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High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations
2010
Biophysical Journal
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Next, in an effort to expose novel conformations of the binding site that might be missed experimentally, we use a theoretical source: molecular dynamics (MD) simulation. ...
Despite the FDA-approval of four NNRTIs to date, the side-effects of drug toxicity and the emergence of drug-resistance mutations demand further drug discovery endeavors. ...
of this transporter.
2381-Pos High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations Noriaki Okimoto 1 , Noriyuki Futatsugi 1 , Hideyoshi Fuji ...
doi:10.1016/j.bpj.2009.12.2502
fatcat:kimxeoh27baatenktifrnqwl4y
High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations
2009
PLoS Computational Biology
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This result indicates that the application of molecular dynamics simulations to virtual screening for lead discovery is both effective and practical. ...
In this study, we used massive molecular dynamics simulations of protein-ligand conformations obtained by molecular docking in order to improve the enrichment performance of molecular docking. ...
In this paper, we report an effective method for computational screening; this method is a combination of molecular docking and massive-scale molecular dynamics simulations. ...
doi:10.1371/journal.pcbi.1000528
pmid:19816553
pmcid:PMC2746282
fatcat:axmdksi4djgodkwkf35ofijxla
Applying high-performance computing in drug discovery and molecular simulation
2016
National Science Review
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This review mainly focuses on the application of HPC to the fields of drug discovery and molecular simulation at the Chinese Academy of Sciences, including virtual drug screening, molecular dynamics simulation ...
Computational drug discovery and design, which is based on HPC and combines pharmaceutical chemistry and computational biology, has become a critical approach in drug research and development and is financially ...
and dynamic simulation projects. ...
doi:10.1093/nsr/nww003
pmid:32288960
pmcid:PMC7107815
fatcat:bhur7mu3lfap5a4lhczgtrbmzm
Perspective of drug design with high-performance computing
2021
National Science Review
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high-performance computing. ...
The representative applications, recent advances and possible future directions of computational drug design were summarized, aiming to accelerate the drug discovery with the assistance of the fast-developing ...
Binding prediction, virtual screening, molecular dynamics simulations, and protein folding are the crucial applications of computational drug design to accelerate the drug discovery ( Fig. 1 ). ...
doi:10.1093/nsr/nwab105
pmid:34992787
pmcid:PMC8692934
fatcat:birxtwxfwvgwjbwwmbwdd3jt5q
Pandemic Drugs at Pandemic Speed: Infrastructure for Accelerating COVID-19 Drug Discovery with Hybrid Machine Learning- and Physics-based Simulations on High Performance Computers
[article]
2021
arXiv
pre-print
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Here, we present an innovative infrastructural development that combines both approaches to accelerate drug discovery. ...
The race to meet the challenges of the global pandemic has served as a reminder that the existing drug discovery process is expensive, inefficient and slow. ...
We acknowledge excellent support from Don Maxwell, Bronson Messier and Sean Wilkinson at OLCF. We also wish to thank Dan Stanzione and Jon Cazes at Texas Advanced Computing Center. ...
arXiv:2103.02843v2
fatcat:k2x6by6ojrgqlkdhb4lpoq7cj4
Pandemic drugs at pandemic speed: infrastructure for accelerating COVID-19 drug discovery with hybrid machine learning- and physics-based simulations on high-performance computers
2021
Interface Focus
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Here, we present an innovative infrastructural development that combines both approaches to accelerate drug discovery. ...
The race to meet the challenges of the global pandemic has served as a reminder that the existing drug discovery process is expensive, inefficient and slow. ...
We acknowledge excellent support from Don Maxwell, Bronson Messer and Sean Wilkinson at OLCF. We also wish to thank Dan Stanzione and Jon Cazes at Texas Advanced Computing Center. ...
doi:10.1098/rsfs.2021.0018
pmid:34956592
pmcid:PMC8504892
fatcat:rvalq6bwkfcmfapzwnowova6se
Computational methods in drug discovery
2016
Beilstein Journal of Organic Chemistry
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Advances in virtual high-throughput screening, protein structure prediction methods, protein-ligand docking, pharmacophore modeling and QSAR techniques are reviewed. ...
Here we present an overview of computational methods used in different facets of drug discovery and highlight some of the recent successes. ...
have been built mainly for molecular dynamics simulations. ...
doi:10.3762/bjoc.12.267
pmid:28144341
pmcid:PMC5238551
fatcat:le2kn3lcojgjthfg2qxn5lk3vu
Molecular Docking: Shifting Paradigms in Drug Discovery
2019
International Journal of Molecular Sciences
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Molecular docking is an established in silico structure-based method widely used in drug discovery. ...
In this review, we describe how molecular docking was firstly applied to assist in drug discovery tasks. ...
Considering the high attrition rates characterizing drug discovery [203, 204] , the possibilities offered by docking in combination with the approaches outlined here will be important to reduce time and ...
doi:10.3390/ijms20184331
pmid:31487867
pmcid:PMC6769923
fatcat:pxh6aqni2vehxk7kyjwujciwf4
Ensemble Docking in Drug Discovery
2018
Biophysical Journal
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Ensemble docking corresponds to the generation of an "ensemble" of drug target conformations in computational structure-based drug discovery, often obtained by using molecular dynamics simulation, that ...
This approach is now well established in the field of early-stage drug discovery. ...
Hence, the field of early stage drug discovery pivoted somewhat to the combination of combinatorial chemistry and experimental high-throughput screening. ...
doi:10.1016/j.bpj.2018.02.038
pmid:29606412
pmcid:PMC6129458
fatcat:6kyspe4scneenklkuotmzs7xhe
Molecular dynamics-driven drug discovery: leaping forward with confidence
2017
Drug Discovery Today
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Molecular dynamics (MD) has become a particularly 6 important tool in drug design and discovery. ...
1 Given the high costs and time in developing a commercial drug, it remains important to 2 constantly reform the drug discovery pipeline with novel technologies that can narrow 3 down on the most promising ...
Journal of Chemical Information and Modeling 54 (7), 2127-2138 24 45 Ge, H. et al. (2013) Molecular Dynamics-Based Virtual Screening: Accelerating 25 the Drug Discovery Process by High-Performance Computing ...
doi:10.1016/j.drudis.2016.11.001
pmid:27890821
fatcat:k4hkw2mklfbg5dle24vsy5r5me
Computational Approaches for Drug Discovery
2019
Molecules
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Computational approaches represent valuable and essential tools in each step of the drug discovery and development trajectory [...] ...
Acknowledgments: I wish to thank the Editorial Board of Molecules for the opportunity to become the Guest Editor of the Special Issue "Computational Approaches for Drug Discovery". ...
The current status of high-performance computing applications in the general area of drug discovery has been reviewed. ...
doi:10.3390/molecules24173061
pmid:31443558
pmcid:PMC6749237
fatcat:cl3teejrlfdzze3ct7wm7sht7q
Automated discovery of GPCR bioactive ligands
2019
Current Opinion in Structural Biology
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2018 pre-print arXiv:1812.06400v1 fatcat:2noehybncfhyndkpn56sr6ipu4Other Versions
Along with highlighting the recent advances in structure-based ligand discovery, including docking and molecular dynamics, this article focuses on the latest advances for automating the discovery of bioactive ...
Because of the involvement of GPCRs in various signaling pathways and physiological roles, the identification of endogenous ligands as well as designing novel drugs is of high interest to the research ...
Since computational capabilities are rapidly advancing as well, docking studies are now often accompanied by molecular dynamics simulations, which allow more detailed studies of the GPCR-recognition process ...
doi:10.1016/j.sbi.2019.02.011
pmid:30909105
fatcat:tm5pfuy4z5dexdsnnlca7rzmgm
Hierarchical virtual screening approaches in small molecule drug discovery
2015
Methods
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Hierarchical combination of ligand and structure-based virtual screening approaches has received noteworthy success in numerous drug discovery campaigns. ...
In this review, we focus on different hierarchical virtual screening strategies and their application in the discovery of small molecule modulators of important drug targets. ...
Acknowledgments We thank members of our laboratory for help and discussions. We acknowledge RIKEN, Japan for funding. ...
doi:10.1016/j.ymeth.2014.07.007
pmid:25072167
pmcid:PMC7129923
fatcat:t5mu2qmh5ncz3gwu3k2wnfr3t4
Molecular Docking in Drug Discovery
2021
Journal of Pharmaceutical Research International
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The docking score is analysed by using computer-based drug design software. ...
In last few years the Computer Aided Drug Design and Discovery is many success rates. In academics and many pharmaceutical industries for drug lead discovery they adopt the Computational Drug Design. ...
[Combining docking and molecular dynamic
simulations in drug design. Med Res
Rev. 2006;26(5):531-
568. [PubMed] [Google Scholar]
33. Sander T, Liljefors T, Balle T. ...
doi:10.9734/jpri/2021/v33i30b31639
fatcat:dvvvpjjcmbhthhcvfasybcb2je
Computational Methods in Drug Discovery
2013
Pharmacological Reviews
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The optimization process can be accelerated by the use of computational methods like molecular docking, molecular dynamics simulation, and quantum-mechanical simulations. 8 . ...
Table 2 illustrates some examples of drug discovery campaigns in which systematic docking algorithms have been used. 2. Molecular Dynamics Simulations. ...
doi:10.1124/pr.112.007336
pmid:24381236
pmcid:PMC3880464
fatcat:4dzrdkspkjecnombnchznma2ny
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