Software for molecular docking: a review
NS Pagadala, K Syed, J Tuszynski - Biophysical reviews, 2017 - Springer
Molecular docking methodology explores the behavior of small molecules in the binding site
of a target protein. As more protein structures are determined experimentally using X-ray …
of a target protein. As more protein structures are determined experimentally using X-ray …
Molecular dynamics simulations and novel drug discovery
X Liu, D Shi, S Zhou, H Liu, H Liu… - Expert opinion on drug …, 2018 - Taylor & Francis
Introduction: Molecular dynamics (MD) simulations can provide not only plentiful dynamical
structural information on biomacromolecules but also a wealth of energetic information …
structural information on biomacromolecules but also a wealth of energetic information …
Comparative assessment of scoring functions: the CASF-2016 update
In structure-based drug design, scoring functions are often employed to evaluate protein–
ligand interactions. A variety of scoring functions have been developed so far, and thus …
ligand interactions. A variety of scoring functions have been developed so far, and thus …
Computational methods in drug discovery
Computer-aided drug discovery/design methods have played a major role in the
development of therapeutically important small molecules for over three decades. These …
development of therapeutically important small molecules for over three decades. These …
DFT and molecular docking study of the effect of a green solvent (water and DMSO) on the structure, MEP, and FMOs of the 1-ethylpiperazine-1, 4-diium bis …
M Medimagh, CB Mleh, N Issaoui… - Journal of Molecular …, 2023 - Elsevier
We report in this study the influence of green solvents (water and DMSO) effect in structural
parameters, frontier molecular orbital's (FMO's) and molecular electrostatic potential surface …
parameters, frontier molecular orbital's (FMO's) and molecular electrostatic potential surface …
Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein− ligand complexes
RA Friesner, RB Murphy, MP Repasky… - Journal of medicinal …, 2006 - ACS Publications
A novel scoring function to estimate protein− ligand binding affinities has been developed
and implemented as the Glide 4.0 XP scoring function and docking protocol. In addition to …
and implemented as the Glide 4.0 XP scoring function and docking protocol. In addition to …
Docking and scoring in virtual screening for drug discovery: methods and applications
DB Kitchen, H Decornez, JR Furr… - Nature reviews Drug …, 2004 - nature.com
Computational approaches that'dock'small molecules into the structures of macromolecular
targets and'score'their potential complementarity to binding sites are widely used in hit …
targets and'score'their potential complementarity to binding sites are widely used in hit …
[HTML][HTML] Calendulaglycoside A showing potential activity against SARS-CoV-2 main protease: Molecular docking, molecular dynamics, and SAR studies
Background and aim The discovery of drugs capable of inhibiting SARS-CoV-2 is a priority
for human beings due to the severity of the global health pandemic caused by COVID-19. To …
for human beings due to the severity of the global health pandemic caused by COVID-19. To …
Comparative assessment of scoring functions on an updated benchmark: 2. Evaluation methods and general results
Our comparative assessment of scoring functions (CASF) benchmark is created to provide
an objective evaluation of current scoring functions. The key idea of CASF is to compare the …
an objective evaluation of current scoring functions. The key idea of CASF is to compare the …
Using autodock for ligand‐receptor docking
This unit describes how to set up and analyze ligand‐protein docking calculations using
AutoDock and the graphical user interface, AutoDockTools (ADT). The AutoDock scoring …
AutoDock and the graphical user interface, AutoDockTools (ADT). The AutoDock scoring …