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
Hierarchical virtual screening approaches in small molecule drug discovery
Ashutosh Kumar,Kam Y. J. Zhang +1 more
TL;DR: This review focuses on different hierarchical virtual screening strategies and their application in the discovery of small molecule modulators of important drug targets.
Journal ArticleDOI
Free Energy Methods in Drug Design: Prospects of "Alchemical Perturbation" in Medicinal Chemistry
TL;DR: It is concluded that al chemical methods are becoming a feasible reality in medicinal chemistry research due to improved computational resources and algorithms and that alchemical free energy predictions methods are close to becoming a mainstream tool for medicinal chemists.
Journal ArticleDOI
Theory and Applications of Covalent Docking in Drug Discovery: Merits and Pitfalls
TL;DR: This review is the first account that highlights different aspects of covalent docking with its merits and pitfalls, and believes that the method and applications highlighted in this study will help future efforts towards the design of irreversible inhibitors.
Journal ArticleDOI
Integrated approach to structure-based enzymatic drug design: molecular modeling, spectroscopy, and experimental bioactivity.
Bahareh Honarparvar,Thavendran Govender,Glenn E. M. Maguire,Mahmoud E. S. Soliman,Hendrik G. Kruger +4 more
Journal ArticleDOI
Receptor-based virtual screening protocol for drug discovery.
Nuno M. F. S. A. Cerqueira,Diana S. Gesto,Eduardo F. Oliveira,Diogo Santos-Martins,Natércia F. Brás,Sérgio F. Sousa,Pedro A. Fernandes,Maria J. Ramos +7 more
TL;DR: This chapter provides a comprehensive overview of the receptor-based virtual screening process and of its importance in the present drug discovery and development paradigm.
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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