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High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations

Noriaki Okimoto, Noriyuki Futatsugi, Hideyoshi Fuji, Atsushi Suenaga, Gentaro Morimoto, Ryoko Yanai, Yosuske Ohno, Tetsu Narumi, Makoto Taiji
2010 Biophysical Journal  
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

Noriaki Okimoto, Noriyuki Futatsugi, Hideyoshi Fuji, Atsushi Suenaga, Gentaro Morimoto, Ryoko Yanai, Yousuke Ohno, Tetsu Narumi, Makoto Taiji, David Case
2009 PLoS Computational Biology  
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

Tingting Liu, Dong Lu, Hao Zhang, Mingyue Zheng, Huaiyu Yang, Yechun Xu, Cheng Luo, Weiliang Zhu, Kunqian Yu, Hualiang Jiang
2016 National Science Review  
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

Zhe Li, Hui Li, Kunqian Yu, Hai-Bin Luo
2021 National Science Review  
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]

Agastya P. Bhati, Shunzhou Wan, Dario Alfè, Austin R. Clyde, Mathis Bode, Li Tan, Mikhail Titov, Andre Merzky, Matteo Turilli, Shantenu Jha, Roger R. Highfield, Walter Rocchia (+17 others)
2021 arXiv   pre-print
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

Agastya P. Bhati, Shunzhou Wan, Dario Alfè, Austin R. Clyde, Mathis Bode, Li Tan, Mikhail Titov, Andre Merzky, Matteo Turilli, Shantenu Jha, Roger R. Highfield, Walter Rocchia (+17 others)
2021 Interface Focus  
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

Sumudu P Leelananda, Steffen Lindert
2016 Beilstein Journal of Organic Chemistry  
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

Luca Pinzi, Giulio Rastelli
2019 International Journal of Molecular Sciences  
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

Rommie E. Amaro, Jerome Baudry, John Chodera, Özlem Demir, J. Andrew McCammon, Yinglong Miao, Jeremy C. Smith
2018 Biophysical Journal  
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

Aravindhan Ganesan, Michelle L. Coote, Khaled Barakat
2017 Drug Discovery Today  
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

Brogi
2019 Molecules  
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

Sebastian Raschka
2019 Current Opinion in Structural Biology  
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

Ashutosh Kumar, Kam Y.J. Zhang
2015 Methods  
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

Rani T. Bhagat, Santosh R. Butle, Deepak S. Khobragade, Sagar B. Wankhede, Chandani C. Prasad, Divyani S. Mahure, Ashwini V. Armarkar
2021 Journal of Pharmaceutical Research International  
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

G. Sliwoski, S. Kothiwale, J. Meiler, E. W. Lowe
2013 Pharmacological Reviews  
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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