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AFD: an application for bi-molecular interaction using axial frequency distribution

  • Saad Raza
  • Syed Sikander Azam
Original Paper
  • 95 Downloads

Abstract

Conformational flexibility and generalized structural features are responsible for specific phenomena existing in biological pathways. With advancements in computational chemistry, novel approaches and new methods are required to compare the dynamic nature of biomolecules, which are crucial not only to address dynamic functional relationships but also to gain detailed insights into the disturbance and positional fluctuation responsible for functional shifts. Keeping this in mind, axial frequency distribution (AFD) has been developed, designed, and implemented. AFD can profoundly represent distribution and density of ligand atom around a particular atom or set of atoms. It enabled us to obtain an explanation of local movements and rotations, which are not significantly highlighted by any other structural and dynamical parameters. AFD can be implemented on biological models representing ligand and protein interactions. It shows a comprehensive view of the binding pattern of ligand by exploring the distribution of atoms relative to the x-y plane of the system. By taking a relative centroid on protein or ligand, molecular interactions like hydrogen bonds, van der Waals, polar or ionic interaction can be analyzed to cater the ligand movement, stabilization or flexibility with respect to the protein. The AFD graph resulted in the residual depiction of bi-molecular interaction in gradient form which can yield specific information depending upon the system of interest.

Keywords

Molecular dynamics simulation Conformational analysis Software Axial frequency distribution Radial distribution function Binding pattern 

Notes

Acknowledgments

The authors would like to acknowledge the valuable insight and testing done by Klaus R. Liedl and Julian E. Fuch at Theoretical Chemistry, Faculty of Chemistry and Pharmacy, Center for Molecular Biosciences, Leopold-Franzens-University Innsbruck. The authors would also like to acknowledge Higher Education Commission, Pakistan, International Foundation for Science and Ernst Mach follow-up grant for financial assistance.

Author contributions

SSA designed, conceived and drafted the manuscript. SR programmed and debugged the software and also drafted the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare no conflict of interest.

Supplementary material

894_2018_3601_MOESM1_ESM.docx (14 kb)
ESM 1 (DOCX 13 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Computational Biology Lab, National Center for BioinformaticsQuaid-i-Azam UniversityIslamabadPakistan

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