ENRI: A tool for selecting structure‐based virtual screening target conformations

R Akbar, SA Jusoh, RE Amaro… - Chemical Biology & Drug …, 2017 - Wiley Online Library
Finding pharmaceutically relevant target conformations from an arbitrary set of protein
conformations remains a challenge in structure‐based virtual screening (SBVS). The growth …

Identifying and characterizing promiscuous targets: implications for virtual screening

VI Pérez-Nueno, DW Ritchie - Expert opinion on drug discovery, 2012 - Taylor & Francis
Introduction: Ligand-based shape matching approaches have become established as
important and popular virtual screening (VS) techniques. However, despite their relative …

Selecting machine-learning scoring functions for structure-based virtual screening

PJ Ballester - Drug discovery today: technologies, 2019 - Elsevier
Interest in docking technologies has grown parallel to the ever increasing number and
diversity of 3D models for macromolecular therapeutic targets. Structure-Based Virtual …

A practical guide to machine-learning scoring for structure-based virtual screening

VK Tran-Nguyen, M Junaid, S Simeon, PJ Ballester - Nature Protocols, 2023 - nature.com
Abstract Structure-based virtual screening (SBVS) via docking has been used to discover
active molecules for a range of therapeutic targets. Chemical and protein data sets that …

Structure-based virtual screening

Q Li, S Shah - Protein Bioinformatics: From Protein Modifications and …, 2017 - Springer
Abstract Structure-based virtual screening (SBVS) is a computational approach used in the
early-stage drug discovery campaign to search a chemical compound library for novel …

Improving virtual screening performance against conformational variations of receptors by shape matching with ligand binding pocket

HS Lee, CS Lee, JS Kim, DH Kim… - Journal of chemical …, 2009 - ACS Publications
In this report, we present a novel virtual high-throughput screening methodology to assist in
computer-aided drug discovery. Our method, designated as SLIM, involves ligand-free …

Generation of receptor structural ensembles for virtual screening using binding site shape analysis and clustering

DJ Osguthorpe, W Sherman… - Chemical biology & drug …, 2012 - Wiley Online Library
Accounting for protein flexibility is an essential yet challenging component of structure‐
based virtual screening. Whereas an ideal approach would account for full protein and …

Efficient virtual screening using multiple protein conformations described as negative images of the ligand-binding site

SI Virtanen, OT Pentikäinen - Journal of chemical information …, 2010 - ACS Publications
The protein structure-based virtual screening is typically accomplished using a molecular
docking procedure. However, docking is a fairly slow process that is limited by the available …

Combined strategies in structure-based virtual screening

Z Wang, H Sun, C Shen, X Hu, J Gao, D Li… - Physical Chemistry …, 2020 - pubs.rsc.org
The identification and optimization of lead compounds are inalienable components in drug
design and discovery pipelines. As a powerful computational approach for the identification …

Pharmacophore-based virtual screening

H Sun - Current medicinal chemistry, 2008 - ingentaconnect.com
Virtual screening (VS) is an important component of cheminformatics and molecular
modeling. An abundance of structural information, indicated by both the ever-increasing …