Biasing conformational ensembles towards bioactive-like conformers for ligand-based drug design

B Musafia, H Senderowitz - Expert opinion on drug discovery, 2010 - Taylor & Francis
Importance of the field: In silico or virtual screening has become a common practice in
contemporary computer-aided drug discovery efforts and currently constitutes a reasonably …

[PDF][PDF] Virtual screening strategies in drug design–methods and applications

E Bielska, X Lucas, A Czerwoniec, JM Kasprzak… - …, 2011 - journals.pan.pl
Virtual screening (VS) overcomes the limitations of traditional high-throughput screening
(HTS) by applying computer-based methods in drug discovery. VS takes advantage of fast …

Cheminformatics meets molecular mechanics: a combined application of knowledge-based pose scoring and physical force field-based hit scoring functions improves …

JH Hsieh, S Yin, XS Wang, S Liu… - Journal of chemical …, 2012 - ACS Publications
Poor performance of scoring functions is a well-known bottleneck in structure-based virtual
screening (VS), which is most frequently manifested in the scoring functions' inability to …

A hybrid virtual screening protocol based on binding mode similarity

A Anighoro, J Bajorath - Rational Drug Design: Methods and Protocols, 2018 - Springer
In structure-based virtual screening (SBVS), a scoring function is usually applied to rank a
database of docked compounds. Docking programs are often successful in reproducing …

Target-biased scoring approaches and expert systems in structure-based virtual screening

JM Jansen, EJ Martin - Current opinion in chemical biology, 2004 - Elsevier
Structure-based virtual screening followed by selection of a top fraction of the rank-ordered
result list suffers from many false positives and false negatives because the general scoring …

USR-VS: a web server for large-scale prospective virtual screening using ultrafast shape recognition techniques

H Li, KS Leung, MH Wong, PJ Ballester - Nucleic acids research, 2016 - academic.oup.com
Abstract Ligand-based Virtual Screening (VS) methods aim at identifying molecules with a
similar activity profile across phenotypic and macromolecular targets to that of a query …

DockBench: an integrated informatic platform bridging the gap between the robust validation of docking protocols and virtual screening simulations

A Cuzzolin, M Sturlese, I Malvacio, A Ciancetta, S Moro… - Molecules, 2015 - mdpi.com
Virtual screening (VS) is a computational methodology that streamlines the drug discovery
process by reducing costs and required resources through the in silico identification of …

Improving classical substructure-based virtual screening to handle extrapolation challenges

T Biniashvili, E Schreiber, Y Kliger - Journal of chemical …, 2012 - ACS Publications
Target-oriented substructure-based virtual screening (sSBVS) of molecules is a promising
approach in drug discovery. Yet, there are doubts whether sSBVS is suitable also for …

Structure-based virtual screening

SS Chauhan, T Jamal, A Singh, A Sehrawat… - … , QSAR and Machine …, 2023 - Elsevier
Drug development is challenging for the pharmaceutical sector, as it is time-consuming and
cost extensive to complete all the phases necessary to transform a chemical into a new drug …

How to optimize shape-based virtual screening: choosing the right query and including chemical information

J Kirchmair, S Distinto, P Markt… - Journal of chemical …, 2009 - ACS Publications
Shape-based molecular similarity approaches have been established as important and
popular virtual screening techniques. Recent applications have shown successful screening …