Journal ArticleDOI
Latest developments in molecular docking: 2010-2011 in review.
TLDR
The main developments in docking in this period, covered in this review, are receptor flexibility, solvation, fragment docking, postprocessing, docking into homology models, and docking comparisons.Abstract:
The aim of docking is to accurately predict the structure of a ligand within the constraints of a receptor binding site and to correctly estimate the strength of binding. We discuss, in detail, methodological developments that occurred in the docking field in 2010 and 2011, with a particular focus on the more difficult, and sometimes controversial, aspects of this promising computational discipline. The main developments in docking in this period, covered in this review, are receptor flexibility, solvation, fragment docking, postprocessing, docking into homology models, and docking comparisons. Several new, or at least newly invigorated, advances occurred in areas such as nonlinear scoring functions, using machine-learning approaches. This review is strongly focused on docking advances in the context of drug design, specifically in virtual screening and fragment-based drug design. Where appropriate, we refer readers to exemplar case studies.read more
Citations
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Journal ArticleDOI
Deciphering inhibitory activity of flavonoids against tau protein kinases: a coupled molecular docking and quantum chemical study.
Hassan Rasouli,Seyed Mohammad Bagher Hosseini Ghazvini,Reza Yarani,Ali Altıntaş,Saber Ghafari Nikoo Jooneghani,Teodorico C. Ramalho +5 more
TL;DR: A coupled docking and quantum study was applied to determine the binding mode of flavonoids and three protein kinases involved in the pathogenesis of AD, and suggested that all docked metabolites showed considerable binding affinity to interact with target receptors, but some compounds possessed higher binding energy values.
Journal ArticleDOI
Synthesis, characterization, anti-diabetic potential and DFT studies of 7-hydroxy-4-methyl-2-oxo-2H-chromene-8-carbaldehyde oxime.
Seyed Mohammad Bagher Hosseini Ghazvini,Parvin Safari,Akbar Mobinikhaledi,Hassan Moghanian,Hassan Rasouli +4 more
TL;DR: Computational finding suggests that this compound has a potential to be used as a supplementary agent in the pre-management of diabetes mellitus and a good binding affinity to interact with the active sites of human α-glucosidase and α-amylase.
Journal ArticleDOI
Computational Assessment and Pharmacological Property Breakdown of Eight Patented and Candidate Drugs against Four Intended Targets in Alzheimer’s Disease
Bishajit Sarkar,Syed S. Islam,Md. Asad Ullah,Sohana Hossain,Md. Nazmul Islam Prottoy,Yusha Araf,Masuma Afrin Taniya +6 more
TL;DR: Investigation of Docking results, Druglikeness properties and ADME/T testing results suggest that the best findings of this experiment are memantine, hymenialdisine, dihydrospiro[a,d][7]annulene-5,4’-imidazol] and harmol, that could be the best possible drugs for the treatment of AD.
Journal ArticleDOI
A biased random key genetic algorithm for the protein–ligand docking problem
TL;DR: The proposed method, BRKGA-DOCK, developed a Biased Random Key Genetic Algorithm as a sampling strategy to search the protein–ligand conformational space and proved to be efficient and a good alternative for the molecular docking problem.
Journal ArticleDOI
Dipeptidyl Peptidase-4 Is a Target Protein of Epigallocatechin-3-Gallate.
TL;DR: Data provide a theoretical basis for intervention in glucose metabolism with EGCG, and target Dipeptidyl peptidase-4 was identified following this approach.
References
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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
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.
Journal ArticleDOI
Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy.
Richard A. Friesner,Jay L. Banks,Robert B. Murphy,Thomas A. Halgren,Jasna Klicic,Daniel T. Mainz,Matthew P. Repasky,Eric H. Knoll,Mee Shelley,Jason K. Perry,David E. Shaw,Perry Francis,Peter S Shenkin +12 more
TL;DR: Glide approximates a complete systematic search of the conformational, orientational, and positional space of the docked ligand to find the best docked pose using a model energy function that combines empirical and force-field-based terms.
Journal ArticleDOI
Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening.
Thomas A. Halgren,Robert B. Murphy,Richard A. Friesner,Hege S. Beard,Leah L. Frye,W. Thomas Pollard,Jay L. Banks +6 more
TL;DR: Comparisons to results for the thymidine kinase and estrogen receptors published by Rognan and co-workers show that Glide 2.5 performs better than GOLD 1.1, FlexX 1.8, or DOCK 4.01.
Journal ArticleDOI
A Fast Flexible Docking Method using an Incremental Construction Algorithm
TL;DR: This work presents an automatic method for docking organic ligands into protein binding sites that combines an appropriate model of the physico-chemical properties of the docked molecules with efficient methods for sampling the conformational space of the ligand.
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