on structural information critical for mechanistic
analyses; however, it is restricted to describing low energy conformations of …

PIPER: an FFT‐based protein docking program with pairwise potentials

D Kozakov, R Brenke, SR Comeau… - … Structure, Function, and …, 2006 - Wiley Online Library
Abstract The Fast Fourier Transform (FFT) correlation approach to protein–protein docking
can evaluate the energies of billions of docked conformations on a grid if the energy is …

FireDock: a web server for fast interaction refinement in molecular docking

E Mashiach, D Schneidman-Duhovny… - Nucleic acids …, 2008 - academic.oup.com
Structural details of protein–protein interactions are invaluable for understanding and
deciphering biological mechanisms. Computational docking methods aim to predict the …

FireDock: fast interaction refinement in molecular docking

N Andrusier, R Nussinov… - … : Structure, Function, and …, 2007 - Wiley Online Library
Here, we present FireDock, an efficient method for the refinement and rescoring of rigid‐
body docking solutions. The refinement process consists of two main steps:(1) …

The B30. 2 domain of pyrin, the familial Mediterranean fever protein, interacts directly with caspase-1 to modulate IL-1β production

JJ Chae, G Wood, SL Masters… - Proceedings of the …, 2006 - National Acad Sciences
Familial Mediterranean fever (FMF) is a recessively inherited autoinflammatory disorder with
high carrier frequencies in the Middle East. Pyrin, the protein mutated in FMF, regulates …

Automated and efficient generation of general molecular aggregate structures

C Plett, S Grimme - Angewandte Chemie International Edition, 2023 - Wiley Online Library
Modeling intermolecular interactions of complex non‐covalent structures is important in
many areas of chemistry. To facilitate the generation of reasonable dimer, oligomer, and …

ZRANK: reranking protein docking predictions with an optimized energy function

B Pierce, Z Weng - Proteins: Structure, Function, and …, 2007 - Wiley Online Library
Protein–protein docking requires fast and effective methods to quickly discriminate correct
from incorrect predictions generated by initial‐stage docking. We have developed and …