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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DissertationDOI
Neue N-substituierte 3-Chlorkenpaullone als Wirkstoffe gegen Trypanosomen
TL;DR: Paullonen et al. as mentioned in this paper used 3-Chlorkenpaullone as a Wirkstoffe gegen T. Brucei-Brucei-Homogenat.
Posted ContentDOI
Comprehensive Genome Based Analysis of Vibrio parahaemolyticus for Identifying Novel Drug and Vaccine Molecules: Subtractive Proteomics and Vaccinomics Approach
Mahmudul Hasan,Kazi Faizul Azim,Abdus Shukur Imran,Ishtiak Malique Chowdhury,Shah Rucksana Akhter Urme,Sorwer Alam Parvez,Bashir Uddin,Syed Sayeem Uddin Ahmed +7 more
TL;DR: The predicted drug molecules and vaccine constructs could be further studied to combat V. parahaemolyticus associated infections and exhibited deformability at a minimum level that strengthened the prediction.
Book ChapterDOI
In Silico Modeling of Anticancer Drugs: Recent Advances
Smriti Sharma,Vinayak Bhatia +1 more
TL;DR: In this paper, the authors focus on the importance and latest advances of in-silicon modeling for the design of new and potent anti-cancer drugs, and present a review of the most recent advances in this area.
Journal ArticleDOI
The Development of Classical Swine Fever Marker Vaccines in Recent Years
Fangfang Li,Bingke Li,Xinni Niu,Wenxian Chen,Yuwan Li,Keke Wu,Xiaowen Li,Hongxing Ding,Mingqiu Zhao,Jinding Chen,Lin Yi +10 more
TL;DR: The progress of the new CSF marker vaccine is summarized and a detailed overview of the vaccine design ideas and immunization effects are provided, which provides a methodology for the development of a new generation of vaccines for CSF and vaccine development for other significant epidemics.
Book ChapterDOI
CADD Studies Applied to Secondary Metabolites in the Anticancer Drug Research
Luciana Scotti,Nagendra Sastry Yarla,Francisco J. B. Mendonça Filho,José Maria Barbosa Filho,Marcelo Sobral da Silva,Josean Fechine Tavares,Marcus Tullius Scotti +6 more
TL;DR: The aim of present chapter is to discuss the use of computational approaches such as ADMET, molecular docking, molecular dynamics simulation, and QSAR to asses and predict the safety, efficacy, potency, and identification of natural potent anticancer molecules.
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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