Dr. Pratiti Bhadra

Address

Email: pratiti.bhadra@bioinformatik.uni-saarland.de ; pratiti.bhadra@gmail.com
Telephone:
Postal address: Center for Bioinformatics
Gebäude E2 1, R. 303
P.O. Box 15 11 50
D-66041 Saarbrücken
Germany

Curriculum Vitae

Research Areas

  • Biomolecular simulations and docking
  • Application of machine learning algorithms
  • Parameterization of biomolecular force field

Publications

"Quantitative proteomics and differential protein abundance analysis after depletion of putative mRNA receptors in the ER membrane of human cells identifies novel aspects of mRNA targeting to the ER" Pratiti Bhadra; Monika Lerner, Stefan Schorr, Duy Nguyen, Johanna Dudek, Friedrich Förster, Volkhard Helms, Sven Lang, Richard Zimmermann. Molecules (accepted) (2021)

"Mycolactone enhances the Ca2+ leakage from endoplasmic reticulum by trapping Sec61 translocons in a Ca2+ permeable state."  Bhadra, Pratiti, Scott Dos Santos, Igor Gamayun, Tillman Pick, Joy Ogbechi, Belinda S. Hall, Richard Zimmermann, Volkhard Helms, Rachel E. Simmonds, and Adolfo Cavalie. bioRxiv (2021).

How does the presence/absence of Sec63 affect the Sec61α conformations in yeast?” Pratiti Bhadra; Lalitha Yadhanapudi; Karin Römisch; Volkhard Helms. Plos. Comp. Bio. 2021) 17(3), e1008855.

Effect of concentration, chain length, hydrophobicity, and external electric fields on growth of mixed alkanethiol self-assembled monolayers: A molecular dynamics study” Pratiti Bhadra; Shirley W. I. Siu. Langmuir 37, 5, 1913-1924 (2021)

Deep-AmPEP30: Improve short antimicrobial peptides prediction with deep learning” JieluYan;Pratiti Bhadra; Ang Li; Pooja Sethiya; Longguang Qin; Hio Kuan Tai; Koon HoWong; Shirley W. I. Siu. Molecular Therapy - Nucleic Acids Volume 20, Pages 882-894(2020)

A Refined Empirical Force Field to Model Protein-SAM Interactions Based on AMBER14and GAFF”Pratiti Bhadraand Shirley W. I. Siu.Langmuir35, 29, 9622-9633(2019)

AmPEP: Sequence-based prediction of antimicrobial peptides using distribution patterns ofamino acid properties and random forest”Pratiti Bhadra, Jielu Yan, Jinyan Li, SimonFong, and Shirley W. I. Siu.ScientificReports8 1697(2018)

TNF Receptor Type II as an Emerging Drug Target for the Treatment of Cancer, Autoim-mune Diseases, and Graft-Versus-Host Disease: Current Perspectives and In silico Search forSmall Molecule Binders” Faraz Shaikh, Jiang He,Pratiti, Bhadra, Xin Chen, Shirley W.I. SiuFrontiers in Immunology, 9, 1382,(2018)

Comparison of Biomolecular Force Fields for Alkanethiol Self-Assembled Monolayer Simulations”Pratiti Bhadraand Shirley W.I. Siu.J. Phys. Chem. C, 121 (47), pp 2634026349(2017)

Molecular dynamics information improves cis-peptide based function annotation of proteins.” Sreetama Das,Pratiti Bhadra, S. Ramakumar and Debnath Pal.Journal ofProteome Research, 16, 2936-2946(2017).

Pipeline for inferring protein function from dynamics using coarse-grained molecular mechanics forcefield”Pratiti Bhadra, Debnath Pal.Computer in Biology and Medicine.83, 134-142(2017)

De novo inference of protein function from coarse-grained dynamics" Pratiti Bhadra, Deb-nath Pal.Protiens: Structure, Function and Bioinformatics. 82:24432454(2014

Teaching

  • Teaching
  • Mentoring (co-supervisor)
    • 2020: Mohan Dash, MSc thesis, Center of Bioinformatics, MSc thesis, Saarland University, Germany
    • 2017-18:  Jielu Yan, MSc thesis, Department of Computer and Information Science, University of Macau, Macau