Publications
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A yeast system for discovering optogenetic inhibitors of eukaryotic translation initiation
H Lu, M Mazumder, ASI Jaikaran, A Kumar, EK Leis, X Xu, M Altmann, ...
ACS synthetic biology 8 (4), 744-757
IDeAS: automated design tool for hetero-chiral protein folds
R Ranbhor, A Kumar, A Tendulkar, K Patel, V Ramakrishnan, S Durani
Physical Biology 15 (6), 066005
A Kumar, S Nokhrin, RM Woloschuk, GA Woolley
Biochemistry 57 (28), 4093-4104
Automated design evolution of stereochemically randomized protein foldamers
R Ranbhor, A Kumar, K Patel, V Ramakrishnan, S Durani
Physical biology 15 (3), 036001
Effect of tacticity-derived topological constraints in bactericidal peptides
PK Hazam, G Jerath, A Kumar, N Chaudhary, V Ramakrishnan
Biochimica et Biophysica Acta (BBA)-Biomembranes 1859 (8), 1388-1395
B Goyal, A Kumar, KR Srivastava, S Durani
Journal of Biomolecular Structure and Dynamics 35 (9), 1923-1935
Automated protein design: Landmarks and operational principles
A Kumar, R Ranbhor, K Patel, V Ramakrishnan, S Durani
Progress in biophysics and molecular biology 125, 24-35
KR Srivastava, B Goyal, A Kumar, S Durani
RSC Advances 7 (45), 27981-27991
B Goyal, KR Srivastava, A Kumar, GN Patwari, S Durani
RSC Advances 6 (114), 113611-113619
B Goyal, A Kumar, KR Srivastava, S Durani
RSC Advances 6 (78), 74162-74176 (2016)
Origins of the Intermediate Spectral Form in M100 Mutants of Photoactive Yellow Protein
A Kumar, GA Woolley
Photochemistry and photobiology 91 (4), 985-991 (2015)
Photo-control of DNA binding by an engrailed homeodomain–photoactive yellow protein hybrid
A Kumar, AM Ali, GA Woolley
Photochemical & Photobiological Sciences 14 (9), 1729-1736 (2015)
Engineering Photo-Control Of Translation Initiation Using Photoactive Yellow Protein Hybrids
A Kumar, AS Jaikaran, A Bah, J Forman-Kay, GA Woolley
PROTEIN SCIENCE 23, 124-124 (2014)
A circularly permuted photoactive yellow protein as a scaffold for photoswitch design
A Kumar, DC Burns, MS Al-Abdul-Wahid, GA Woolley
Biochemistry 52 (19), 3320-3331 (2013)
Structure-Based Design of Circularly Permutated and Frame-Shifted Photoactive Yellow Proteins
A Woolley, A Kumar, S Al-Abdul-Wahid
Biophysical Journal 102 (3), 25a (2012)
KR Srivastava, A Kumar, B Goyal, S Durani
The Journal of Physical Chemistry B 115 (20), 6700-6708 (2011)
KR Srivastava, A Kumar, S Durani
Biophysical Journal 100 (3), 209a (2011)
K Patel, B Goyal, A Kumar, N Kishore, S Durani
The Journal of Physical Chemistry B 114 (50), 16887-16893 (2010)
Creating novel protein scripts beyond natural alphabets
A Kumar, V Ramakrishnan
Systems and synthetic biology 4 (4), 247-256 (2010)
Homochiral stereochemistry: the missing link of structure to energetics in protein folding
A Kumar, V Ramakrishnan, R Ranbhor, K Patel, S Durani
The Journal of Physical Chemistry B 113 (51), 16435-16442 (2009)
Analysis of the structural consensus of the zinc coordination centers of metalloprotein structures
K Patel, A Kumar, S Durani
Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics 1774 (10), 1247-1253 (2007)
The interplay of sequence and stereochemistry in defining conformation in proteins and polypeptides
R Ranbhor, V Ramakrishnan, A Kumar, S Durani
Biopolymers: Original Research on Biomolecules 83 (5), 537-545 (2006)
V Ramakrishnan, R Ranbhor, A Kumar, S Durani
The Journal of Physical Chemistry B 110 (18), 9314-9323 (2006)
Communicated/Under Preparation
Anil Kumar, Punam Ghosh, Kirti Patel, and Susheel Durani. "Stereochemical Design of "paper-clip" with L- and D-alpha-amino acid alphabet and its serendipitous assembly as a nanotube." 2023
RESEARCH TALK
9. Department of Biosciences & Bioengineering, IIT Bombay, Mumbai, India
Invited Talk, March 4th, 2016
"Designing light-switchable proteins"
8. Department of Chemistry, IIT Patna, Patna, India
Invited Talk, Feb 26th, 2016
"Designing light-switchable proteins"
7. 13th CBP-2014 (Chemical Biophysics Symposium), Canada
University of Toronto, Toronto, Canada, May 2-4th, 2014
"Photo-control of cap-dependent translation"
6. MOOT XXVI NMR Symposium, Canada
Queen's University, Kingston, Ontario, Canada October 26-27th, 2013
"A Circularly Permuted Photoactive Yellow Protein as a Scaffold for Photoswitch Design:
5. IBS-2009 (National Symposium on Cellular & Molecular Biophysics)
CCMB, Hyderabad, India January 22-24th, 2009
“Homochirality and Protein-Folding Principles: Experimental and Theoretical Studies of Ac-Lys-Ala3-Lys-Ala3-Lys-NHMe Isomeric in Structure.”
4. IBS-2007 (National Symposium on Biophysics: Trends in Biomedical Research)
New Delhi, India Feburary 13-15th, 2007
“Molecular Dynamics of Blocked Octa-L-alanine Implicates Inter-Peptide Electrostatics as Possible Speed Barrier in Protein Folding.”
3. Department of Chemistry, IIT Bombay, India
Spring Semester 2004
“Theoretical studies of kinetics of protein folding pathway”
2. Department of Chemistry, IIT Bombay, India
Spring Semester 2004
“Magnetic Resonance Imaging (MRI) and its application”
1. Department of Chemistry, IIT Bombay, India
Autumn Semester 2003
“Total synthesis of Diazonamide”
RESEARCH POSTERS
International Conference Proceedings (Selected ones)
• 8th Young Investigators' Meeting, India
YIM - 2016, Gurgaon, New Delhi, Feb 27-Mar 3rd, 2016,
• 98th Canadian Chemistry Conference, Canada
CSC-Meeting 2015, Ottawa, Canada, June 13-17th, 2015
"Structure-based design of a photo-controlled Engrailed DNA binding protein."
• The Protein Society Symposium, USA
28th Symposium of the protein society, San Diego, CA, USA, July 27-30th 2014
"Engineering photo-control of translation initiation using photoactive yellow protein hybrids."
• Protein Engineering Canada Conference, Canada
1st PEC, Ottawa, Ontario, Canada, June 20-22nd, 2014
"Towards photo-control of translation using photoactive yellow protein."
• 12th Chemical Biophysics Symposium
CBP - 2013, University of Toronto, Canada, April 19-21st, 2013
"Structure-based design of photoswitchable translation initiation regulator of 4E-binding protein"
• PrPCANADA 2012 & Protein Folding and Disease Conference
PrPCANADA Meeting - 2012, Toronto, Canada, June 25-27th 2012
“A circularly permuted photoactive yellow proteins”
• 94th Canadian Chemistry Conference
CSC-Meeting 2011, Montreal, Canada, June 5-9th 2011
“Structure-based design of circularly permutated and frame-shifted photoactive yellow proteins”
• 55th Annual meeting of Biophysical Society
Baltimore, Maryland, USA, March 5-9th 2011
“Stereochemistry and Protein Folding: Spectroscopic and Molecular Dynamics Studies of Homopolypeptides in DMSO”
• Fluorescence 2009, An International Conference of Fluorescence in Biology
TIFR, Mumbai, India, March 16-19th, 2009
“Analysis of Folding in the Minimal Protein Model Ac-ERYDNDFQWK-NH2”
• ISCB-2009, 13th ISCBC International Conference on Interplay of Chemical and Biological Sciences: Impact on Health and Environment
University of Delhi, India, February 26th- March 1st, 2009
“Poly-L Stereochemistry and Protein Folding: Enquiry with a simple Peptide Model”
• 51st Annual Meeting of Biophysical Society
California, Long Beach, USA, Biophys. J. 94: 195. 2008
“Poly-L Stereochemistry and Conformational Landscapes of Protein Folding. Explicit Solvent MD of Poly-L and Alternating-L,D Octa-alanines.”
• 21st Symposium of The Protein Society
MA, USA, Protein Science S. 16, 107, 2007
“Simulated Dynamics of Blocked Octa-L-alanine Implicates Inter-Peptide Interaction as Possible Speed Barrier in Protein Folding.”
• 5th International Conference on Bioinformatics
New Delhi, India December 18-20th, 2006
“Inter-peptide Interaction and Protein Folding Mechanism. Molecular Dynamics of blocked Octa-L-Alanine in Explicit Solvent.”
• Joint International Conference on Building Bridges, Forging Bonds for 21st Century Organic Chemistry and Chemical Biology,
Jointly organized by ACS, USA and CSIR, India. National Chemical Laboratory, Pune, India 2006
“De novo Protein Design with Diversification of Molecular Tacticity.”
National Conference Proceedings (Selected ones out of 20)
• Symposium on Recent Trends in Biophysics
BHU, Varanasi, India, February 13-15, 2010
“Stereochemical Design of “Hairclip” with L- and D-a-Amino-Acid Alphabet and its Serendipitous Assembly as a Nanotube”
• Symposium on Frontiers in Computational Biology
C-DAC, Pune, India, July 23-24, 2009
“Stereochemistry and Protein Folding: A Comparative Study of the Peptide Models Homochiral and Heterochiral”
(Selected for First Prize)
• RSC-IITB Symposium on Chemical Sciences
Jointly organized by Dept. of Chemistry, IIT Bombay, India and Royal Society of Chemistry, UK, IRCC Auditorium, IIT Bombay, India February 3rd, 2009
“The Stereochemical bias of Nature: Enquiries of its Relevance to Protein Folding
• In-house symposium
Department of Chemistry, IIT Bombay, India September 27th, 2008
“Probing Protein Folding in its Stereochemical Logic. NMR, CD, and MD Studies of Ac-Lys-Ala3-Lys-Ala3-Lys-NHMe.”
• Western Regional Humboldt Kolleg 2007
Jaipur, Rajasthan, India September 28-30th, 2007
“Poly-L Structure and Peptide Dipolar Interaction in Protein Folding Speed and Specificity.”
• In-house symposium
Department of Chemistry, IIT Bombay, India August 19th, 2006
“Inter-Peptide Interaction and Protein Folding Mechanisms: A Molecular Dynamics Study of Blocked Octa-L-Alanine in Explicit Solvent.”
"Education is a progressive discovery of our ignorance"
- Will Durant
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