3d-nus: A Web Server For Automated Modeling And Visualization Of Non-canonical 3-dimensional Nucleic Acid Structures
Project Description :

The inherent conformational flexibility of nucleic acids (dna, rna etc.) facilitate the formation of a range of conformations such as duplex, triplex, quadruplex etc., which play crucial roles in biological processes such as mismatch repair, replication, recombination, transcription, translation, gene regulations etc. these unconventional base pairing and structural conformations on dna/rna structures at different sequence contexts also induce abruptions in normal cell function which can lead to deformities and diseases (cancer, fragile x syndrome, etc.). to understand the role of these unusual nucleic acid structures in aforementioned biological phenomena and diseases, structural details at atomic level is indispensable. but, experimental methods (such as x-ray crystallography, nmr etc.) are not always successful in determining structural details and are very expensive. further, structural insights about nucleic acid triplexes, which are generally not tractable to structure determination by x-ray crystallography or nmr techniques, are essential to establish their biological function(s). a web server, namely 3d-nus (, has been developed to generate energy minimized models of 80 different types of triplexes, 64 types of g-quadruplexes, left handed z-dna/rna duplexes, rna-dna hybrid duplex along with inter- and intra-molecular dna or rna duplexes comprising a variety of mismatches and their chimeric forms for any user defined sequence and length. it also generates an ensemble of conformations corresponding to the modeled structure. these structures may serve as good starting models for docking proteins & small molecules with nucleic acids, nmr structure determination, cryo-electron microscope modeling, dna/rna nanotechnology applications and molecular dynamics simulation studies. this server will also generate aforementioned structures with modified nucleic acids such as pna, lna etc.

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Project Details :
  • Date : Nov 04,2017
  • Innovator : L Ponoop Prasad Patro
  • Team Members : Narendar Kolimi,Abhishek Kumar
  • Guide Name : Dr Thenmalarchelvi Rathinavelan
  • University : Indian Institutes of Technology Hyderabad
  • Submission Year : 2018
  • Category : Bioengineering / Biotech
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