Metal–ligand interactions in drug design

L Riccardi, V Genna, M De Vivo - Nature Reviews Chemistry, 2018 - nature.com
The fast-growing body of experimental data on metalloenzymes and organometallic
compounds is fostering the exploitation of metal–ligand interactions for the design of new …

Robust and efficient implicit solvation model for fast semiempirical methods

S Ehlert, M Stahn, S Spicher… - Journal of Chemical …, 2021 - ACS Publications
We present a robust and efficient method to implicitly account for solvation effects in modern
semiempirical quantum mechanics and force fields. A computationally efficient yet accurate …

Advances in docking

VB Sulimov, DC Kutov… - Current medicinal …, 2019 - benthamdirect.com
Background: Design of small molecules which are able to bind to the protein responsible for
a disease is the key step of the entire process of the new medicine discovery. Atomistic …

Comprehensive evaluation of ten docking programs on a diverse set of protein–ligand complexes: the prediction accuracy of sampling power and scoring power

Z Wang, H Sun, X Yao, D Li, L Xu, Y Li… - Physical Chemistry …, 2016 - pubs.rsc.org
As one of the most popular computational approaches in modern structure-based drug
design, molecular docking can be used not only to identify the correct conformation of a …

Assessing the accuracy of across-the-scale methods for predicting carbohydrate conformational energies for the examples of glucose and α-maltose

M Marianski, A Supady, T Ingram… - Journal of chemical …, 2016 - ACS Publications
A big hurdle when entering the field of carbohydrate research stems from the complications
in the analytical and computational treatment. In effect, this extremely important class of …

Docking paradigm in drug design

VB Sulimov, DC Kutov, AS Taschilova… - Current Topics in …, 2021 - ingentaconnect.com
Docking is in demand for the rational computer aided structure based drug design. A review
of docking methods and programs is presented. Different types of docking programs are …

Benchmarking of semiempirical quantum-mechanical methods on systems relevant to computer-aided drug design

K Kriz, J Řezáč - Journal of Chemical Information and …, 2020 - ACS Publications
The semiempirical quantum mechanical (SQM) methods used in drug design are commonly
parametrized and tested on data sets of systems that may not be representative models for …

farPPI: a webserver for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB (GB) SA methods

Z Wang, X Wang, Y Li, T Lei, E Wang, D Li… - …, 2019 - academic.oup.com
Protein-protein interactions (PPIs) have been regarded as an attractive emerging class of
therapeutic targets for the development of new treatments. Computational approaches …

Quantum chemical approaches in structure-based virtual screening and lead optimization

CN Cavasotto, NS Adler, MG Aucar - Frontiers in chemistry, 2018 - frontiersin.org
Today computational chemistry is a consolidated tool in drug lead discovery endeavors. Due
to methodological developments and to the enormous advance in computer hardware …

Interaction nature and computational methods for halogen bonding: a perspective

Z Zhu, Z Xu, W Zhu - Journal of Chemical Information and …, 2020 - ACS Publications
Halogen bonds are noncovalent interactions that have been widely used in many fields,
including drug design, crystal engineering, and material sciences. A clear understanding of …