Journal ArticleDOI
Molecular Docking: Challenges, Advances and its Use in Drug Discovery Perspective
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TLDR
In this review, the prime focus has been laid on the challenges of docking and troubleshooters in existing programs, underlying algorithmic background of docking, preferences regarding the use of docking programs for best results illustrated with examples, comparison of performance for existing tools and algorithms, state of art in docking.Abstract:
Molecular docking is a process through which small molecules are docked into the macromolecular structures for scoring its complementary values at the binding sites. It is a vibrant research area with dynamic utility in structure-based drug-designing, lead optimization, biochemical pathway and for drug designing being the most attractive tools. Two pillars for a successful docking experiment are correct pose and affinity prediction. Each program has its own advantages and drawbacks with respect to their docking accuracy, ranking accuracy and time consumption so a general conclusion cannot be drawn. Moreover, users don't always consider sufficient diversity in their test sets which results in certain programs to outperform others. In this review, the prime focus has been laid on the challenges of docking and troubleshooters in existing programs, underlying algorithmic background of docking, preferences regarding the use of docking programs for best results illustrated with examples, comparison of performance for existing tools and algorithms, state of art in docking, recent trends of diseases and current drug industries, evidence from clinical trials and post-marketing surveillance are discussed. These aspects of the molecular drug designing paradigm are quite controversial and challenging and this review would be an asset to the bioinformatics and drug designing communities.read more
Citations
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Journal ArticleDOI
Network pharmacology and molecular docking analyses on Lianhua Qingwen capsule indicate Akt1 is a potential target to treat and prevent COVID-19.
Qi-Dong Xia,Yang Xun,Jun-Lin Lu,Yuchao Lu,Yuanyuan Yang,Peng Zhou,Jia Hu,Cong Li,Shaogang Wang +8 more
TL;DR: This study is aimed to discover the molecular mechanism of coronavirus disease 2019 and provide potential drug targets to discover its molecular mechanism and provide possible drug targets.
Journal ArticleDOI
Network pharmacology and molecular docking analysis on molecular targets and mechanisms of Huashi Baidu formula in the treatment of COVID-19.
TL;DR: Baicalein and quercetin in HSBDF may regulate multiple signaling pathways through ACE2, which might play a therapeutic role on COVID-19.
Journal ArticleDOI
Tackling Antibiotic Resistance with Compounds of Natural Origin: A Comprehensive Review.
TL;DR: The antimicrobial activity of the most representative natural products of animal, bacterial, fungal and plant origin, including phytochemicals, have been reviewed, showing synergistic capacity with antibiotics.
Book ChapterDOI
Docking with SwissDock.
TL;DR: This chapter describes how to use UCSF Chimera and SwissDock to perform protein-ligand docking simulations and describes the molecular docking of the competitive inhibitor roscovitine against the structure of human cyclin-dependent kinase 2.
Journal ArticleDOI
Pimenta dioica (L.) Merr. Bioactive Constituents Exert Anti-SARS-CoV-2 and Anti-Inflammatory Activities: Molecular Docking and Dynamics, In Vitro, and In Vivo Studies.
Heba A. El Gizawy,Sylvia A. Boshra,Ahmed Mostafa,Sara H. Mahmoud,Muhammad I. Ismail,Aisha A. Alsfouk,Azza T. Taher,Ahmed A. Al-Karmalawy +7 more
TL;DR: In this article, four bioactive compounds, namely ferulic acid 1, rutin 2, gallic acid 3, and chlorogenic acid 4 were isolated from the leaves of Pimenta dioica (L.) Merr (ethyl acetate extract) and identified using spectroscopic evidence.
References
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Journal ArticleDOI
The Protein Data Bank
Helen M. Berman,John D. Westbrook,Zukang Feng,Gary L. Gilliland,Talapady N. Bhat,Helge Weissig,Ilya N. Shindyalov,Philip E. Bourne +7 more
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Journal ArticleDOI
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
Oleg Trott,Arthur J. Olson +1 more
TL;DR: AutoDock Vina achieves an approximately two orders of magnitude speed‐up compared with the molecular docking software previously developed in the lab, while also significantly improving the accuracy of the binding mode predictions, judging by tests on the training set used in AutoDock 4 development.
Journal ArticleDOI
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
Garrett M. Morris,Ruth Huey,William Lindstrom,Michel F. Sanner,Richard K. Belew,David S. Goodsell,Arthur J. Olson +6 more
TL;DR: AutoDock4 incorporates limited flexibility in the receptor and its utility in analysis of covalently bound ligands is reported, using both a grid‐based docking method and a modification of the flexible sidechain technique.
Proceedings ArticleDOI
A new optimizer using particle swarm theory
TL;DR: The optimization of nonlinear functions using particle swarm methodology is described and implementations of two paradigms are discussed and compared, including a recently developed locally oriented paradigm.
Journal ArticleDOI
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
Garrett M. Morris,David S. Goodsell,Robert Scott Halliday,Ruth Huey,William E. Hart,Richard K. Belew,Arthur J. Olson +6 more
TL;DR: It is shown that both the traditional and Lamarckian genetic algorithms can handle ligands with more degrees of freedom than the simulated annealing method used in earlier versions of AUTODOCK, and that the Lamarckia genetic algorithm is the most efficient, reliable, and successful of the three.
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