Expanding the boundaries of ligand–target modeling by exascale calculations

Molecular simulations and molecular docking are widely used tools to investigate ligand/target interactions and in drug design. High‐performance computing (HPC) is boosting both the accuracy and predictive power of these approaches. With the advent of exascale computing, HPC may become standardly ap...

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Published inWiley interdisciplinary reviews. Computational molecular science Vol. 11; no. 4
Main Authors Bolnykh, Viacheslav, Rossetti, Giulia, Rothlisberger, Ursula, Carloni, Paolo
Format Journal Article
LanguageEnglish
Published Hoboken, USA Wiley Periodicals, Inc 01.07.2021
Subjects
drug design
exascale computing
ligand‐target modeling
molecular dynamics
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ISSN1759-0876
1759-0884
DOI10.1002/wcms.1535

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Abstract Molecular simulations and molecular docking are widely used tools to investigate ligand/target interactions and in drug design. High‐performance computing (HPC) is boosting both the accuracy and predictive power of these approaches. With the advent of exascale computing, HPC may become standardly applied in many drug design campaigns and pharmacological applications. This review discusses how innovative HPC algorithms and hardware are being exploited in current simulations and docking codes, pointing also at some of the limitations of these approaches. The focus is on technical aspects which might not be all that familiar to the computational pharmacologist. This article is categorized under: Software > Molecular Modeling Software > Simulation Methods Structure and Mechanism > Computational Biochemistry and Biophysics High‐performance computing in the upcoming exascale era will accelerate tremendously computer‐aided drug design.
AbstractList Molecular simulations and molecular docking are widely used tools to investigate ligand/target interactions and in drug design. High‐performance computing (HPC) is boosting both the accuracy and predictive power of these approaches. With the advent of exascale computing, HPC may become standardly applied in many drug design campaigns and pharmacological applications. This review discusses how innovative HPC algorithms and hardware are being exploited in current simulations and docking codes, pointing also at some of the limitations of these approaches. The focus is on technical aspects which might not be all that familiar to the computational pharmacologist. This article is categorized under: Software > Molecular Modeling Software > Simulation Methods Structure and Mechanism > Computational Biochemistry and Biophysics High‐performance computing in the upcoming exascale era will accelerate tremendously computer‐aided drug design.
Author Rothlisberger, Ursula
Rossetti, Giulia
Carloni, Paolo
Bolnykh, Viacheslav
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Notes Funding information
Edited by
Modesto Orozco, Associate Editor
Bioexcel‐2; Helmholtz European Partnering; Human Brain Project SGA3, Grant/Award Number: 945539; Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung; Horizon 2020 Framework Programme; European Union; Swiss National Science Foundation; Deutsche Forschungsgemeinschaft
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Snippet Molecular simulations and molecular docking are widely used tools to investigate ligand/target interactions and in drug design. High‐performance computing...
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SubjectTerms drug design
exascale computing
ligand‐target modeling
molecular dynamics
Title Expanding the boundaries of ligand–target modeling by exascale calculations
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