Peer reviewed Journals
1. Jahnu Saikia, Mouli Sarkar and Vibin Ramakrishnan*. Factors affecting physical stability of peptide self assembly in neurodegenerative disorders (2025) Neuropeptides. DOI: 10.1016/j.npep.2025.102517
Publisher: Elsevier
2. Sajitha Sasidharan and Vibin Ramakrishnan*. Single crystal (4-(tritylthio)butylthio) triphenylmethane forming organic nanoflowers (2025) Adv. Nat. Sci.: Nanosci. 16(1) 015017 DOI 10.1088/2043-6262/ad9fff
Publisher: Institute of Physics IOP Science
3. Yvonne Christian, Amay Sanjay Redkar, Naveen Kumar, Shine Varghese Jancy, Aneesh Chandrasekharan, Thankayyan Retnabai Santhoshkumar, Vibin Ramakrishnan*, Structural Regression Modelling of Peptide based Drug Delivery Vectors for the Treatment of Triple-Negative Breast Cancer. (2024) Drug Delivery and Translational Research. DOI:10.21203/rs.3.rs-4294444/v1.
Publisher: Springer
4. Sayali Shantaram Vikhrankar, Seema Satbhai, Priyanka Kulkarni, Ranjit Ranbhor, Vibin Ramakrishnan, Prashant Kodgire. Enzymatic Routes for Chiral Amine Synthesis: Protein Engineering and Process Optimization. Biologics: Targets and Therapy (2024) DOI:10.2147/BTT.S446712
5. Vivek Prakash, Kalpana Kumari and Vibin Ramakrishnan*. Efficient biosorption of hexavalent chromium from water with human hair. ACS Omega (2022) 10.1021/acsomega.2c06268
Publisher: American Chemical Society
6. Vivek Prakash, Yvonne Christian, Amay Sanjay Redkar, Abhishek Roy, R. Anandalakshmi and Vibin Ramakrishnan*. Antibacterial Hydrogels of Aromatic Tripeptides. Soft Matter (2022) DOI : 10.1039/D2SM00606E/
Publisher: Royal Society of Chemistry
7. 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 (2022) DOI: acs.molpharmaceut.2c00238
Publisher: American Chemical Society
8. Vivek Prakash, Mukesh B, Sajitha Sasidharan, Amay Sanjay Redkar, Abhishek Roy, R. Anandalakshmi and Vibin Ramakrishnan*. Syndiotactic hexamer peptide nanodots. European Biophysics Journal (2022) DOI : 10.1007/s00249-022-01610-3
Publisher: Springer
9. Sasidharan, Sayandeep Ghosh, Rishi Sreedhar, Kalpana Kumari, Subhash Thota, and Vibin Ramakrishnanan* Anisotropic Ferromagnetic Organic Nanoflowers, Journal of Physical Chemistry C (2022) DOI: 10.1021/acs.jpcc.2c01462.
Publisher: American Chemical Society
10. 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 (2022), DOI:10.1021/acsomega.1c07075
Publisher: American Chemical Society
11. Sajitha Sasidharan & Vibin Ramakrishnan. Aromatic interactions directing peptide nano-assembly. Advances in Protein Chemistry and Structural Biology (2022) DOI: 10.1016/bs.apcsb.2022.01.001.
Publisher: Academic Press, Elsevier.
12. Jahnu Saikia, K. Dharmalingam, R. Anandalakshmi, Amay Sanjay Redkar, Venugopal T. Bhat and Vibin Ramakrishnan*, Electric Field Modulated Peptide based Hydrogel Nanocatalyst, Soft Matter (2021) DOI: 10.1039/D1SM00724F
Publisher: Royal Society of Chemistry
13. 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 (2021) DOI : 10.1007/s13346-021-01035-z
Publisher: Springer
14. 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 (2021) DOI: 10.1016/j.jconrel.2021.03.0101
Publisher: Elsevier
15. 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 (2021) DOI: 10.1038/s41540-021-00171-z
Publisher: Nature (npj)
16. Prakash Kishore Hazam, Chimanjita Phukan, R. Akhil, Anjali Singh & Vibin Ramakrishnan Antimicrobial effects of syndiotactic polypeptides, Scientific Reports. (2021) DOI.10.1038/s41598-021-81394-2
Publisher: Nature (npj)
17. Vivek Prakash, Ranjit Ranbhor and Vibin Ramakrishnan "De novo designed Hetero-chiral Blue Fluorescent Protein", ACS Omega (2020) DOI: 10.1021/acsomega.0c02574
Publisher: American Chemical Society
18. 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 (2020). DOI.10.1039/d0md00229a
Publisher: Royal Society of Chemistry
19. 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.
Publisher: Springer
20. Gaurav Jerath, Ruchika Goyal, Vishal Trivedi, T. R. Santhoshkumar and Vibin Ramakrishnan*. Conformationally constrained peptides for drug delivery. Journal of Peptide Science. (2020) DOI: 10.1002/psc.3244
Publisher: Wiley
21. Gaurav Pandey, Sudhir Morla, Sachin Kumar and Vibin Ramakrishnan*. Modulation of tau protein aggregation using ‘Trojan’ sequences. Biochimica et Biophysica Acta, BBA - General Subjects (2020). DOI: 10.1016/j.bbagen.2020.129569.
Publisher: Elsevier
22. Gaurav Pandey, Sudhir Morla, Sachin Kumar and Vibin Ramakrishnan*. Modulating Aβ Fibrillogenesis with ‘Trojan’ peptides. Neuropeptides (2020) DOI: 10.1016/j.npep.2020.102030.
Publisher: Elsevier
23. Gaurav Pandey, Prem Prakash Das and Vibin Ramakrishnan*. Directive effect of chain length in modulating peptide nano-assemblies. Protein & Peptide Letters (2020) DOI: 10.2174/0929866527666200224114627.
Publisher: Bentham Science
24. 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, 2019, 142, 10 – 18.
Publisher: Elsevier
25. 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. (2019), doi:10.1021/acschemneuro.8b00490.
Publisher: American Chemical Society
26. 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. (2019), doi: 10.1039/c8ra09993f.
Publisher: Royal Society of Chemistry
27.Gaurav Jerath, Ruchika Goyal, Vishal Trivedi T.R. Santhoshkumar and Vibin Ramakrishnan*. Syndiotactic Peptides for Targeted Delivery. Acta Biomaterialia. (2019), doi: 10.1016/j.actbio.2019.01.036.
Publisher: Elsevier
28.Sooram Banesh, Vibin Ramakrishnan, and Vishal Trivedi. Mapping of phosphatidylserine recognition region on CD36 ectodomain. Archives of Biochemistry and Biophysics. (2018), doi::10.1016/j.abb.2018.10.005.
Publisher: Elsevier
29.Praksah Kishore Hazam, Ruchika Goyal, Vibin Ramakrishnan*. Peptide based Antimicrobials: Design Strategies and Therapeutic Potential. Progress in Biophysics and Molecular Biology. (2018) DOI: 10.1016/j.pbiomolbio.2018.08.006
Publisher: Elsevier
30.Ranbhor Ranjit, Anil Kumar, Abhijit Tendulkar, Kirti Patel, Vibin Ramakrishnan*, and Susheel Durani. IDeAS: Automated Design Tool for Hetero-chiral Protein Folds. Physical biology. (2018), doi::10.1088/1478-3975/aacdc3.
Publisher: Institute of Physics (IOP)
31.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. (2018), doi:10.1007/s10989-018-9690-0.
Publisher: Springer
32.Ranbhor Ranjit, Anil Kumar, Kirti Patel, Vibin Ramakrishnan*, and Susheel Durani. Automated design evolution of stereo-chemically randomized protein foldamers. Physical biology. (2018), doi:10.1088/1478-3975/aaac9a
Publisher: Institute of Physics (IOP)
33.Sajitha Sasidharan, Shyni P. C., Nitin Chaudhary, and Vibin Ramakrishnan*.Single Crystal Organic Nanofowers. Scientific Reports. (2017), doi:10.1038/s41598-017-17538-0.
Publisher: Nature (npg)
34.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. (2017), doi:10.1007/s10989-017-9615-3
Publisher: Springer
35.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. (2017), doi:10.1016/j.bbamem.2017.05.002.
Publisher: Elsevier
36.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. (2017). doi:10.1038/s41598-017-02609-z
Publisher: Nature (npg)
37.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. (2017), 7, 42994. DOI:10.1038/srep42994.
Publisher: Nature (npg)
38.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. (2017) 121, 404−411. DOI: 10.1021/acs.jpcb.6b09474.
Publisher: American Chemical Society
39.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. (2016). DOI: 10.1016/j.pbiomolbio.2016.12.002
Publisher: Elsevier
40.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 Des. (2016) DOI:10.1111/cbdd.12921.
Publisher: Wiley
41.Gaurav Jerath, Prakash Kishore Hazam, Shashi Shekhar, Vibin Ramakrishnan*. Mapping the Geometric Evolution of Protein Folding Motor. PLOS ONE. (2016) 11(10): e0163993. DOI:10.1371/journal.pone.0163993.
Publisher: PLOS
42.A. Mehra, Gaurav Jerath, Vibin Ramakrishnan, Vishal Trivedi. Characterization of ICAM-1 biophore to design cytoadherence blocking peptides. Journal of Molecular Graphics & Modelling. (2015) 57, 27–35.
Publisher: Elsevier
43.Gaurav Jerath, Prakash Kishore Hazam and Vibin Ramakrishnan*. bPE toolkit: toolkit for computational protein engineering. Systems and Synthetic Biology. (2014) 8:337–341.
Publisher: Springer
44.Rahul Metri, Gaurav Jerath, Govind Kailas, Adityabarna Pal & Vibin Ramakrishnan*. Structure Based Barcoding of Proteins. Protein Science (2014) 23, 117-120.
Publisher: Wiley
45.Gaurav Jerath & Vibin Ramakrishnan*. Web-resources in Post Genomic Era. Health Sciences (2014) 1(3), JS002A.
46.Kimjolly Lhouvum.; Vibin Ramakrishnan & Vishal Trivedi. Insight into structural and biochemical determinants of substrate specificity of PFI1625c: Correlation analysis of protein-peptide molecular models. Journal of Molecular Graphics & Modelling (2013) 43, 21-30.
Publisher: Elsevier
47.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 (2012), 80, 920-934.
Publisher: Wiley
48.Anil Kumar and Vibin Ramakrishnan*. Alternate protein scripts with unnatural alphabets. Systems & Synthetic Biology (2010), 4(4), 247-256.
Publisher: Springer
49.Aimy Sebastian, Andreas Bender and Vibin Ramakrishnan*; Virtual Activity Profiling of Bioactive Molecules by 1D Fingerprinting. Molecular Informatics, 51 (2010) 29, 773-779.
Publisher: Wiley
50.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 (2009) 113 (51), pp 16435–16442.
Publisher: American Chemical Society
51.Ranjit Ranbhor; Vibin Ramakrishnan; Anil Kumar and Susheel Durani. The Interplay of Sequence and Stereochemistry in defining Conformation in Proteins and Polypeptides. Biopolymers (2006) 83, 537-545.
Publisher: Wiley
52.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 (2006) 110, 9314-9323.
Publisher: American Chemical Society
53.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 (2005) 78, 96-105.
Publisher: Wiley
54.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 (2004) 126, 16332-16333.
Publisher: American Chemical Society
Book Chapters
55.Ruchika Goyal & Vibin Ramakrishnan. Peptide-Based Drug Delivery Systems. Characterization and Biology of Nano materials for Drug Delivery. Elsevier (Book Chapter, 2018). ISBN: 978-0-12-814031-4
Publisher: Elsevier
56.Aimy Sebastian & Vibin Ramakrishnan*. Computational Biology Applications. Nutri Horti-culture. Ed. K. V. Peter. DPH New Delhi. (2012) pp 123-142.
Publisher: NIPA.
57. Amay Redkar and Vibin Ramakrishnan Modeling and Simulation of peptides. De novo peptide design: Principles and Applications, Academic Press, ISBN: 9780323999175, Page 35-56. DOI: 10.1016/B978-0-323-99917-5.00009-3.
58. Jahnu Saikia and Vibin Ramakrishnan Peptide Nanocatalysts. De novo peptide design: Principles and Applications, Academic Press, ISBN: 9780323999175, Page 35-56. DOI: 10.1016/B978-0-323-99917-5.00006-8.
59. Ruchika Goyal and Vibin Ramakrishnan. Peptide based antibiotics. De novo peptide design: Principles and Applications, Academic Press, ISBN: 9780323999175, Page 35-56. DOI: 10.1016/B978-0-323-99917-5.00006-4
60. Vivek Prakash and Vibin Ramakrishnan. Bioinspired functional molecular constructs. De novo peptide design: Principles and Applications, Academic Press, ISBN: 9780323999175, Page 35-56. DOI: 10.1016/B978-0-323-99917-5.00006-2
61. Amit Bhandari and Vibin Ramakrishnan. Molecular Docking, Springer Protocols, ISBN: 978-1-0716-3404-2 https://doi.org/10.1007/978-1-0716-3405-9
62. Amay Sanjay Redkar and Vibin Ramakrishnan, Molecular Dynamics Simulations, Springer Protocols, ISBN: 978-1-0716-3404-2 https://doi.org/10.1007/978-1-0716-3405-9
63. Ilackeya Bhavananthi and Vibin Ramakrishnan, Mass Spectrometry, Springer Protocols, ISBN: 978-1-0716-3404-2 https://doi.org/10.1007/978-1-0716-3405-9
64. Kalpana Kumari and Vibin Ramakrishnan, Circular Dichroism Spectroscopy, Springer Protocols, ISBN: 978-1-0716-3404-2 https://doi.org/10.1007/978-1-0716-3405-9
65. Kalpana Kumari and Vibin Ramakrishnan, Fourier Transform IR Spectroscopy, Springer Protocols, ISBN: 978-1-0716-3404-2 https://doi.org/10.1007/978-1-0716-3405-9
66. Yvonne Christian, Dikshita Hazarika and Vibin Ramakrishnan, Cell culture for cell penetrating peptides, Springer Protocols, ISBN: 978-1-0716-3404-2 https://doi.org/10.1007/978-1-0716-3405-9
67. Yvonne Christian, and Vibin Ramakrishnan, Cellular uptake of peptides by Flow Cytometry, Springer Protocols, ISBN: 978-1-0716-3404-2 https://doi.org/10.1007/978-1-0716-3405-9
68. Ruchika Goyal and Vibin Ramakrishnan, Penetration in 3D tumorospheres, Springer Protocols, ISBN: 978-1-0716-3404-2 https://doi.org/10.1007/978-1-0716-3405-9
69. Ruchika Goyal and Vibin Ramakrishnan, TMRM Cytotoxicity Assay, Springer Protocols, ISBN: 978-1-0716-3404-2 https://doi.org/10.1007/978-1-0716-3405-9
70. Ruchika Goyal, Khushboo Bhagat and Vibin Ramakrishnan, Cell Death by Apoptosis, Springer Protocols, ISBN: 978-1-0716-3404-2 https://doi.org/10.1007/978-1-0716-3405-9
71. Dikshita Hazarika, Yvonne Christian and Vibin Ramakrishnan, Hemolytic Activity, Springer Protocols, ISBN: 978-1-0716-3404-2 https://doi.org/10.1007/978-1-0716-3405-9
72. Amay Sanjay Redkar and Vibin Ramakrishnan, Antimicrobial assay, Springer Protocols, ISBN: 978-1-0716-3404-2 https://doi.org/10.1007/978-1-0716-3405-9
73. Vivek Prakash and Vibin Ramakrishnan, Antimicrobial assay with peptide based hydrogels, Springer Protocols, ISBN: 978-1-0716-3404-2 https://doi.org/10.1007/978-1-0716-3405-9
74. Kalpana Kumari and Vibin Ramakrishnan, Rheology of Peptide based hydrogels, Springer Protocols, ISBN: 978-1-0716-3404-2 https://doi.org/10.1007/978-1-0716-3405-9
75. Jahnu Saikia and Vibin Ramakrishnan, Estimation of aggregation kinetics, Springer Protocols, ISBN: 978-1-0716-3404-2 https://doi.org/10.1007/978-1-0716-3405-9
76. Laxmi Raman Adil and Vibin Ramakrishnan, Assessment of amyloid morphology using electron microscopy, Springer Protocols, ISBN: 978-1-0716-3404-2 https://doi.org/10.1007/978-1-0716-3405-9
77. Kalpana Kumari and Vibin Ramakrishnan, Catalytic efficiency of designed peptides, Springer Protocols, ISBN: 978-1-0716-3404-2 https://doi.org/10.1007/978-1-0716-3405-