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Ramakrishnan Vibin

Professor

vibin@iitg.ac.in

Research Areas:

Computational Biology, Bioinformatics, Biophysics, Bio-Organic Chemistry, Bio-nanotechnology.

Web page: https://fac.iitg.ac.in/vibin/



Journals

1. Vivek Prakash, Mukesh B, Sajitha Sasidharan, Amay Sanjay Redkar, Abhishek Roy, R. Anandalakshmi and Vibin Ramakrishnan "Syndiotactic hexamer peptide nanodots", European Biophysics Journal, DOI.10.1007/s00249-022-01610-3, Vol., , P.P - , (2022)

2. Gaurav Jerath, Pramod Darvin, Yvonne Christian, Vishal Trivedi, T. R. Santhosh Kumar and Vibin Ramakrishnan* "Delivery of Small Molecules by Syndiotactic Peptides for Breast Cancer Therapy", Molecular Pharmaceutics, DOI.acs.molpharmaceut.2c00238, Vol., , P.P - , (2022)

3. Vivek Prakash, Yvonne Christian, Amay Sanjay Redkar, Abhishek Roy, R. Anandalakshmi and Vibin Ramakrishnan* "Antibacterial Hydrogels of Aromatic Tripeptides.", Soft Matter, DOI.10.1039/D2SM00606E/, Vol., , P.P - , (2022)

4. Sajitha Sasidharan, Sayandeep Ghosh, Rishi Sreedhar, Kalpana Kumari, Subhash Thota, and Vibin Ramakrishnanan "Anisotropic Ferromagnetic Organic Nanoflowers", Journal of Physical Chemistry C , DOI.10.1021/acs.jpcc.2c01462., Vol., , P.P - , (2022)

5. Jahnu Saikia, Venugopal T Bhat, Lokeswara Rao Potnuru, Amay S Redkar, Vipin Agarwal, Vibin Ramakrishnan "Minimalist de novo design of an artificial enzyme", ACS Omega , DOI.DOI:10.1021/acsomega.1c07075, Vol., , P.P - , (2022)

6. Sajitha Sasidharan & Vibin Ramakrishnan "Aromatic interactions directing peptide nano-assembly", Advances in Protein Chemistry and Structural Biology , DOI.10.1016/bs.apcsb.2022.01.001, Vol., , P.P - , (2022)

7. Prakash Kishore Hazam, Chimanjita Phukan, R. Akhil, Anjali Singh & Vibin Ramakrishnan "Antimicrobial effects of syndiotactic polypeptides", Scientific Reports, DOI.10.1038/s41598-021-81394-2, Vol.11, , P.P 1823- , (2021)

8. Aparna Rai, Vikas Kumar, Gaurav Jerath, C. C. Kartha & Vibin Ramakrishnan "Mapping drug-target interactions and synergy in multi-molecular therapeutics for pressure-overload cardiac hypertrophy", npj Systems Biology and Applications, DOI.10.1038/s41540-021-00171-z, Vol.7, , P.P 11- , (2021)

9. Ruchika Goyal, Gaurav Jerath, Akhil R., Aneesh Chandrasekharan, Eswara Rao Puppala, Srikanth Ponneganti, Anupam Sarma, V.G.M. Naidu, T. R. Santhoshkumar, and Vibin Ramakrishnanan "Geometry Encoded Functional Programming of Tumor Homing Peptides for Targeted Drug Delivery", Journal of Controlled Release, DOI.10.1016/j.jconrel.2021.03.010, Vol.333, , P.P 16-27 , (2021)

10. Ruchika Goyal, Gaurav Jerath, Aneesh Chandrasekharan, Yvonne Christian, T. R. Santhoshkumar, and Vibin Ramakrishnanan "Molecular hybridization combining tumor homing and penetrating peptide domains for cellular targeting", Drug Delivery and Translational Research, DOI.10.1007/s13346-021-01035-z, Vol., , P.P - , (2021)

11. Jahnu Saikia, K. Dharmalingam, R. Anandalakshmi, Amay Sanjay Redkar, Venugopal T. Bhat and Vibin Ramakrishnan "Electric Field Modulated Peptide based Hydrogel Nanocatalyst", Soft Matter , DOI.10.1039/D1SM00724F, Vol., , P.P - , (2021)

12. Gaurav Pandey, Prem Prakash Das and Vibin Ramakrishnan* "Directive effect of chain length in modulating peptide nano-assemblies", Protein & Peptide Letters, DOI.10.2174/0929866527666200224114627., Vol., , P.P - , (2020)

13. Gaurav Pandey, Sudhir Morla, Sachin Kumar and Vibin Ramakrishnan* "Modulating A? Fibrillogenesis with ‘Trojan’ peptides", Neuropeptides, DOI.10.1016/j.npep.2020.102030, Vol., , P.P - , (2020)

14. Gaurav Pandey, Sudhir Morla, Sachin Kumar and Vibin Ramakrishnan* "Modulation of tau protein aggregation using ‘Trojan’ sequences", Biochimica et Biophysica Acta, BBA - General Subjects, DOI.10.1016/j.bbagen.2020.129569, Vol., , P.P - , (2020)

15. Gaurav Jerath, Ruchika Goyal, Vishal Trivedi, T. R. Santhoshkumar and Vibin Ramakrishnan* "Conformationally constrained peptides for drug delivery", Journal of Peptide Science, DOI.10.1002/psc.3244, Vol., , P.P - , (2020)

16. Gaurav Pandey & Vibin Ramakrishnan* "Invasive and non-invasive therapies for Alzheimer’s disease and other amyloidosis", Biophysical Reviews , DOI.10.1007/s12551-020-00752-y, Vol., , P.P - , (2020)

17. Ruchika Goyal, Gaurav Jerath, Aneesh Chandrasekharan, T. R. Santhosh Kumar and Vibin Ramakrishnan* "Peptide-based delivery vectors with pre-defined geometrical locks", RSC Medicinal Chemistry, DOI.10.1039/d0md00229a, Vol., , P.P - , (2020)

18. Vivek Prakash, Ranjit Ranbhor and Vibin Ramakrishnan "De novo designed Hetero-chiral Blue Fluorescent Protein", ACS Omega, DOI.10.1021/acsomega.0c02574, Vol., , P.P - , (2020)

19. Praksah Kishore Hazam, Akhil, R. , Gaurav Jerath, Jahnu Saikia and Vibin Ramakrishnan* "Topological effects on the designability and bactericidal potency of antimicrobial peptides", Biophysical Chemistry, DOI., Vol.248, , P.P 1-8 , (2019)

20. Jahnu Saikia, Gaurav Pandey, Sajitha Sasidharan, Ferrin Antony, Harshal B. Nemade, Sachin Kumar, Nitin Chaudhary, and Vibin Ramakrishnan "Electric Field Disrupts Amyloid Aggregation; Potential Non-invasive Therapy for Alzheimer’s Disease", ACS Chemical Neuroscience, DOI., Vol.10, 5, P.P 2250-2262 , (2019)

21. Gaurav Pandey, Sudhir Morla, Harshal B. Nemade, Sachin Kumar and Vibin Ramakrishnan "Modulation of Aggregation with Electric Field; Scientific Roadmap for a Potential Non-Invasive Therapy Against Tauopathies.", RSC Advances, DOI., Vol.9, , P.P 4744-4750 , (2019)

22. Gaurav Jerath, Ruchika Goyal, Vishal Trivedi T.R. Santhoshkumar and Vibin Ramakrishna "Syndiotactic Peptides for Targeted Delivery", Acta Biomaterialia, DOI., Vol.87, , P.P 130-139 , (2019)

23. Praksah Kishore Hazam, Ruchika Goyal, Vibin Ramakrishnan "Peptide based antimicrobials: Design strategies and therapeutic potential", Progress in Biophysics and Molecular Biology, DOI., Vol.142, , P.P 10-22 , (2019)

24. Prakash Kishore Hazam, Anjali Singh, Nitin Chaudhary and Vibin Ramakrishnan "Bactericidal Potency and Extended Serum Life of Stereo-Chemically Engineered Peptides Against Mycobacterium", International Journal of Peptide Research and Therapeutics., DOI., Vol.25, 2, P.P 465-472 , (2019)

25. Sooram Banesh, Vibin Ramakrishnan, and Vishal Trivedi "Mapping of phosphatidylserine recognition region on CD36 ectodomain", Archives of Biochemistry and Biophysics, DOI., Vol.660, , P.P 1-10 , (2018)

26. Ranbhor Ranjit, Anil Kumar, Abhijit Tendulkar, Kirti Patel, Vibin Ramakrishnan*, and Susheel Durani. "IDeAS: Automated Design Tool for Hetero-chiral Protein Folds. Physical biology", Physical Biology, DOI., Vol.15, 6, P.P doi::10.10- , (2018)

27. Ranbhor Ranjit, Anil Kumar, Kirti Patel, Vibin Ramakrishnan "Automated design evolution of stereo-chemically randomized protein foldamers", Physical Biology, DOI., Vol.15, 3, P.P doi: 10.10- , (2018)

28. Prakash Kishore Hazam, Gaurav Jerath, Nitin Chaudhary, and Vibin Ramakrishnan "Peptido-mimetic Approach in the Design of Syndiotactic Antimicrobial Peptides", International Journal of Peptide Research and Therapeutics, DOI., Vol.24, 2, P.P 299-307 , (2018)

29. Karabi Saikia, Yalavarthi Durga Sravani, Vibin Ramakrishnan, and Nitin Chaudhary "Highly potent antimicrobial peptides from N-terminal membrane-binding region of E. coli MreB", Scientific Reports, DOI., Vol.doi:10.1038/srep42994, , P.P - , (2017)

30. Sajitha Sasidharan, Prakash Kishore Hazam and Vibin Ramakrishnan*. "Symmetry Directed Self-Organization in Peptide Nano-Assemblies Through Aromatic pi-pi Interactions. ", The Journal of Physical Chemistry B, DOI., Vol.121, 2, P.P 404-411 , (2017)

31. Anil Kumar, Ranjit Ranbhor, Kirti Patel, Vibin Ramakrishnan*, Susheel Durani "Automated Protein and Peptide Design: Landmarks and Operational Principles", Progress in Biophysics and Molecular Biology., DOI., Vol.125, , P.P 24-35 , (2017)

32. Suman Jyoti Deka, Ashalata Roy, Vibin Ramakrishnan, Debasis Manna and Vishal Trivedi. "Danazol has potential to cause pkc translocation, cell-cycle dysregulation and apoptosis in breast cancer cells.", Chem. Biol. Drug Design, DOI., Vol.89, , P.P 953-963 , (2017)

33. Sajitha Sasidharan, Shyni P. C., Nitin Chaudhary, and Vibin Ramakrishnan " Single Crystal Organic Nanofowers", Scientific Reports, DOI., Vol., , P.P doi::10.10- , (2017)

34. Prakash Kishore Hazam, Gaurav Jerath, Anil Kumar, Nitin Chaudhary, and Vibin Ramakrishnan "Effect of tacticity-derived topological constraints in bactericidal peptides", Biochimica et Biophysica Acta. Biomembranes, DOI., Vol.1859, , P.P 1388-1395 , (2017)

35. Gaurav Pandey, Jahnu Saikia, Sajitha Sasidharan, Deep C. Joshi, Subhash Thota, Harshal B. Nemade, Nitin Chaudhary, and Vibin Ramakrishnan "Modulation of Peptide Based Nano-Assemblies with Electric and Magnetic Fields", Scientific Reports, DOI., Vol., , P.P doi:10.103- , (2017)

36. Gaurav Jerath, Prakash Kishore Hazam, Shashi Shekhar, Vibin Ramakrishnan "Mapping the Geometric Evolution of Protein Folding Motor", Plos One, DOI., Vol.10.1371/journal.pone.0163993., , P.P - , (2016)

37. A. Mehra, Gaurav Jerath, Vibin Ramakrishnan, Vishal Trivedi. "Characterization of ICAM-1 biophore to design cytoadherence blocking peptides", Journal of Molecular Graphics & Modelling, DOI., Vol.57, , P.P 27-35 , (2015)

38. Gaurav Jerath, Prakash Kishore Hazam and Vibin Ramakrishnan "bPE toolkit: toolkit for computational protein engineering", Systems and Synthetic Biology, DOI., Vol.8, , P.P 337-341 , (2014)

39. Rahul Metri, Gaurav Jerath, Govind Kailas, Adityabarna Pal & Vibin Ramakrishnan* "Structure Based Barcoding of Proteins", Protein Science , DOI., Vol.23, , P.P 117-120 , (2014)

40. Gaurav Jerath & Vibin Ramakrishnan* " Web-resources in Post Genomic Era. ", Health Sciences , DOI., Vol.1, 3, P.P JS002A- , (2014)

41. Kimjolly Lhouvum.; Vibin Ramakrishnan & Vishal Trivedi. "Insight into structural and biochemical determinants of substrate specificity of PFI1625c", Journal of Molecular Graphics & Modelling , DOI., Vol.43, , P.P 21-30 , (2013)

42. Vibin Ramakrishnan, Saeed Salem; Saipraveen Srinivasan, Mohammed Zaki, Suzanne Mathews, Wilfredo Colon and Christopher Bystroff "Developing a detailed mechanistic model for protein unfolding", Proteins: Structure Function & Bioinformatics , DOI., Vol.80, , P.P 920-934 , (2012)

43. Anil Kumar and Vibin Ramakrishnan "Alternate protein scripts with unnatural alphabets", Systems & Synthetic Biology , DOI., Vol.4, 4, P.P 247-256 , (2010)

44. Aimy Sebastian, Andreas Bender and Vibin Ramakrishnan "Virtual Activity Profiling of Bioactive Molecules by 1D Fingerprinting", Molecular Informatics , DOI., Vol.29, , P.P 773-779 , (2010)

45. Anil Kumar; Vibin Ramakrishnan; Ranjit Ranbhor and Susheel Durani. "Homochiral Stereochemistry: The Missing Link of Structure to Energetics in Protein Folding. ", Journal of Physical Chemistry B , DOI., Vol.113, 51, P.P 16435-16442 , (2009)

46. Ranjit Ranbhor; Vibin Ramakrishnan; Anil Kumar and Susheel Durani. " The Interplay of Sequence and Stereochemistry in defining Conformation in Proteins and Polypeptides. ", Biopolymers, DOI., Vol.83, , P.P 537-545 , (2006)

47. Vibin Ramakrishnan; Ranjit Ranbhor; Anil Kumar and Susheel Durani "The link between Sequence and Conformation in Protein Structures appears to be Stereochemically Established.", The Journal of Physical Chemistry B , DOI., Vol.110, , P.P 9314-9323 , (2006)

48. Vibin Ramakrishnan; Ranjit Ranbhor and Susheel Durani "Probing Main Chain Roles in Protein Structure and Folding Stereochemically. A Simulated Annealing Folding Study of Isotactic, Syndiotactic and Heterotactic Polypeptides", Biopolymers, DOI., Vol.78, , P.P 96-105 , (2005)

49. Vibin Ramakrishnan; Ranjit Ranbhor and Susheel Durani. "Existence of Specific "Folds" in Polyproline-II Ensembles of an Unfolded Alanine Peptide Detected by Molecular Dynamics", Journal of the American Chemical Society , DOI., Vol.126, , P.P 16332-16333 , (2004)

Conference Publication

No Data Available!

Book

1. Vibin Ramakrishnan, Kirti Patel, Ruchika Goyal "De Novo Peptide Design: Principles and Applications", Academic Press, Elsevier. Vol., 9780323999175, P.P 296- , (2022)

Book Chapter

1. Aimy Sebastian & Vibin Ramakrishnan "Nutri Horti-culture", DPH. Vol., 978-8170357766, P.P 123 - 142- , (2013)

2. Ruchika Goyal & Vibin Ramakrishnan "Nanoscience and Nanotechnology in Drug Delivery", Elsevier. Vol., 978-0-12-814031-4, P.P 25 - 45- , (2019)

3. Amay Redkar, Vibin Ramakrishnan "De Novo Peptide Design: Principles and Applications ", Academic Press. Vol., 9780323999175, P.P 35-56- , (2022)

4. Jahnu Saikia, Vibin Ramakrishnan "De Novo Peptide Design: Principles and Applications", Academic Press. Vol., 9780323999175, P.P 173-206- , (2022)

5. Ruchika Goyal, Vibin Ramakrishnan "De Novo Peptide Design Principles and Applications", Academic Press. Vol., 9780323999175, P.P 79-103- , (2022)

6. Vivek Prakash, Vibin Ramakrishnan "De Novo Peptide Design Principles and Applications", Academic Press. Vol., 9780323999175, P.P 207-254- , (2022)



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