VirtualFlow Ants—Ultra-Large Virtual Screenings with Artificial Intelligence Driven Docking Algorithm Based on Ant Colony Optimization

Autor: Gerhard Wagner, Christoph Gorgulla, Patrick D. Fischer, Konstantin Fackeldey, Haribabu Arthanari, Süleyman Selim Çınaroğlu
Jazyk: angličtina
Rok vydání: 2021
Předmět:
0301 basic medicine
structure based virtual screening
Protein Conformation
Computer science
On the fly
Cloud computing
Ligands
01 natural sciences
Swarm intelligence
Biology (General)
Spectroscopy
Kelch-Like ECH-Associated Protein 1
Drug discovery
swarm intelligence
Ant colony optimization algorithms
food and beverages
General Medicine
artificial intelligence
Computer Science Applications
Molecular Docking Simulation
Chemistry
Key factors
Thermodynamics
Algorithm
Algorithms
Protein Binding
NF-E2-Related Factor 2
QH301-705.5
Article
Catalysis
drug discovery
Inorganic Chemistry
03 medical and health sciences
ddc:570
CADD
computer aided drug design
Physical and Theoretical Chemistry
Molecular Biology
QD1-999
Virtual screening
business.industry
Organic Chemistry
fungi
Computational Biology
Reproducibility of Results
molecular docking
0104 chemical sciences
KEAP1
010404 medicinal & biomolecular chemistry
030104 developmental biology
Docking (molecular)
business
Zdroj: International Journal of Molecular Sciences, Vol 22, Iss 5807, p 5807 (2021)
International Journal of Molecular Sciences
Volume 22
Issue 11
ISSN: 1661-6596
1422-0067
Popis: The docking program PLANTS, which is based on ant colony optimization (ACO) algorithm, has many advanced features for molecular docking. Among them are multiple scoring functions, the possibility to model explicit displaceable water molecules, and the inclusion of experimental constraints. Here, we add support of PLANTS to VirtualFlow (VirtualFlow Ants), which adds a valuable method for primary virtual screenings and rescoring procedures. Furthermore, we have added support of ligand libraries in the MOL2 format, as well as on the fly conversion of ligand libraries which are in the PDBQT format to the MOL2 format to endow VirtualFlow Ants with an increased flexibility regarding the ligand libraries. The on the fly conversion is carried out with Open Babel and the program SPORES. We applied VirtualFlow Ants to a test system involving KEAP1 on the Google Cloud up to 128,000 CPUs, and the observed scaling behavior is approximately linear. Furthermore, we have adjusted several central docking parameters of PLANTS (such as the speed parameter or the number of ants) and screened 10 million compounds for each of the 10 resulting docking scenarios. We analyzed their docking scores and average docking times, which are key factors in virtual screenings. The possibility of carrying out ultra-large virtual screening with PLANTS via VirtualFlow Ants opens new avenues in computational drug discovery.
Databáze: OpenAIRE
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