Recognition of Errors in the Refinement and Validation of Three-Dimensional Structures of AC1 Proteins of Begomovirus Strains by Using ProSA-Web | Zendy

Rajneesh Prajapat | Zendy; Avinash Marwal | Zendy; Rajarshi Kumar Gaur | Zendy

Open Access

Recognition of Errors in the Refinement and Validation of Three-Dimensional Structures of AC1 Proteins of Begomovirus Strains by Using ProSA-Web

Author(s) -

Rajneesh Prajapat,

Avinash Marwal,

Rajarshi Kumar Gaur

Publication year - 2014

Publication title -

journal of viruses

Language(s) - English

Resource type - Journals

eISSN - 2356-7716

pISSN - 2314-646X

DOI - 10.1155/2014/752656

Subject(s) - in silico , begomovirus , computational biology , docking (animal) , computer science , structural bioinformatics , protein structure , biology , biological system , genetics , gene , genome , biochemistry , nursing , medicine

The structural model of begomovirus AC1 protein is useful for understanding biological function at molecular level and docking study. For this study we have used the ProSA program (Protein Structure Analysis) tool to establish the structure prediction and modeling of protein. This tool was used for refinement and validation of experimental protein structures. Potential problems of protein structures based on energy plots are easily seen by ProSA and are displayed in a three-dimensional manner. In the present study we have selected different AC1 proteins of begomovirus strains (YP_003288785, YP_002004579, and YP_003288773) for structural analysis and display of energy plots that highlight potential problems spotted in protein structures. The 3D models of Rep proteins with recognized errors can be effectively used for in silico docking study for development of potential ligand molecules against begomovirus infection.

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