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Faculty Dr Naga Bhushana Rao Karampudi

Dr Naga Bhushana Rao Karampudi

Assistant Professor

Department of Biological Sciences

Contact Details

nagabhushan.k@srmap.edu.in

Office Location

Education

2017
PhD
Indian Institute of Technology Kharagpur
India
2011
MTech
Indian Institute of Technology Kharagpur
India
2008
BTech
JNTU Hyderabad,
India

Experience

  • 2020-2021 – Postdoctoral Research Associate – University of Lausanne, Lausanne, Switzerland
  • 2016-2019 – Postdoctoral Research Associate – Texas Tech University, Lubbock, Texas, USA

Research Interest

  • Computational analysis of transcriptomics data to identify the candidate genes and their gene network dynamics, emphasizing on the adaptation mechanisms triggered in transgressive segregants in response to abiotic stress.
  • Computational structural analysis of macromolecules and their complexes to understand molecular basis of interactions.
  • Databases and Web-applications development.
  • Molecular dynamics simulation studies of Intrinsically disordered proteins to decipher the molecular plasticity and its role in selecting multiple binding partner molecules.
  • Computational estimation of ancestral genomes using gene synteny.

Awards

  • 2017 – Distinguished academic Achievement – Texas Tech University
  • 2016 – Full funded International Workshop on Advanced computing – ICTP, Trieste, Italy
  • 2009-2011 – M.Tech Fellowship – IIT Kharagpur
  • 2011-2016 – Ph.D Fellowship – IIT Kharagpur

Memberships

No data available

Publications

  • Sampled Surface and Shape DataBase (SSSDb): A database of deterministically sampled surface and a spectrum of shape representations of biomolecular structures

    Dr Naga Bhushana Rao Karampudi

    Source Title: Research square, DOI Link

    View abstract ⏷

    Computational tools and techniques have come a long way in analyzing biomolecular structures. However, there are still limitations in how far we can exhaustively utilize the structural information of molecules in applications like whole database docking studies, achieving microsecond simulations , performing pairwise comparisions of entire molecular repositories. Coarse Grained models biomolecular structures have potential applications in many such methodologies as they help reduce the computational loads. SSSDb is a resource of such reduced representations of biomole-cular structures and provides surface and a spectrum of deterministically sampled shapes at varied fineness. Phase I of SSSDb provides 9,88,124 (? 1 million) coarse grained structures of 31,885 CATH protein domains. To cater the different possible needs of users the database is also provisioned to be accessible through four different options: (1) CATH ID based queires, (2) precompiled data clusters, (3) entire database download as single zip file and (4) customizable and automated downloads using programming script. In near future, SSSDb will be expanded to include all the biomolecular structures of Protein, DNA, RNA and their complexes. The entire database is available freely and openly for both academic and non-academic purposes

Patents

Projects

Scholars

Doctoral Scholars

  • Vanajakshi Kunchala
  • Siva Bhavani Gollapalli
  • Kiruthiga Shankar Kumar

Interests

  • Computational analysis of Genomic and Transcriptomics data
  • Computational Biology

Thought Leaderships

There are no Thought Leaderships associated with this faculty.

Top Achievements

Education
2008
BTech
JNTU Hyderabad,
India
2011
MTech
Indian Institute of Technology Kharagpur
India
2017
PhD
Indian Institute of Technology Kharagpur
India
Experience
  • 2020-2021 – Postdoctoral Research Associate – University of Lausanne, Lausanne, Switzerland
  • 2016-2019 – Postdoctoral Research Associate – Texas Tech University, Lubbock, Texas, USA
Research Interests
  • Computational analysis of transcriptomics data to identify the candidate genes and their gene network dynamics, emphasizing on the adaptation mechanisms triggered in transgressive segregants in response to abiotic stress.
  • Computational structural analysis of macromolecules and their complexes to understand molecular basis of interactions.
  • Databases and Web-applications development.
  • Molecular dynamics simulation studies of Intrinsically disordered proteins to decipher the molecular plasticity and its role in selecting multiple binding partner molecules.
  • Computational estimation of ancestral genomes using gene synteny.
Awards & Fellowships
  • 2017 – Distinguished academic Achievement – Texas Tech University
  • 2016 – Full funded International Workshop on Advanced computing – ICTP, Trieste, Italy
  • 2009-2011 – M.Tech Fellowship – IIT Kharagpur
  • 2011-2016 – Ph.D Fellowship – IIT Kharagpur
Memberships
No data available
Publications
  • Sampled Surface and Shape DataBase (SSSDb): A database of deterministically sampled surface and a spectrum of shape representations of biomolecular structures

    Dr Naga Bhushana Rao Karampudi

    Source Title: Research square, DOI Link

    View abstract ⏷

    Computational tools and techniques have come a long way in analyzing biomolecular structures. However, there are still limitations in how far we can exhaustively utilize the structural information of molecules in applications like whole database docking studies, achieving microsecond simulations , performing pairwise comparisions of entire molecular repositories. Coarse Grained models biomolecular structures have potential applications in many such methodologies as they help reduce the computational loads. SSSDb is a resource of such reduced representations of biomole-cular structures and provides surface and a spectrum of deterministically sampled shapes at varied fineness. Phase I of SSSDb provides 9,88,124 (? 1 million) coarse grained structures of 31,885 CATH protein domains. To cater the different possible needs of users the database is also provisioned to be accessible through four different options: (1) CATH ID based queires, (2) precompiled data clusters, (3) entire database download as single zip file and (4) customizable and automated downloads using programming script. In near future, SSSDb will be expanded to include all the biomolecular structures of Protein, DNA, RNA and their complexes. The entire database is available freely and openly for both academic and non-academic purposes
Contact Details

nagabhushan.k@srmap.edu.in

Scholars

Doctoral Scholars

  • Vanajakshi Kunchala
  • Siva Bhavani Gollapalli
  • Kiruthiga Shankar Kumar

Interests

  • Computational analysis of Genomic and Transcriptomics data
  • Computational Biology

Education
2008
BTech
JNTU Hyderabad,
India
2011
MTech
Indian Institute of Technology Kharagpur
India
2017
PhD
Indian Institute of Technology Kharagpur
India
Experience
  • 2020-2021 – Postdoctoral Research Associate – University of Lausanne, Lausanne, Switzerland
  • 2016-2019 – Postdoctoral Research Associate – Texas Tech University, Lubbock, Texas, USA
Research Interests
  • Computational analysis of transcriptomics data to identify the candidate genes and their gene network dynamics, emphasizing on the adaptation mechanisms triggered in transgressive segregants in response to abiotic stress.
  • Computational structural analysis of macromolecules and their complexes to understand molecular basis of interactions.
  • Databases and Web-applications development.
  • Molecular dynamics simulation studies of Intrinsically disordered proteins to decipher the molecular plasticity and its role in selecting multiple binding partner molecules.
  • Computational estimation of ancestral genomes using gene synteny.
Awards & Fellowships
  • 2017 – Distinguished academic Achievement – Texas Tech University
  • 2016 – Full funded International Workshop on Advanced computing – ICTP, Trieste, Italy
  • 2009-2011 – M.Tech Fellowship – IIT Kharagpur
  • 2011-2016 – Ph.D Fellowship – IIT Kharagpur
Memberships
No data available
Publications
  • Sampled Surface and Shape DataBase (SSSDb): A database of deterministically sampled surface and a spectrum of shape representations of biomolecular structures

    Dr Naga Bhushana Rao Karampudi

    Source Title: Research square, DOI Link

    View abstract ⏷

    Computational tools and techniques have come a long way in analyzing biomolecular structures. However, there are still limitations in how far we can exhaustively utilize the structural information of molecules in applications like whole database docking studies, achieving microsecond simulations , performing pairwise comparisions of entire molecular repositories. Coarse Grained models biomolecular structures have potential applications in many such methodologies as they help reduce the computational loads. SSSDb is a resource of such reduced representations of biomole-cular structures and provides surface and a spectrum of deterministically sampled shapes at varied fineness. Phase I of SSSDb provides 9,88,124 (? 1 million) coarse grained structures of 31,885 CATH protein domains. To cater the different possible needs of users the database is also provisioned to be accessible through four different options: (1) CATH ID based queires, (2) precompiled data clusters, (3) entire database download as single zip file and (4) customizable and automated downloads using programming script. In near future, SSSDb will be expanded to include all the biomolecular structures of Protein, DNA, RNA and their complexes. The entire database is available freely and openly for both academic and non-academic purposes
Contact Details

nagabhushan.k@srmap.edu.in

Scholars

Doctoral Scholars

  • Vanajakshi Kunchala
  • Siva Bhavani Gollapalli
  • Kiruthiga Shankar Kumar