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
Docking optimization, variance and promiscuity for large-scale drug-like chemical space using high performance computing architectures
Richard E. Trager,Paul Giblock,Sherwin Soltani,Amit A. Upadhyay,Bhanu Rekapalli,Yuri K. Peterson +5 more
TL;DR: Wrappers provide faster docking speeds when compared with the naive multi-threading system MPI-DOCK, making future endeavors in large-scale docking more feasible; in addition, eliminating highly variant or promiscuous compounds will make databases more useful.
Journal ArticleDOI
Virus-Host Interactions: New Insights and Advances in Drug Development Against Viral Pathogens
Minakshi Prasad,Koushlesh Ranjan,Basanti Brar,Ikbal Shah,Upendra Lalmbe,Manimegalai J,Bhavya Vashisht,Madhusudan Gaury,Pawan Kumar,Sandip Kumar Khurana,Gaya Prasad,Jagveer Rawat,Vikas Yadav,Sunil Kumar,Rekha Rao +14 more
TL;DR: The present review is aimed at providing an update on research and development efforts being made to create effective antiviral chemotherapeutic agents and approaches to their delivery to appropriate targeted cells or tissues.
Book ChapterDOI
In Silico Structure-Based Prediction of Receptor–Ligand Binding Affinity: Current Progress and Challenges
TL;DR: The dependence of binding affinity on pH, estimation of entropy along with enthalpy in binding affinity, inclusion of conformational entropy of ligand and receptor, and modulation of flexibilities during complex formation are important challenges lying ahead.
Journal ArticleDOI
Biological Activities Evaluation of Enantiopure Isoxazolidine Derivatives: In Vitro, In Vivo and In Silico Studies.
Habib Mosbah,Hassiba Chahdoura,Asma Mannai,Mejdi Snoussi,Kaïss Aouadi,Rui M V Abreu,Ali Bouslama,Lotfi Achour,Boulbaba Selmi +8 more
TL;DR: A series of enantiopure isoxazolidines synthesized by 1,3-dipolar cycloaddition between a (−)-menthone-derived nitrone and various terminal alkenes was found to be the most potent antimicrobial agent as compared to the standard drug.
Journal ArticleDOI
A neutral polysaccharide from green tea: Structure, effect on α-amylase activity and hydrolysis property.
TL;DR: Molecular docking analysis revealed that the various behaviors of TPSN to α-amylase could be attributed to that the different chain segments of T PSN combined with different amino acid residues of α- amylase.
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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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