2023
''Computational Drug Discovery – A Primer” N. Sukumar, Harishchander Anandaram and Pratiti Bhadra (in press, Ion Cures Press, 2023) .
2022
"Effect of Sec62 on the conformation of the Sec61 channel in yeast." Pratiti Bhadra, Karin Römisch, and Volkhard Helms. Biochimica et Biophysica Acta (BBA)-Biomembranes 1864.12 (2022): 184050.
``Synthesis, Biological Evaluation and Docking Studies of Ring-Opened Analogues of Ipomoeassin F" Sarah O’Keefe, Pratiti Bhadra, Kwabena B. Duah, Guanghui Zong, Levise Tenay, Lauren Andrews, Hayden Schneider, Ashley Anderson, Zhijian Hu, Hazim S. Aljewari, Belinda S. Hall, Rachel E. Simmonds, Volkhard Helms, Stephen High, Wei Q. Shi Molecules MDPI 27.14 (2022): 4419.
"Signal peptide features determining the substrate specificities of targeting and translocation components in human ER protein import." Sven Lang, Duy Nguyen, Pratiti Bhadra, Martin Jung, Volkhard Helms and Richard Zimmermann, Frontiers in Physiology, vol 13 no. 833540.
"Phenylbutyrate rescues the transport defect of the Sec61α mutations V67G and T185A for renin." Sicking, Mark, Martina Živná, Pratiti Bhadra, Veronika Barešová, Andrea Tirincsi, Drazena Hadzibeganovic, Kateřina Hodaňová et al. Life Science Alliance 5, no. 4 (2022).
2021
``Mycolactone enhances the Ca2+ leakage from endoplasmic reticulum by trapping Sec61 translocons in a Ca2+ permeable state." Pratiti Bhadra, Scott Dos Santos, Igor Gamayun, Tillman Pick, Joy Ogbechi, Belinda S. Hall, Richard Zimmermann, Volkhard Helms, Rachel E. Simmonds, and Adolfo Cavalie. Biochemistry Journal. 478 (22): 4005–4024
``Molecular modeling of signal peptide recognition by eukaryotic Sec complexes" Pratiti Bhadra, Volkhard Helms; International Journal of Molecular Sciences, 22, 10705.
``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 26(12):3591
``How does the presence/absence of Sec63 affect the Sec61a conformations in yeast?" Pratiti Bhadra; Lalitha Yadhanapudi; Karin Romisch; Volkhard Helms. PLoS Computational Biology 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
2020
``Deep-AmPEP30: Improve short antimicrobial peptides prediction with deep learning" Jielu Yan; Pratiti Bhadra; Ang Li; Pooja Sethiya; Longguang Qin; Hio Kuan Tai; Koon Ho Wong; Shirley W. I. Siu. Molecular Therapy - Nucleic Acids 20, 882-894.
2019
``A Refined Empirical Force Field to Model Protein-SAM Interactions Based on AMBER14 and GAFF" Pratiti Bhadra and Shirley W. I. Siu. Langmuir 35, 29, 9622-9633.
2018
``AmPEP: Sequence-based prediction of antimicrobial peptides using distribution patterns of amino acid properties and random forest" Pratiti Bhadra , Jielu Yan, Jinyan Li, Simon Fong, and Shirley W. I. Siu. Scientific Reports 8 1697.
``TNF Receptor Type II as an Emerging Drug Target for the Treatment of Cancer, Autoimmune Diseases, and Graft-Versus-Host Disease: Current Perspectives and In silico Search for Small Molecule Binders" Faraz Shaikh, Jiang He, Pratiti, Bhadra, Xin Chen, Shirley W. I. Siu Frontiers in Immunology, 9, 1382.
2017
``Comparison of Biomolecular Force Fields for Alkanethiol Self-Assembled Monolayer Simulations" Pratiti Bhadra and Shirley W.I. Siu. Journal of Physical Chemistry C, 121 (47), pp 26340–26349.
``Molecular dynamics information improves cis-peptide based function annotation of proteins." Sreetama Das, Pratiti Bhadra, S. Ramakumar and Debnath Pal. Journal of Proteome Research, 16, 2936-2946.
``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.
2014
``De novo inference of protein function from coarse-grained dynamics” Pratiti Bhadra, Debnath Pal. Protiens: Structure, Function and Bioinformatics. 82:2443–2454