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Dr. Pratiti Bhadra

Assistant Professor (SG), Center for Computational Engineering and Networking, Amrita Vishwa Vidapeetham, Coimbatore

Qualification: B-Tech, Ph.D
b_pratiti@cb.amrita.edu
Google Scholar Profile
Scopus ID
Research Interest: Application of artificial intelligence in drug discovery and structural bioinformatics, Biomolecular simulation, docking and virtual screening, Coarse-grain modelling of biomolecules, Omics data science, Application of ML/DL in Drug Discovery (therapeutic peptide and small molecule) , Computational Structural Bioinformatics ,Application of ML/DL in Biomedical Research Area,Clinical diagnosis support system,Transcriptomics data-analysis

Nature of Association: Regular

Bio

Dr. Pratiti Bhadra joined the Center for Computational Engineering and Networking (School of AI) Amrita Vishwa Vidapeetham, Coimbatore, India, as Assistant Professor (Selection Grade) from January 2023. Before, she served PharmCADD Pvt. Ltd. (in-silico drug discovery) as a senior scientist in R&D from 2021 to 2022. She pursued her PhD in Computational Biology from the Indian Institute of Science (IISc), India, in 2015. Between 2016 and 2021, she was involved in research as post-doctoral research fellow at the Centre for Bioinformatics of Saarland University, Germany (2019-2021) and the University of Macau, Macau (2016-2018). Her area of research covers various problems in computational structural biology and drug discovery (application of machine/deep learning approach, distance topology approach, MD simulation, docking and modelling). To date, she developed a new knowledge-based coarse-grained molecular mechanics force field (CGMM) to study the conformation dynamics of proteins. She presented topological distance-based dynamic signature of molecular function (DynFunc).

She predicted antimicrobial peptides using machine learning (AmPEP and Deep-AMPEP30) and activators for pathogen-sensing receptors. Using molecular dynamics and molecular docking simulations, she explained the functional mechanism of protein translocation, the orientation of protein on the surface, the formation of self-assembled monolayers to form efficient biosensors and disease-related protein-ligand interaction. Besides, she used deep learning and machine learning methods to identify target peptides and predict the loop geometry of protein. Her research works were published in reputed journals, namely Comp. Biol. Med.; J.Proteome Res.; Prot. Struc. Func. and Bio.; Nature Sci. Rep.; J. Phy. Chem. C; Langmuir; Mol. Ther. Nuc. Aci.; Front. imm; Plos. Comp. Bio.; Biochem. J; IJMS, BBA-Biomembranes and Molecules. She has collaboration with Saarland University (Germany), Macao Polytechnic University (Macau, ), Renji Hospital, Shanghai Jiaotong University, School of Medicine (China), IISc, IIT Palakkad, NIPER Hyderabad, Koneru Lakshmaiah Education Foundation University, Government medical college Kota, , Amrita Faridabad, Amrita Kochi, Amrita Bangalore.

Experience(s)/Qualification(s): 

Post-doctoral Experience

  • Institute Post-doctoral Fellow
    – Indian Institute of Science, Bangalore (2015), Institute fellowship
  • Post-doctoral Scholar
    – Centre for Bioinformatics, Saarland University, Saarbrucken, Germany (2019-2021)(Deutsche Forschungsgemeinschaft (DFG) – project fellowship)
    – Faculty of Science and Technology, Macau University, Macau, China (2016-2019)
  • PhD (Year): 2009-2015
    Specialization: Computational Structural Bioinformatics
    Thesis title:  A new coarse-grained molecular mechanics for protein dynamics and its application on dynamics-function correlation”
Publications

Journal Article

Year : 2022

Phenylbutyrate rescues the transport defect of the Sec61α mutations V67G and T185A for renin

Cite this Research Publication : Mark Sicking, Martina Živná, Pratiti Bhadra, Veronika Barešová,, Andrea Tirincsi, Drazena Hadzibeganovic, Kateřina Hodaňová, Petr Vyleťal, Jana Sovová, Ivana Jedličková Martin Jung; Thomas Bell, Volkhard Helms, Anthony J Bleyer, Stanislav Kmoch, Adolfo Cavalié Sven Lang "Phenylbutyrate rescues the transport defect of the Sec61α mutations V67G and T185A for renin", Life Science Alliance 5.4 (2022)

Year : 2022

Signal Peptide Features Determining the Substrate Specificities of Targeting and Translocation Components in Human ER Protein Import

Cite this Research Publication : Sven Lang, Duy Nguyen, Pratiti Bhadra, Martin Jung, Volkhard Helms, Richard Zimmermann "Signal Peptide Features Determining the Substrate Specificities of Targeting and Translocation Components in Human ER Protein Import", Frontiers in Physiology, 2022, vol 13 no. 833540.

Year : 2022

Synthesis, Biological Evaluation and Docking Studies of Ring-Opened Analogues of Ipomoeassin F

Cite this Research Publication : 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 "Synthesis, Biological Evaluation and Docking Studies of Ring-Opened Analogues of Ipomoeassin F" .) Molecules 27.14 (2022): 4419

Year : 2021

How does the presence/absence of Sec63 affect the Sec61α conformations in yeast?

Cite this Research Publication : Pratiti Bhadra; Lalitha Yadhanapudi; Karin R¨omisch; Volkhard Helms “How does the presence/absence of Sec63 affect the Sec61α conformations in yeast?” . PLoS computational biology 17.3 (2021): e1008855.

Year : 2021

AmPEP: Sequence-based prediction of antimicrobial peptides using distribution patterns of amino acid properties and random forest

Cite this Research Publication : Pratiti Bhadra, Jielu Yan, Jinyan Li, Simon Fong & Shirley W. I. Siu, "AmPEP: Sequence-based prediction of antimicrobial peptides using distribution patterns of amino acid properties and random forest" Scientific Reports volume 8, Article number: 1697 (2018)

Year : 2021

A Refined Empirical Force Field to Model Protein-SAM Interactions Based on AMBER14 and GAFF

Cite this Research Publication : Pratiti Bhadra, Shirley W I Siu "Refined Empirical Force Field to Model Protein-Self-Assembled Monolayer Interactions Based on AMBER14 and GAFF", Langmuir, 2019

Year : 2021

Effect of Concentration, Chain Length, Hydrophobicity, and an External Electric Field on the Growth of Mixed Alkanethiol Self-Assembled Monolayers: A Molecular Dynamics Study

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

Year : 2021

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

Cite this Research Publication : Monika Lerner, Stefan Schorr, Duy Nguyen, Johanna Dudek, Friedrich Förster, Volkhard Helms, Sven Lang, Richard Zimmermann., "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", Molecules. 2021

Year : 2021

De novo inference of protein function from coarse-grained dynamics

Cite this Research Publication : Pratiti Bhadra, Debnath Pal "De novo inference of protein function from coarse-grained dynamics, Proteins, 2014

Year : 2021

Molecular Modeling of Signal Peptide Recognition by Eukaryotic Sec Complexes

Cite this Research Publication : Sreetama Das, Pratiti Bhadra, S. Ramakumar and Debnath Pal "Molecular Modeling of Signal Peptide Recognition by Eukaryotic Sec Complexes", Journal of Proteome Research, 16, 2017, 2936-2946

Year : 2021

Mycolactone enhances the Ca2+ leakage from endoplasmic reticulum by trapping Sec61 translocons in a Ca2+ permeable state

Cite this Research Publication : Pratiti Bhadra, Scott Dos Santos, Igor Gamayun, Tillman Pick, Joy Ogbechi, Belinda S. Hall, Richard Zimmermann, Volkhard Helms, Rachel E. Simmonds, and Adolfo Cavalie "Mycolactone enhances the Ca2+ leakage from endoplasmic reticulum by trapping Sec61 translocons in a Ca2+ permeable state", Biochemistry Journal. 478 (22): 4005–4024

Year : 2020

Deep-AmPEP30: Improve short antimicrobial peptides prediction with deep learning

Cite this Research Publication : Jielu Yan; Pratiti Bhadra; Ang Li; Pooja Sethiya; Longguang Qin; Hio Kuan Tai; Koon Ho Wong; Shirley W. I. Siu., "Deep-AmPEP30: Improve Short Antimicrobial Peptides Prediction with Deep Learning" Volume 20, 5 June 2020, Pages 882-894

Year : 2020

Effect of Sec62 on the conformation of the Sec61 channel in yeast

Cite this Research Publication : Pratiti Bhadra a, Karin Römisch b, Volkhard Helms, "Chakraborty, S., Ravikumar, A. Substrate induced electronic phase transitions of CrI3 based van der Waals heterostructures.", Biochimica et Biophysica Acta (BBA)Volume 1864, Issue 12, 1 December 2022, 184050

Year : 2018

Highly accurate sequenced-based antimicrobial peptide prediction using random

Cite this Research Publication : Dr. Pratiti Bhadra and Dr. Volkhard Helms "Highly accurate sequenced-based antimicrobial peptide prediction using random ", German Conference on Bioinformatics (GCB2019), 2018

Year : 2018

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

Cite this Research Publication : Faraz Shaikh, Jiang He, Pratiti, Bhadra, Xin Chen, Shirley W. I. Siu "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", Frontiers in Immunology, 9, 1382, 2018

Year : 2017

Comparison of Biomolecular Force Fields for Alkanethiol Self-Assembled Monolayer Simulations

Cite this Research Publication : Pratiti Bhadra and Shirley W.I. Siu. J. , Comparison of Biomolecular Force Fields for Alkanethiol Self-Assembled Monolayer Simulations” Phys. Chem. C, 121 (47), pp 26340–26349 (2017)

Year : 2017

Molecular Dynamics Information Improves cis-Peptide-Based Function Annotation of Proteins

Cite this Research Publication : Sreetama Das, Pratiti Bhadra, Suryanarayanarao Ramakumar, Debnath Pal "Molecular Dynamics Information Improves cis-Peptide-Based Function Annotation of Proteins", Journal of Proteome Research 16(8), June 2017

Year : 2017

Pipeline for inferring protein function from dynamics using coarse-grained molecular mechanics forcefield

Cite this Research Publication : Pratiti Bhadra, Debnath Pal "Pipeline for inferring protein function from dynamics using coarse-grained molecular mechanics forcefield", Computer in Biology and Medicine, 2017 .83, 134-142

Year : 2012

A new Ca atom-based force-field for coarse-grained protein dynamics correlated

Cite this Research Publication : Pratiti Bhadra and Dr. Debanth Pal "A new Ca atom-based force-field for coarse-grained protein dynamics correlated well with experimental data", Humboldt kollege on Interdisciplinary Science: Catalyst for Sustainable Progress, 2012

Conference Paper

Year : 2024

International Conference on Computations and Data Science

Cite this Research Publication : K Sivappriya, Pratiti Bhadra, “International Conference on Computations and Data Science”, , Internation Conference on Computations and Data Science (organized by IIT Roorkee) 2024

Year : 2024

Community Detection Using Graph Attention Networks Clustering Algorithm

Cite this Research Publication : Ippatapu Venkata Srichandra, Pratiti Bhadra. “Community Detection Using Graph Attention Networks Clustering Algorithm”, IEEE 2024 9th International Conference for Convergence in Technology (I2CT).

Book Chapter

Year : 2023

Computational Drug Discovery – A Primer

Cite this Research Publication : N. Sukumar, Harishchander Anandaram and Pratiti Bhadra, “Computational Drug Discovery – A Primer” (Ion Cures Press, 2023)

Poster

Year : 2019

A deep learning approach to short antimicrobial peptide prediction

Cite this Research Publication : Pratiti Bhadra, "A deep learning approach to short antimicrobial peptide prediction", 2019

Year : 2019

Modulating the conformation of the Sec61 protein translocation pore

Cite this Research Publication : "Pratiti Bhadra and Volkhard Helms", Cell Physics 2019, Germany

Year : 2015

Protein dynamics and function correlation using a new knowledge based coarse grained force field

Cite this Research Publication : Pratiti Bhadra and Dr. Debanth Pal "Protein dynamics and function correlation using a new knowledge based coarse grained force field", Humboldt kollege on Interdisciplinary Science: Catalyst for Sustainable, 2015

Positions

(A) Current Positions
1. Assistant Professor (SG), Center of Computational Engineering and Networking (CEN), School of AI, Amrita Vishwa Vidyapeetham, Coimbatore
(B) Past Positions 
1. Senior Scientist, PharmCADD Pvt. Ltd. Busan, South Korea (Nov 2022 – Dec 2022)
2. Senior Scientist, PharmCADD Pvt. Ltd. Hyderabad, India (Aug 2021- Oct 2022)
3. Post Doctoral Research Fellow, Saarland University, Saarbrucken, Germany (Jan 2019 – Jul 2021)
4. Post Doctoral Research Fellow, University of Macau, Macau, China (Jan 2016 – Nov 2018)
5. Senior Research Associate, Indian Institute of Science, Bangalore, India (July 2015 – Dec 2015)
6. Junior Research Associate, Indian Institute of Science, Bangalore, India (July 2014 – June 2015)
7. Project Assistant, Society for Innovation and Development, Indian Institute of Science (IISc), Bangalore, India (Apr 2008 – June 2009)
8. Associate System Engineer, IBM India Pvt. Ltd. (July 2007 – March 2008)

Invited Talks

Invited Talks/ Seminars/ Workshops/ Session Chairs

  1. ISE Science Seminar 2023; Host: Dr. Shirley W.I Su ; “How do accessory proteins affect the conformation of Sec61 translocon?” The university of saint joseph, Macau, Macau.
Reviewers

Reviewers (National/International Journals; Conferences)

1. Reviewer of MDPI-publisher (Journal: Energy, Diagnostics, Applied Science, Sensors, Journal of personalized medicine, Biomedicines, Biology, Current Oncology, Healthcare)
2. Programme Committee: The 7th international conference on Computational System-Biology and Bioinformat ics CSBio2016
3. Reviewer: Bioinformatics Advances Journal
4. Programme Committee: COMSYS2022, COMSY2023
5. Bioinformatics Advances JournalJournal of Biomolecular Structure & DynamicsJournal of chemical information and modelling.

Teaching 

Courses taught (Name, Year, UG/PG)

UG 

2023 Even Sem:

  • Data Structure and Algorithm 1 (Core, Credit:4 Student: 135)

2023 Odd Sem:

  • Intelligent Biological System (Core, Credit:2 Student 135)

PG 

2023 Odd Sem:

  • Deep Learning in Life Science (Elective, Credit:3; Student: 3, share with another 3 course instructors)

2023 Even Sem:

  • Data structure and algorithm for Data Science (Core; Student: 28)
  • Deep Learning in Genomics and Biomedicine (Elective; Credit:4; Student:18, share with another course teacher)

2024 Odd Sem:

  • Statistical Modelling (Core, Credit:3; Student:28)

Doctoral advisor (Thesis title, Year)

  • Mr. Sathiyajith JN (Join 2023, Full-time): therapeutic peptides
  • Mr. Prasad Balachandran (Join 2023, Full-time): Clinical diagnostic decision support system
  • Mrs. Sruthi S (Join 2023, Part-time): Borol cluster application in drug delivery

Conferences/Workshops/Webinars organized (Chairman/Convener/Others) 

  • Webinar (Series):  Artificial Intelligence and Statistical Mechanics in Biomedical Research (AISMBR) https://sites.google.com/view/aismbr/ (from 09/09/2023)
  • Workshop: (2-day) “Introduction to Material Informatics” (27th-28th January 2024)
Projects
  • Sponsored Projects
    Amrita Seed Grant 2022 “In silico design and prediction of blood-brain barrier penetrative peptide to treat CNS-associated disease” (~23 lakh)
Awards

Awards/Honors/Recognition 

  • First Prize in Oral Presentation. ”A machine-learning approach to antimicrobial peptide prediction, leading a novel antibacterial in wet-lab”;  Amrita Pharmacon-2023, International Conference on “Innovations in Antimicrobial Therapeutics”
  • In 2014, 18 month more scholarship from IISc due to submission of thesis with in 5 years of PhD registration; Institute Research Associate (28th July 2014 to 31st Dec 2015)

Membership/Associations

  • IEEE
  • BIOinformatics CLUb for Experimenting Scientists
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