Publications
1.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 American Chemical Society (2004) 126, 16332- 16333.
Publisher: American Chemical Society
2.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
3.Vibin Ramakrishnan; Ranjit Ranbhor; Anil Kumar and Susheel Durani. The link between Sequence and Conformation in Protein Structures appears to be Stereochemically Established.
Journal of Physical Chemistry B (2006) 110, 9314-9323.
Publisher: American Chemical Society
4.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
5.Vibin Ramakrishnan, Saeed Salem, Saipraveen Srinivasan, Wilfredo Colon, Mohammed Zaki & Christopher Bystroff. GEOFOLD: A Mechanistic Model to Study the Effect of Topology on Protein Unfolding Pathways and Kinetics.
3DSig. Structural Biology & Comptational Biophysics. (2008) 25-26.
Publisher: ISCB
6.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) 16435-16442.
Publisher: American Chemical Society
7.Aimy Sebastian, Andreas Bender and Vibin Ramakrishnan; Virtual Activity Profiling of Bioactive Molecules by 1D Fingerprinting.
Molecular Informatics (2010) 29, 773-779.
Publisher: WILEY
8.Anil Kumar and Vibin Ramakrishnan. Alternate protein scripts with unnatural alphabets.
Systems & Synthetic Biology (2010), 4(4), 247-256.
Publisher: Springer
9.Aimy Sebastian and Vibin Ramakrishnan; Computational Biology Applications. Science of Horticulture, VOl 3, Ed: K V Peter. NIPA New Delhi (Book Chapter).
Publisher: NIPA
10.Vibin Ramakrishnan; Saeed Salem; Saipraveen Srinivasan, Mohammed Zaki, Suzanne Mathews, Wilfredo Colon and Christopher Bystroff. GeoFold: Topology-based protein unfolding pathways capture the effects of engineered disulfides on kinetic stability
Proteins. Structure Function & Bio-informatics (2012) 80, 920-934.
Publisher: WILEY
11.Anil Kumar, Bhupesh Goyal, Vibin Ramakrishnan, Ranjit Ranbhor, Kinshuk Srivastava, Pooja Gupta and Susheel Durani. Homochiral Stereochemistry and Protein Folding: Topological Blocks of Folding Path may manifest Φ,Ψ Dispersal under effect of poly-L Structure" Under Review.
12.Ranjit Ranbhor, Anil Kumar, Abhijit Tendulkar Vibin Ramakrishnan, and Susheel Durani IDeAS: Protein-Design Software for Applying Side Chains to Chirality of Interest Under Review
IMPORTANT TOOLS
1. GeoFOLD (Rensselaer, New York): Tool for predicting protein folding kinetics, mechanism and pathways based on protein topology. Developed in Bystroff lab, center for Bioinformatics at RPI, NY.
2. IDeAS (IIT Bombay): IDeAS is a tool for sequence optimization, developed and calibrated against a set of small to medium sized proteins. The program applies Dead End Elimination and Monte Carlo based search algorithms for optimization of sequences of chosen folds, using molecular mechanics based force fields. Developed in Durani Lab at IIT Bombay
2. IDeAS (IIT Bombay): IDeAS is a tool for sequence optimization, developed and calibrated against a set of small to medium sized proteins. The program applies Dead End Elimination and Monte Carlo based search algorithms for optimization of sequences of chosen folds, using molecular mechanics based force fields. Developed in Durani Lab at IIT Bombay
Conference Proceedings (International)
1. Vibin Ramakrishnan, Ranjit Ranbhor and Susheel Durani. Stereochemical origins of compactness and stability in proteins. A simulated annealing study of poly L and alternating L, D diastereomer variants of Ac-Ala30-NHMe. 48th Annual Meeting of Biophysical Society, Baltimore, Maryland, USA. Biophys. J S. 2004, 86,621.
2. Ranjit Ranbhor, Vibin Ramakrishnan, Anil Kumar, Abhijit Tendulkar and Susheel Durani. Heterochiral Proteins. De novo Design by Stereochemical Control of Folding. The 19th Annual Symposium of Protein Society, USA. 2005. Boston, USA. Protein Science S. 2005, 14, 105.
3. Anil Kumar; Ranjit Ranbhor; Vibin Ramakrishnan; Susheel Durani. “Simulated Dynamics of Blocked Octa-L-alanine Implicates Inter-Peptide Interaction as Possible Speed Barrier in Protein Folding.” The 21st Annual Symposium of Protein Society, USA. Boston, U.S.A. July 21-25, 2007.
4. Anil kumar, Vibin Ramakrishnan, Ranjit Ranbhor; Susheel Durani. “Poly-L stereochemistry and conformational landscapes of protein folding. Explicit solvent MD of Poly-L and Alternating-L,D octa-alanines.” 51st Annual Meeting of Biophysical Society, CA, USA Biophys. J. 94: 195. 2008.
5. Vibin Ramakrishnan; Saeed Salem; Mohammed Zaki and Christopher Bystroff. Simulation of Protein Folding Pathways and Folding Kinetics using Statistical Mechanical Model. 5th International Conference on Bioinformatics December 18 - 20, InCoB 2006, New Delhi.
Conference Proceedings (National)
6. Vibin Ramakrishnan, Ranjit Ranbhor and Susheel Durani. Stereochemical origins of compactness and stability in proteins. A systematic modeling study of poly L and alternating L, D diastereomer variants of Ac-Ala8-NHMe. NCBS Symposium on Molecules, Machines and Networks 2004 National Centre for Biological Sciences, TIFR, GKVK Campus, Bangalore.
7. Vibin Ramakrishnan, Ranjit Ranbhor, Anil Kumar and Susheel Durani. Seeds of protein folding in polyproline-II ensembles of unfolded polypeptides. The Second Indian Symposium of Protein Society- Protein Structure and Function. 2004. IIT-Bombay.
8. Ranjit Ranbhor, Vibin Ramakrishnan, Anil Kumar and Susheel Durani. De novo design of heterotactic mini-protein. The Second Indian Symposium of Protein Society- Protein Structure and Function. 2004 IIT-Bombay.
9. Anil Kumar, Ranjit Ranbhor, Abhijit Tendulkar, Kirti Patel, Vibin Ramakrishnan and Susheel Durani. De novo Design with Diversification of Molecular Tacticity. Joint International Conference by American Chemical Society and Council of Scientific and Industrial Research. 2006. National Chemical Laboratory, Pune.
10.Ranjit Ranbhor, Vibin Ramakrishnan, Anil Kumar and Susheel Durani. The Link between Sequence and Conformation in Protein Structures could be Stereochemically Established. The Eighth Symposium of Chemical Research Society of India. 2006. IIT-Bombay, Mumbai.
11.Anil Kumar, Ranjit Ranbhor, Vibin Ramakrishnan and Susheel Durani. Inter-peptide Interaction and Protein Folding Mechanisms: A Molecular Dynamics Study of Blocked Octa-L-Alanine in Explicit Solvent. In-House Symposium. August 19, 2006. Department of Chemistry, IIT-Bombay, Mumbai.
12.Ranjit Ranbhor, Vibin Ramakrishnan, Anil Kumar, Abhijit Tendulkar and Susheel Durani. Computational Design of Heterochiral Protein Assemblies. 75th Annual Meeting, Society of Biological Chemists (India) December 8 - 11, 2006 at Jawaharlal Nehru University, New Delhi.
13.Ranjit Ranbhor, Anil Kumar, Vibin Ramakrishnan, Abhijit Tendulkar and Susheel Durani. Computational Design of Protein Dimers in C2-Symmetry. 5th International Conference on Bioinformatics December 18 - 20, 2006 at Hotel Ashok, New Delhi.
14.Anil Kumar, Vibin Ramakrishnan, Ranjit Ranbhor and Susheel Durani. Inter-peptide Interaction and Protein Folding Mechanism. Molecular Dynamics of Blocked Octa-L-Alanine in Explicit Solvent. 5th International Conference on Bioinformatics December 18 - 20, 2006 at Hotel Ashok, New Delhi.
15.Anil Kumar; Ranjit Ranbhor; Vibin Ramakrishnan; Susheel Durani. “Molecular Dynamics of Blocked Octa-L-alanine Implicates Inter-Peptide Electrostatics as Possible Speed Barrier in Protein Folding.” Indian Biophysical Society-2007 (National Symposium on Biophysics: Trends in Biomedical Research) New Delhi, Feburary 13-15, 2007
16.Anil Kumar; Ranjit Ranbhor; Vibin Ramakrishnan; Susheel Durani. “Poly-L Structure and Peptide Dipolar Interaction in Protein Folding Speed and Specificity.” Western Regional Humboldt Kolleg 2007 Jaipur, Rajasthan, September 28-30, 2007.
17.Ranjit Ranbhor; Ashish Tendulkar; Anil Kumar; Vibin Ramakrishnan; Kirti Patel; Susheel Durani. “Towards Evolutionary Design in the Combined Alphabet of Chemical and Stereochemical Structure.” Vth In-house symposium Department of Chemistry, IIT Bombay, September 22, 2007.
INVITED LECTURES
• Canonicalization of Molecular Structures for Virtual Activity Profiling. National Seminar on "Current Trends in Genomics & Proteomics ", September 21-23, 2011. Pondicherry Central University.
• "A 'reductionist' approach in virtual activity profiling of drug molecules" ICDDT, 2011. 3rd International Conference on Drug Discovery and Therapy, Feb 7-10, 2011 Dubai, UAE.
• "Computational Protein Design", ADCOM 2009 International Conference on advanced computing and communication 14-17 Dec 2009. Indian Institute of Science Bangalore.
• National Seminar on Molecular Modeling and Drug Design, Pondicherry Central University. October 14-16 2008.
• PRATHYARTH 2008, SASTRA Thanjavur. October 11, 2008