Molecular simulation methods for selecting thrombin-binding aptamers

Jangam Vikram Kumar, Wen Yih Chen, Jeffrey J.P. Tsai, Wen Pin Hu

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

6 Scopus citations

Abstract

To study and compare the simulation methods on the different scoring functions to analyze the consistency of the Docking score between the aptamers and protein. Thrombin is well characterized and has been studied with the thrombin binding aptamer (TBA) and mutated TBA sequences in a previous report, which finds three representative aptamers have best, medium, and worst binding interactions with thrombin. Discovery Studio 3.5 is a useful modeling and simulation software. The ZDOCK in this package incorporates a simple and novel scoring function: Pairwise Shape Complementarity. By using ZDOCK, we also can evaluate the differences in the binding ability between the interactions of the thrombin and aptamers. Basically, our results are consistent with the previous report. From this study, we make sure that the ZDOCK can provide reliable results and able be used as an alternative method in performing in silico selection of aptamer.

Original languageEnglish
Title of host publicationInformation Technology Convergence
Subtitle of host publicationSecurity, Robotics, Automations and Communication
PublisherSpringer Verlag
Pages743-749
Number of pages7
ISBN (Print)9789400769953
DOIs
StatePublished - 2013
Event5th FTRA International Conference on Information Technology Convergence and Services, ITCS 2013 and the 3rd International Conference on Intelligent Robotics, Automations, Telecommunication Facilities, and Applications, IRoA 2013 - Fukuoka, Japan
Duration: 8 Jul 201310 Jul 2013

Publication series

NameLecture Notes in Electrical Engineering
Volume253 LNEE
ISSN (Print)1876-1100
ISSN (Electronic)1876-1119

Conference

Conference5th FTRA International Conference on Information Technology Convergence and Services, ITCS 2013 and the 3rd International Conference on Intelligent Robotics, Automations, Telecommunication Facilities, and Applications, IRoA 2013
Country/TerritoryJapan
CityFukuoka
Period8/07/1310/07/13

Keywords

  • Aptamers
  • Molecular simulation
  • Pairwise shape complementarity
  • Selection
  • Thrombin

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