Scaffold Hopping Using Two-Dimensional Fingerprints: True Potential, Black Magic, or a Hopeless Endeavor? Guidelines for Virtual Screening

2010 ◽  
Vol 53 (15) ◽  
pp. 5707-5715 ◽  
Author(s):  
Martin Vogt ◽  
Dagmar Stumpfe ◽  
Hanna Geppert ◽  
Jürgen Bajorath
Keyword(s):  
Virtual Screening ◽  
Scaffold Hopping ◽  
Two Dimensional ◽  
Black Magic

Discovery of Novel Small Molecule Inhibitors of Dengue Viral NS2B-NS3 Protease Using Virtual Screening and Scaffold Hopping

2012 ◽  
Vol 55 (14) ◽  
pp. 6278-6293 ◽  
Author(s):  
Jing Deng ◽  
Ning Li ◽  
Hongchuan Liu ◽  
Zhili Zuo ◽  
Oi Wah Liew ◽  
...  
Keyword(s):  
Virtual Screening ◽  
Small Molecule ◽  
Small Molecule Inhibitors ◽  
Scaffold Hopping ◽  
Ns3 Protease

scholarly journals Identification of new SUMO activating enzyme 1 inhibitors using virtual screening and scaffold hopping

2016 ◽  
Vol 26 (4) ◽  
pp. 1218-1223 ◽  
Author(s):  
Ashutosh Kumar ◽  
Akihiro Ito ◽  
Mikako Hirohama ◽  
Minoru Yoshida ◽  
Kam Y.J. Zhang
Keyword(s):  
Virtual Screening ◽  
Scaffold Hopping

Virtual Screening and Scaffold Hopping Based on GRID Molecular Interaction Fields

2005 ◽  
Vol 45 (5) ◽  
pp. 1313-1323 ◽  
Author(s):  
Marie M. Ahlström ◽  
Marianne Ridderström ◽  
Kristina Luthman ◽  
Ismael Zamora
Keyword(s):  
Virtual Screening ◽  
Molecular Interaction ◽  
Scaffold Hopping ◽  
Molecular Interaction Fields

scholarly journals InterLig: improved ligand-based virtual screening using topologically independent structural alignments

2020 ◽  
Vol 36 (10) ◽  
pp. 3266-3267
Author(s):  
Claudio Mirabello ◽  
Björn Wallner
Keyword(s):  
Drug Discovery ◽  
Virtual Screening ◽  
Small Molecules ◽  
Supplementary Information ◽  
Scaffold Hopping ◽  
Supplementary Data ◽  
Protein Target ◽  
The Past ◽  
3D Methods ◽  
Structural Alignments

Abstract Motivation In the past few years, drug discovery processes have been relying more and more on computational methods to sift out the most promising molecules before time and resources are spent to test them in experimental settings. Whenever the protein target of a given disease is not known, it becomes fundamental to have accurate methods for ligand-based virtual screening, which compares known active molecules against vast libraries of candidate compounds. Recently, 3D-based similarity methods have been developed that are capable of scaffold hopping and to superimpose matching molecules. Results Here, we present InterLig, a new method for the comparison and superposition of small molecules using topologically independent alignments of atoms. We test InterLig on a standard benchmark and show that it compares favorably to the best currently available 3D methods. Availability and implementation The program is available from http://wallnerlab.org/InterLig. Supplementary information Supplementary data are available at Bioinformatics online.

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