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

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 Simula-tions”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 pro-teins.” 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 me-chanicsforcefield”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
    • SS 2020: “Bioinformatics: Processing Biological Data” assignment discussion class of ”Deep learning”,  Center of Bioinformatics, University Saarland, Germany
    • WS 2019/2020: “Bioinformatics II” assignment discussion class of "Graph and Pathways of Metabolic Networks" and "Dynamics Simulation of Networks",  Center of Bioinformatics, University Saarland, Germany
    • WS 2018/2019: “Bioinformatics: Processing Biological Data” assignment discussion class of ”Molecular Dynamics simulation, Center of Bioinformatics, University Saarland, Germany
  • 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