Unconventional 2D Shape Similarity Method Affords Comparable Enrichment as a 3D Shape Method in Virtual Screening Experiments

2009 ◽  
Vol 49 (6) ◽  
pp. 1313-1320 ◽  
Author(s):  
Jerry Osagie Ebalunode ◽  
Weifan Zheng
Keyword(s):  
Virtual Screening ◽  
Shape Similarity ◽  
3D Shape ◽  
Screening Experiments ◽  
Similarity Method

Performance Evaluation of 2D Fingerprint and 3D Shape Similarity Methods in Virtual Screening

2012 ◽  
Vol 52 (5) ◽  
pp. 1103-1113 ◽  
Author(s):  
Guoping Hu ◽  
Guanglin Kuang ◽  
Wen Xiao ◽  
Weihua Li ◽  
Guixia Liu ◽  
...  
Keyword(s):  
Performance Evaluation ◽  
Virtual Screening ◽  
Shape Similarity ◽  
3D Shape

scholarly journals A Free Web-Based Protocol to Assist Structure-Based Virtual Screening Experiments

2019 ◽  
Vol 20 (18) ◽  
pp. 4648 ◽  
Author(s):  
Nathalie Lagarde ◽  
Elodie Goldwaser ◽  
Tania Pencheva ◽  
Dessislava Jereva ◽  
Ilza Pajeva ◽  
...  
Keyword(s):  
Drug Discovery ◽  
Virtual Screening ◽  
Web Service ◽  
Molecular Mechanics ◽  
In Silico ◽  
Chemical Biology ◽  
In Silico Screening ◽  
Web Based ◽  
Screening Experiments ◽  
The Web

Chemical biology and drug discovery are complex and costly processes. In silico screening approaches play a key role in the identification and optimization of original bioactive molecules and increase the performance of modern chemical biology and drug discovery endeavors. Here, we describe a free web-based protocol dedicated to small-molecule virtual screening that includes three major steps: ADME-Tox filtering (via the web service FAF-Drugs4), docking-based virtual screening (via the web service MTiOpenScreen), and molecular mechanics optimization (via the web service AMMOS2 [Automatic Molecular Mechanics Optimization for in silico Screening]). The online tools FAF-Drugs4, MTiOpenScreen, and AMMOS2 are implemented in the freely accessible RPBS (Ressource Parisienne en Bioinformatique Structurale) platform. The proposed protocol allows users to screen thousands of small molecules and to download the top 1500 docked molecules that can be further processed online. Users can then decide to purchase a small list of compounds for in vitro validation. To demonstrate the potential of this online-based protocol, we performed virtual screening experiments of 4574 approved drugs against three cancer targets. The results were analyzed in the light of published drugs that have already been repositioned on these targets. We show that our protocol is able to identify active drugs within the top-ranked compounds. The web-based protocol is user-friendly and can successfully guide the identification of new promising molecules for chemical biology and drug discovery purposes.

scholarly journals PSOVina: The hybrid particle swarm optimization algorithm for protein–ligand docking

2015 ◽  
Vol 13 (03) ◽  
pp. 1541007 ◽  
Author(s):  
Marcus C. K. Ng ◽  
Simon Fong ◽  
Shirley W. I. Siu
Keyword(s):  
Particle Swarm Optimization ◽  
Virtual Screening ◽  
Particle Swarm ◽  
Ligand Docking ◽  
Conformational Search ◽  
Search Problem ◽  
Data Set ◽  
Swarm Optimization ◽  
Screening Experiments ◽  
Hybrid Particle Swarm Optimization

Protein–ligand docking is an essential step in modern drug discovery process. The challenge here is to accurately predict and efficiently optimize the position and orientation of ligands in the binding pocket of a target protein. In this paper, we present a new method called PSOVina which combined the particle swarm optimization (PSO) algorithm with the efficient Broyden–Fletcher–Goldfarb–Shannon (BFGS) local search method adopted in AutoDock Vina to tackle the conformational search problem in docking. Using a diverse data set of 201 protein–ligand complexes from the PDBbind database and a full set of ligands and decoys for four representative targets from the directory of useful decoys (DUD) virtual screening data set, we assessed the docking performance of PSOVina in comparison to the original Vina program. Our results showed that PSOVina achieves a remarkable execution time reduction of 51–60% without compromising the prediction accuracies in the docking and virtual screening experiments. This improvement in time efficiency makes PSOVina a better choice of a docking tool in large-scale protein–ligand docking applications. Our work lays the foundation for the future development of swarm-based algorithms in molecular docking programs. PSOVina is freely available to non-commercial users at http://cbbio.cis.umac.mo .

scholarly journals Virtual screening web servers: designing chemical probes and drug candidates in the cyberspace

2020 ◽  
Author(s):  
Natesh Singh ◽  
Ludovic Chaput ◽  
Bruno O Villoutreix
Keyword(s):  
Virtual Screening ◽  
Drug Repositioning ◽  
Pharmaceutical Research ◽  
Bioactive Molecules ◽  
Screening Methods ◽  
Web Servers ◽  
Web Based ◽  
Drug Candidates ◽  
Screening Experiments ◽  
Molecule Docking

Abstract The interplay between life sciences and advancing technology drives a continuous cycle of chemical data growth; these data are most often stored in open or partially open databases. In parallel, many different types of algorithms are being developed to manipulate these chemical objects and associated bioactivity data. Virtual screening methods are among the most popular computational approaches in pharmaceutical research. Today, user-friendly web-based tools are available to help scientists perform virtual screening experiments. This article provides an overview of internet resources enabling and supporting chemical biology and early drug discovery with a main emphasis on web servers dedicated to virtual ligand screening and small-molecule docking. This survey first introduces some key concepts and then presents recent and easily accessible virtual screening and related target-fishing tools as well as briefly discusses case studies enabled by some of these web services. Notwithstanding further improvements, already available web-based tools not only contribute to the design of bioactive molecules and assist drug repositioning but also help to generate new ideas and explore different hypotheses in a timely fashion while contributing to teaching in the field of drug development.

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