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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Book ChapterDOI
Enzyme-encapsulated nanoparticles for biodegradation of materials
TL;DR: The global market for nanocomposites is estimated to reach $7.3 billion by 2022, growing at a compounded annual growth rate of 29.5% for the period of 2017-2022 as discussed by the authors .
Dissertation
Computational modelling of ligand shape and interactions for medicines design
TL;DR: In this article, the feasibility of using quantum mechanical (QM) methods within the two broad categories of in silico ligand-based and structure-based drug design was explored, and an in-house docking scheme based on a Monte Carlo sampling algorithm using the semiempirical PM6/AMBER force field scoring function was compiled for the first time within the Gaussian 09 program.
Journal ArticleDOI
Design and Identification of a Novel Antiviral Affinity Peptide against Fowl Adenovirus Serotype 4 (FAdV-4) by Targeting Fiber2 Protein
Xiao Chen,Qiang Wei,Fusheng Si,Fang Wang,Qingxia Lu,Zhenhua Guo,Yongxiao Chai,Rongfang Zhu,Guangxu Xing,Qianyue Jin,Gaiping Zhang +10 more
TL;DR: In this paper , the C-terminal knob domain of the FAdV-4 Fiber2 protein was expressed and purified, and its trimer structure was determined for the first time.
Journal ArticleDOI
Characterization, Electrochemical Detection, Biological Evaluation and Molecular Modelling of 1,5-Di-O-caffeoylquinic Acid from Artichoke (Cynara scolymus L.) Head Extract
Mahdi Jamshidi,Akram Ranjbar,Sadegh Khazalpour,Dara Dastan,Mojtaba Vakili-Azghandi,Sara Torabi,Ameneh Amani,Hojat Alizadeh,Mahsa Sedaghat +8 more
Book ChapterDOI
In Silico Structure-Based Vaccine Design.
TL;DR: Structure-based vaccine design (SBVD) is an important technique in computational vaccine design that uses structural information on a targeted protein to design novel vaccine candidates as discussed by the authors . But the current challenges and limitations of SBVD are discussed.
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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