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
The smaller heparin fragments bind non-specifically through the IAPP sequence: An in silico study
TL;DR: The findings indicate that the heparin fragments of longer length, >dp7, predominantly interact with IAPP N- and C-termini, resulting in a stable complex with solvent accessible self-recognition element (SRE) of IAPP sequence, however, shorter fragment non-specifically binds through the IAPP sequences, including N-terminus residues and SRE sequences.
Journal ArticleDOI
Molecular docking analysis of piperine with CDK2,CDK4,Cyclin D and Cyclin T proteins.
Umapathy Vidhya Rekha,M. Anita,Govindaraj Jayamathi,K. Sadhana,Subramanian Deepa,Sajid Hussain,J Bhuvaneswari,V. Ramya,Jayaraman Selvaraj,N S Naveenraj +9 more
TL;DR: Piperine is a bioenhancer as it reduces the activity of drug-metabolizing enzymes in rodents and thereby enhancing the plasma concentrations of several drugs, including the Pglycoprotein substrates, so it is of interest to understand the molecular docking interactions of piperine with several cell cycle proteins for further consideration in drug discovery related to oral cancer.
Journal ArticleDOI
The mechanistic insight of a specific interaction between 15d-Prostaglandin-J2 and eIF4A suggests an evolutionary conserved role across species.
So Jeong Yun,Hyunjoon Kim,Seung Hyun Jung,Joon Kim,Jeong Eun Ryu,N. Jiten Singh,Jouhyun Jeon,Jin-Kwan Han,Cheol-Hee Kim,Sanguk Kim,Sung Key Jang,Woo Jae Kim +11 more
TL;DR: The tail region of 15d-PGJ2 plays a important role in modulating the activity of eIF4A protein across species, which implies that the tail area of this prostaglandins can be adapted to design new drugs.
Journal ArticleDOI
Integrating sampling techniques and inverse virtual screening: toward the discovery of artificial peptide-based receptors for ligands
German Perez,Luis A. Salomón,Luis A. Montero-Cabrera,José M. García de la Vega,Marcello Mascini +4 more
TL;DR: A novel heuristic using an iterative select-and-purge strategy that combines statistical techniques for sampling and classification by rigid molecular docking through an inverse virtual screening scheme is proposed for de novo discovery of short peptides that may act as docking receptors for small target molecules when there are no data available about known association complexes between them.
Posted ContentDOI
In Silico Analysis of Some Phytochemicals as Potent Anti-tubercular Agents Targeting Mycobacterium tuberculosis RNA Polymerase and InhA Protein
TL;DR: Two agents, 4hydroxybenzaldehyde and bergapten were considered as the best agents among the five selected agents and they also showed far better results than the two currently used drugs, that function in these pathways, rifampicin (MTB RNA polymerase) and isoniazid (InhA protein).
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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