Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database

D Plewczynski, M Łaźniewski… - Journal of …, 2011 - Wiley Online Library
Docking is one of the most commonly used techniques in drug design. It is used for both
identifying correct poses of a ligand in the binding site of a protein as well as for the …

Recent advances in small organic molecules as DNA intercalating agents: Synthesis, activity, and modeling

A Rescifina, C Zagni, MG Varrica, V Pistarà… - European journal of …, 2014 - Elsevier
The interaction of small molecules with DNA plays an essential role in many biological
processes. As DNA is often the target for majority of anticancer and antibiotic drugs, study …

[HTML][HTML] Evaluation of the binding performance of flavonoids to estrogen receptor alpha by Autodock, Autodock Vina and Surflex-Dock

Q Xue, X Liu, P Russell, J Li, W Pan, J Fu… - … and Environmental Safety, 2022 - Elsevier
Molecular docking is a widely used method to predict the binding modes of small-molecule
ligands to the target binding site. However, it remains a challenge to identify the correct …

[PDF][PDF] An overview of molecular docking

S Agarwal, R Mehrotra - JSM chem, 2016 - researchgate.net
Molecular docking is a kind of computational modeling of the complexes, which is formed
from the interaction of two or more molecules. It predicts the three-dimensional structure of …

[1, 2, 4] Triazolo [4, 3-c] quinazoline and bis ([1, 2, 4] triazolo)[4, 3-a: 4′, 3′-c] quinazoline derived DNA intercalators: Design, synthesis, in silico ADMET profile …

K El-Adl, MK Ibrahim, MSI Alesawy, IH Eissa - Bioorganic & Medicinal …, 2021 - Elsevier
In view of their DNA intercalation activities as anticancer agents, novel fifteen [1, 2, 4] triazolo
[4, 3-c] quinazoline and bis ([1, 2, 4] triazolo)[4, 3-a: 4′, 3′-c] quinazoline derivatives have …

Docking studies on DNA-ligand interactions: building and application of a protocol to identify the binding mode

CG Ricci, PA Netz - Journal of chemical information and modeling, 2009 - ACS Publications
Despite DNA being an important target for several drugs, most of the docking programs are
validated only for proteins and their ligands. In this paper, we used AutoDock 4.0 to perform …

Docking studies on DNA intercalators

Y Gilad, H Senderowitz - Journal of chemical information and …, 2014 - ACS Publications
DNA is an important target for the treatment of multiple pathologies, most notably cancer. In
particular, DNA intercalators have often been used as anticancer drugs. However, despite …

Design, synthesis, molecular modeling and biological evaluation of novel 1H-pyrazolo [3, 4-b] pyridine derivatives as potential anticancer agents

IH Eissa, AM El-Naggar, MA El-Hashash - Bioorganic chemistry, 2016 - Elsevier
In trying to develop new anticancer agents, a series of 1H-pyrazolo [3, 4-b] pyridine
derivatives was designed and synthesized. Fifteen compounds were evaluated in vitro for …

A new, improved hybrid scoring function for molecular docking and scoring based on AutoDock and AutoDock Vina

VY Tanchuk, VO Tanin, AI Vovk… - Chemical biology & drug …, 2016 - Wiley Online Library
Automated docking is one of the most important tools for structure‐based drug design that
allows prediction of ligand binding poses and also provides an estimate of how well small …

Changes in binding affinity between ofloxacin and calf thymus DNA in the presence of histone H1: Spectroscopic and molecular modeling investigations

FD Sani, N Shakibapour, S Beigoli, H Sadeghian… - Journal of …, 2018 - Elsevier
The interaction between ofloxacin (Oflx) and calf thymus DNA (ct DNA) in the presence and
absence of histone H1 was investigated in Tris buffer (pH= 6.8) using UV–vis absorption and …