Use of molecular docking computational tools in drug discovery

F Stanzione, I Giangreco, JC Cole - Progress in medicinal chemistry, 2021 - Elsevier
Molecular docking has become an important component of the drug discovery process.
Since first being developed in the 1980s, advancements in the power of computer hardware …

Structure-based virtual screening for ligands of G protein–coupled receptors: what can molecular docking do for you?

F Ballante, AJ Kooistra, S Kampen, C de Graaf… - Pharmacological …, 2021 - ASPET
G protein–coupled receptors (GPCRs) constitute the largest family of membrane proteins in
the human genome and are important therapeutic targets. During the last decade, the …

Molecular docking and molecular dynamics simulation

S Singh, QB Baker, DB Singh - Bioinformatics, 2022 - Elsevier
Computational drug discovery methods provide valuable insights into the understanding of
protein–ligand interaction systems in a virtual manner. Molecular docking and …

[HTML][HTML] Performance of virtual screening against GPCR homology models: Impact of template selection and treatment of binding site plasticity

M Jaiteh, I Rodríguez-Espigares, J Selent… - PLoS computational …, 2020 - journals.plos.org
Rational drug design for G protein-coupled receptors (GPCRs) is limited by the small
number of available atomic resolution structures. We assessed the use of homology …

Unpacking the Pathogen Box—an open source tool for fighting neglected tropical disease

CGL Veale - ChemMedChem, 2019 - Wiley Online Library
Abstract The Pathogen Box is a 400‐strong collection of drug‐like compounds, selected for
their potential against several of the world's most important neglected tropical diseases …

Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?

J Kapla, I Rodríguez-Espigares, F Ballante… - PLoS Computational …, 2021 - journals.plos.org
The determination of G protein-coupled receptor (GPCR) structures at atomic resolution has
improved understanding of cellular signaling and will accelerate the development of new …

Matrix metalloproteinase 9 (MMP9) in wound healing of diabetic foot ulcer: Molecular target and structure-based drug design

M Hariono, SH Yuliani, EP Istyastono, FDO Riswanto… - Wound Medicine, 2018 - Elsevier
Abstract Matrix Metalloproteinase 9 (MMP9) is one of the many zinc-dependent
endopeptidases found in the body, which is also involved in delaying wound healing by …

Emulating docking results using a deep neural network: a new perspective for virtual screening

S Jastrzebski, M Szymczak, A Pocha… - Journal of Chemical …, 2020 - ACS Publications
Docking is one of the most important steps in virtual screening pipelines, and it is an
established method for examining potential interactions between ligands and receptors …

Molecular interaction fingerprint approaches for GPCR drug discovery

M Vass, AJ Kooistra, T Ritschel, R Leurs… - Current opinion in …, 2016 - Elsevier
Highlights•Interaction fingerprints (IFP) have been effectively used for GPCR ligand
screening.•Machine learning enables IFP and bioactivity data integration.•Binding site …

Structure-based prediction of G-protein-coupled receptor ligand function: a β-adrenoceptor case study

AJ Kooistra, R Leurs, IJP De Esch… - Journal of chemical …, 2015 - ACS Publications
The spectacular advances in G-protein-coupled receptor (GPCR) structure determination
have opened up new possibilities for structure-based GPCR ligand discovery. The structure …