A knowledge-based halogen bonding scoring function for predicting protein-ligand interactions

Y Liu, Z Xu, Z Yang, K Chen, W Zhu - Journal of molecular modeling, 2013 - Springer
Halogen bonding, a non-covalent interaction between the halogen σ-hole and Lewis bases,
could not be properly characterized by majority of current scoring functions. In this study, a …

A quantum mechanics-based halogen bonding scoring function for protein-ligand interactions

Z Yang, Y Liu, Z Chen, Z Xu, J Shi, K Chen… - Journal of molecular …, 2015 - Springer
A quantum mechanics-based scoring function for halogen bonding interaction, namely
XBScore QM, is developed based on 18,135 sets of geometrical and energetical parameters …

AutoDock VinaXB: implementation of XBSF, new empirical halogen bond scoring function, into AutoDock Vina

MR Koebel, G Schmadeke, RG Posner… - Journal of …, 2016 - Springer
Background Halogen bonding has recently come to play as a target for lead optimization in
rational drug design. However, most docking program don't account for halogen bonding in …

The many faces of halogen bonding: A review of theoretical models and methods

LP Wolters, P Schyman, MJ Pavan… - Wiley …, 2014 - Wiley Online Library
Halogen bonds, the formally noncovalent interactions where the halogen acts as a Lewis
acid, have brought several controversies to the theoretical world regarding its nature and …

The underestimated halogen bonds forming with protein side chains in drug discovery and design

Q Zhang, Z Xu, W Zhu - Journal of Chemical Information and …, 2017 - ACS Publications
Halogen bonds (XBs) have been attracting increasing attention in biological systems,
especially in drug discovery and design, for their advantages of both improving drug–target …

Scaffold effects on halogen bonding strength

A Lange, J Heidrich, MO Zimmermann… - Journal of Chemical …, 2019 - ACS Publications
Halogen bonds have become increasingly popular interactions in molecular design and
drug discovery. One of the key features is the strong dependence of the size and magnitude …

Halogen bonding in halocarbon-protein complexes and computational tools for rational drug design

PJ Costa, R Nunes, D Vila-Viçosa - Expert Opinion on Drug …, 2019 - Taylor & Francis
Introduction: Halogens have a prominent role in drug design. Often used as a mean to
improve ADME properties, they are also becoming a tool in protein–ligand recognition given …

Strength and character of halogen bonds in protein–ligand complexes

KE Riley, P Hobza - Crystal growth & design, 2011 - ACS Publications
In this study we investigate the strength and character of eight halogen bonding interactions
from six protein–ligand complexes. The halogen bonding complexes investigated here were …

Molecular docking in halogen bonding

A Suárez-Castro, M Valle-Sánchez… - Molecular …, 2018 - books.google.com
Molecular modeling applies several computational chemistry tools as molecular docking;
this latter has been useful in medicinal chemistry for prediction of interactions between small …

The evaluation of QM/MM-driven molecular docking combined with MM/GBSA calculations as a halogen-bond scoring strategy

R Kurczab - Acta Crystallographica Section B: Structural Science …, 2017 - journals.iucr.org
The combination of quantum mechanics/molecular mechanics-driven (QM/MM) molecular
docking with binding free-energy calculations was successfully used to reproduce the X-ray …