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| Selected List of Publications |
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2012
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B Jayaram, Tanya Singh, Goutam Mukherjee, Abhinav Mathur, Shashank Shekhar, Vandana Shekhar, "Sanjeevini: a freely accessible web-server for target directed lead molecule discovery", BMC Bioinformatics 2012, 13(Suppl 17):S7 (13 December 2012)
doi:10.1186/1471-2105-13-S17-S7
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Nagi B. Kumar, Medha Dhurandhar, Bharat Aggarwal, Shrikant Anant, Kenyon Daniel, Gary Deng, Julie Djeu, Jinhui Dou, Ernest Hawk, B. Jayaram, Libin Jia, Rajendra Joshi, Madhuri Kararala,Devarajan Karunagaran, Omer Kucuk,Lalit Kumar, Mokenge Malafa, G. J. Samathanam, Fazlul Sarkar, Maqsood Siddiqi, Rana P. Singh, Anil Srivastava, Jeffrey D. White, "Proceedings of the Indo-U.S. bilateral workshop on accelerating botanicals/biologics agent development research for cancer chemoprevention, treatment, and survival", Article first published online:27 NOV 2012,
DOI: 10.1002/cam4.42.
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http://onlinelibrary.wiley.com/doi/10.1002/cam4.42/full
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B. Jayaram and Priyanka Dhingra, "Towards creating complete proteomic
structural databases of whole organisms", Current Bioinformatics, 2012, 7(4), 424-435.
Read Abstract
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M. Bansal, B. Jayaram, A. Mittal, "Nucleic Acids in Disease &
Disorder: Understanding the language of life emerging from the 'ABC'
of DNA", J Bio Sc., 2012, 37, 375-378.
http://www.ias.ac.in/jbiosci/jul2012/375.pdf
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B. Jayaram, Aditya Mittal, Avinash Mishra, Chanchal Acharya, Garima Khandelwal
"Universalities In Protein Tertiary Structures: Some New Concepts" GNR special issue on Biomolecular Forms & Functions, 2013, in press.
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Anjali Soni, Khushhali Menaria, Pratima Ray and B. Jayaram. "Genomes to
Hits in Silico - A Country Path Today, A Highway Tomorrow: A Case Study of Chikungunya", Current Pharmaceutical Design, accepted (in press).
Read Abstract
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Abbas G. Shilabin, Liudmila Dzhekieva, Pushpa Misra, B. Jayaram, and R. F. Pratt "4-Quinolones as Noncovalent Inhibitors of High Molecular Mass Penicillin-Binding Proteins", ACS Med. Chem. Lett., Article ASAP, Publication Date (Web): June 4, 2012, DOI: 10.1021/ml3001006.
http://pubs.acs.org/doi/abs/10.1021/ml3001006
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The article "DNA-water interactions distinguish messenger RNA genes from transfer RNA genes" is featured in C&EN as DNA's destiny lies in its solvation.
http://cen.acs.org/articles/90/web/2012/05/DNAs-Destiny-Lies-Solvation.html
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G. Khandelwal, B. Jayaram, "DNA-water interactions distinguish
messenger RNA genes from transfer RNA genes", J. Am. Chem. Soc., 2012,Vol. 134 (21), 8814-8816, DOI:10.1021/ja3020956.
Read Abstract
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Aditya Mittal, B. Jayaram, "A possible molecular metric for
biological evolvability", J. Bio Sc.,37(3), July 2012, 573-577.
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Garima Khandelwal, Jalaj Gupta and B. Jayaram, "DNA energetics based analyses suggest additional genes
in prokaryotes" J Bio Sc., 2012, 37 433-444 DOI 10.1007/s12038-012-9221-7
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B. Jayaram, P. Dhingra, B. Lakhani and S. Shekhar, "Bhageerath - Targeting
the Near Impossible: Pushing the Frontiers of Atomic Models for Protein Tertiary Structure Prediction",
Journal of Chemical Sciences,January 2012 Vol. 124, No. 1, pp. 83.91.
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Aditya K. Padhi, Hirdesh Kumar, Suhas V. Vasaikar, B. Jayaram and James Gomes, "Mechanisms of Loss of Functions of Human Angiogenin Variants Implicated in Amyotrophic Lateral Sclerosis", PLoS One, 2012, 7(2): e32479. doi:10.1371/journal.pone.0032479.
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Saher Afshan Shaikh, Tarun Jain, Gurvisha Sandhu, Anjali Soni and B. Jayaram, "From Drug Target to Leads - Sketching A Physico-chemical Pathway for Lead Molecule Design In Silico", Frontiers in Medicinal Chemistry, Volume 6, 2012, Editor: Atta ur Rahman, Bentham Publishers, in press.
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Prateek Pandya, Surendra P. Gupta, Kumud Pandav, Ritu Barthwal, B. Jayaram and Surat Kumar, "DNA Binding Studies of Vinca Alkaloids: Experimental and Computational Evidence", NPC Natural Product Communications, 2012 Vol. 7, Issue 3, Pages 283-418.
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B. Jayaram, Priyanka Dhingra, Goutam Mukherjee, Vivekanandan Perumal, "Genomes to Hits: The Emerging Assembly LineIn Silico",Proceedings of the Ranbaxy Science Foundation 17th Annual Symposium on "New Frontiers in Drug Design, Discovery and Development" 2012, Chapter 3, pages 13-35.
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2011
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M. M. Gromiha, N. Saranya, S. Selvaraj, B. Jayaram and Kazuhiko Fukui,"Sequence and structural features of binding site residu es in protein-protein complexes: comparison with protein-nucleic acid complexes", Proteome Science, 2011, 9 (Suppl 1),S13, doi:10.1186/1477-5956-9-S1-S13.
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B. Jayaram, Tanya Singh, Marcia Fenley, "DNA-Drug Interactions: A Theoretical Perspective" in "Methods for Studying DNA/Drug Interactions", Editors, Dr. Meni Wanunu & Prof. Yitzhak Tor, 2011,Ch-14, pp 317-338, CRC Press.
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Tanya Singh, D. Biswas, B. Jayaram, AADS - An automated active site
identification, docking and scoring protocol for protein targets based on physico-chemical descriptors., 2011, J. Chem. Inf. Modeling,51 (10), 2515-2527, DOI: 10.1021/ci200193z.
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A. Mittal and B. Jayaram, "Backbones of folded proteins reveal
novel invariant amino-acid neighborhoods", J. Biomol. Struc. Dyn., 2011,
Vol. 28(4), 443-454.
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| A. Mittal and B. Jayaram, "The newest view on protein
folding: stoichiometric and spatial unity in structural and functional diversity", J. Biomol.
Struc. Dyn., 2011, Vol. 28(4), 669-674.
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2010
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A. Mittal, B. Jayaram, S. R. Shenoy and T. S. Bawa,
"A Stoichiometry driven universal spatial organization of backbones of
folded proteins: Are there Chargaff's rules for protein folding ?", J.
Biomol. Struc. Dyn., 2010, Vol. 28 (2), 133-142.
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Download Supplementary files1 Supplementary files2 Primary Contact Data.xls
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M. O. Fenley, R. Harris, B. Jayaram, A. H. Boschitsch,
"Revisiting the association of cationic groove-binding drugs to DNA
using a poisson-boltzmann approach", Biophys J., 2010, 99(3), 879-886.
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G. Khandelwal, B. Jayaram, "A Phenomenological model for predicting
melting temperatures of DNA sequences", PLoS One , 2010, 5(8), e12433.
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G. Mukherjee, N. Patra, P. Barua and B. Jayaram, "A Fast
empirical GAFF compatible partial atomic charge assignment scheme
for modeling interactions of small molecules with biomolecular targets (TPACM4)",
J. Computational Chemistry, Article first published online: 22 OCT 2010; DOI: 10.1002/jcc.21671; 32,893-907 (2011).
DOI:10.1002/jcc.21671. |
P. Pandya, Md. M. Islam, G. S. Kumar, B. Jayaram, S.
Kumar, "DNA minor groove binding of small molecules: experimental and
computational evidence", J. Chemical Sciences, 2010, Vol. 122(2), 247-257.
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S. R. Shenoy and B. Jayaram, "Proteins: sequence to structure and function- current Status", Current Protein and Peptide
Science, 2010, 11(7), 498-514.
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2009
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R. Lavery, K. Zakrzewska, D. L. Beveridge, T. C. Bishop,
D. A. Case, T. Cheatham III, S. Dixit, B. Jayaram, F. Lankas,
C. Laughton, J. H. Maddocks, A. Michon, R. Osman,
M. Orozco, A. Perez, T. Singh, N Spackova and J. Sponer.
"A systematic molecular dynamics study of nearest neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA", Nucleic Acids Research, 2009, Vol. 38(1), 299-313.
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2008
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B. Jayaram, "Decoding the design principles of amino acids and the chemical logic of protein sequences", Nature Precedings. 2008
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Download Supplementary Pdf
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P. Singhal, B. Jayaram, S. B. Dixit and D. L. Beveridge, "Prokaryotic gene finding based on physicochemical characteristics of codons calculated from molecular dynamics simulations", Biophys J., 2008, 94, 11, 4173-4183.
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2007
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A. Gupta, A. Gandhimathi, P. Sharma, B. Jayaram ,"ParDOCK: An all atom energy based monte carlo docking protocol for protein-ligand complexes", Protein and Peptide Letters, 2007, 14, 632-646.
Read Abstract
S. A. Shaikh, T. Jain, G. Sandhu, N. Latha, B. Jayaram, "From drug target to leads-
sketching, A physicochemical pathway for lead molecule
design in silico", Current Pharmaceutical Design, 2007, 13, 3454-3470.
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S. A. Shaikh and B. Jayaram, "A Swift all-atom energy based
computational protocol to predict DNA ligand binding affinity
and ΔTm", J. Med.Chem., 2007, 50, 2240-2244.
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T. Jain, B. Jayaram, "A computational protocol for
predicting the binding affinities of zinc containing metalloprotein-ligand
complexes", PROTEINS: Struct. Funct. Bioinfo., 2007, 67, 1167-1178.
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L. Thukral, S. R. Shenoy, K. Bhusan and B.Jayaram,
"ProRegIn: A regularity index for the selection of native-like tertiary structures of proteins",
Journal of Biosciences, 2007, 32(1), 71-81.
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M. Vidyasagar, et al. BioSuite: A comprehensive bioinfromatics software package ( a unique industry -academia collaboration), Current Science, 2007, 92(1), 29-38.
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2006
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S. Shenoy, B. Jayaram, et al. "From gene to drug:
A proof of concept for a plausible computational pathway".
6th international conference on intelligent systems design
and applications, Jinan, China, Oct. 16-18, 2006, Proceedings,
IEEE Computer Society, 2006, pp., 1147-1152.
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Full Text
B. Jayaram, K. Bhushan, et al., "Bhageerath : An
energy based web enabled computer software suite for limiting
the search space of tertiary structures of small globular
proteins", Nucl. Acids Res., 2006, 34, 6195-6204.
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Full Text
S. Dutta, P. Singhal, P. Agrawal, R. Tomer, Kritee, E. Khurana, and B. Jayaram, "A Physico-chemical model for
analyzing DNA sequences", J. Chem. Inf. Model., 2006, 46(1), 78-85.
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B. Jayaram, N. Latha, T. Jain, P. Sharma, A. Gandhimathi, and V. S. Pandey, "Sanjeevini: A comprehensive Active-Site
directed lead design software", Ind. J. Chem., 2006, 45A, 1834-1837.
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P. Narang, K. Bhushan, S. Bose, B. Jayaram, "Protein
structure evaluation using an all-atom energy based empirical
scoring function", J. Biomol. Str. Dyn., 2006, 23, 385-406.
Read Abstract
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2005
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| T. Jain, and B. Jayaram, "An all atom energy based computational protocol for
predicting binding affinities of protein-ligand complexes",
FEBS Letters, 2005, 579, 6659-6666.
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P. Narang, K. Bhushan, S. Bose and B. Jayaram, "A
computational pathway for bracketing native-like structures
for small alpha helical globular proteins", Phys. Chem.
Chem. Phys., 2005, 7, 2364-2375.
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N. Latha, and B. Jayaram, "A Binding affinity based
computational pathway for active-site directed lead
molecule design: some promises and perspectives", Drug
Des. Rev.-Online, 2005, 2, 145-165.
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Full Text
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2004
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| S. A. Shaikh, S. R. Ahmed, and B. Jayaram, "A molecular thermodynamic view of DNA-drug
interaction: A case study of 25 minor groove binders",
Arch. Biochem. Biophys., 2004, 429, 81-99.
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Full Text
N. Latha, T. Jain, P. Sharma, B. Jayaram, "A free
energy based computational pathway from chemical templates
to lead compounds: a case study of COX-2 inhibitors",
J. Biomol. Struct. Dyn., 2004, 21, 791-804.
Read
Abstract
B. Jayaram and T. Jain, "The role of water in Protein-DNA recognition", Annu. Rev. Biophys. Biomol. Struct, 2004, 33, 343-61.
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2002 and before ( i.e. before inauguration of SCFBio on 31st July, 2002 )
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| Achintya Das, Parul Kalra, N. Latha and B. Jayaram, "In Silico Trends in Thermodynamics and Kinetics of Binding - New Tools for De Novo Drug Design", in Recent Trends in Chemistry, Editors, Dr.M.
M.Srivastava, Shalini Srivastava,2002 Chapter-15, pp 218-234.
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B. Jayaram, K. Mcconnell, S. B. Dixit, D. L. Beveridge, "Free energy componenet analysis of 40 protein-DNA complexes: A consensus view on the thermodynamics of binding at the molecular level", J. Comput. Chem, 2002, 23, 1-14.
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D. C. Kombo, B. Jayaram, K. J. McConnell, and D. L. Beveridge, "Calculation of the affinity of the λ repressor-operator complex based on free energy component analysis", Molecular Simulations, 2002, 28, 187-211.
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P. Kalra, T. V. Reddy, and B. Jayaram, "Free energy component analysis for drug design: A case study of HIV-1 protease-inhibitor binding", J. Med. Chem., 2001, 44, 4325-4338.
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Ch. K. Reddy, A. Das and B. Jayaram, "Do water molecules
mediate protein-DNA recognition?" J. Mol. Biol., 2001, 314,
619-32.
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B. Jayaram, and A. Das, "Partitioning the electrostatic interaction energy between two charge distributions", J. Mol. Struct. (Theochem), 2001, 543, 123-128.
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M S Madhusudhan, and S Vishveshwara, A. Das, P. Kalra and B. Jayaram, "A molecular dynamics study based post facto energy analysis of the binding of bovine angiogenin with UMP and CMP ligands", Ind. J. Biochemistry & Biophysics, 2001, 38, 27-33.
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S. B. Dixit, N. Arora, and B. Jayaram, "How do hydrogen bonds contribute to protein-DNA recognition", J. Biomol. Struc. & Dyn., 2000, 109-112.
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P. Kalra, A. Das, S. B.Dixit, and B. Jayaram, "Free energy analysis of enzyme-inhibitor binding: the carboxypeptidase A-inhibitor complexes", Ind. J. Chemistry A, 2000, 39A, 262-273.
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B. Jayaram, K. J. McConnell, S. B. Dixit, and D. L. Beveridge, "Free energy analysis of protein-DNA
binding: The EcoRI endonuclease - DNA complex", J. Comput.
Phys, 1999, 151, 333-357.
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N. Arora and B. Jayaram, "Energetics of base pairs in B-DNA
in solution: An appraisal of potential functions and dielectric
treatments", J. Phys. Chem. B., 1998, 102, 6139-6144.
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B.Jayaram, "Biomolecular modelling and simulations - The
current status", PINSA A. 1998, 64 , 179-192.
B. Jayaram, D. Sprous, and D. L. Beveridge, "Solvation free energy of biomacromolecules: parameters for a modified
generalized born model consistent with the AMBER force
field", J. Phys. Chem. B., 1998, 102, 9571-9576.
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B. Jayaram, D. Sprous, M. A. Young, and D. L. Beveridge, "Free energy analysis of the conformational preferences of A and B forms of DNA in solution", J. Am. Chem. Soc, 1998, 120, 10629-10633.
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M. A. Young, B. Jayaram, and D. L. Beveridge, "Local dielectric
environment of B-DNA in solution : Results from a 14 ns
molecular dynamics trajectory", J. Phys. Chem. B., 1998, 102, 7666-7669.
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B. Jayaram,Y. Liu, D. L. Beveridge,
"A modification of the generalized Born theory for improved estimates of
solvation energies and pK shifts", J. Chem. Phys., 1998, 109, 1465-1471.
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M. A. Young, B. Jayaram, and D. L. Beveridge, "Intrusion
of counterions into the spine of hydration in the minor
groove of B-DNA: Fractional occupancy of electronegative
pockets", J. Am. Chem. Soc. 1997, 119, 59-69.
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N. Arora, and B. Jayaram, "Strength of hydrogen bonds in
alpha helices", J. Comput. Chem. 1997, 18, 1245-1252.
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Surjit B. Dixit, R. Bhasin, E. Rajasekaran, and B. Jayaram, "Solvation thermodynamics of amino acids : Assessment
of the electrostatic contribution and force-field dependence",
J. Chem. Soc., Faraday Trans. 1997, 93(6), 1105-1113.
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B. Jayaram, "Beyond the wobble: the rule of conjugates",
J. Mol. Evol., 1997, 45, 704-705.
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G. Ravishanker, P. Auffinger, D. R. Langley, B. Jayaram, M. A. Young, and D. L. Beveridge, "Treatment of counterions in computer simulations of DNA", Rev. Comput. Chem., Eds.: K. B. Lipkowitz and D. B. Boyd, 1997, 11, 317-372.
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B. Jayaram and D. L. Beveridge, "Modeling DNA in aqueous
solution: theoretical And computer simulation studies
on the Ion atmosphere of DNA", Annu. Rev. Biophys. Biomol.
Struct., 1996, 25, 367-394.
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B. Jayaram, "Some energeics and kinetics aspects of protein-DNA interaction : A theoretical study on the λ
repressor-operator complex", Biological Structure and Dynamics, Eds., R. H. Sarma and M. H. Sarma, Vol. 1, 1996, 109-120.
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B. Jayaram, "On the acceptance ratio in monte carlo computer simulations", J.Mathematical Chemistry, 1996, 20, 395-397.
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K. B. Roy, D. Vrushank, and B. Jayaram, "Use of isotope dilution phenomenon to advantage in the determination of kinetic constant Km and Kcat for BamH1 restriction endonuclease: An empirical and iterative approach", Analytical Biochemistry, 1994, 220, 160-164.
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E. Rajasekaran, B. Jayaram, and B. Honig, "Electrostatic
interactions in aliphatic dicarboxylic acids: A computational
route to the determination of pKa shifts", J. Am. Chem.
Soc., 1994, 116, 8238-8240.
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E. Rajasekaran and B. Jayaram, "Counterion condensation
in DNA systems : The cylindrical poisson-boltzmann model
revisited", Biopolymers, 1994, 34, 443-445.
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B. Jayaram, "Free energy of solvation, interaction, and
binding of arbitrary charge distributions imbedded in
a dielectric continuum", J. Phys. Chem., 1994, 98, 5773-5777.
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B. Jayaram, N. Aneja, E. Rajasekaran, V. Arora, A. Das, V. Ranganathan and V. Gupta, "Modelling DNA in aqueous solutions", J. Scientific & Industrial Research, 1994, 53, 88-105.
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B. Jayaram, and D. L. Beveridge, "Grand canonical monte carlo simulation studies on aqueous solution of NaCl ana NaDNA: Excess chemical potentials and source of nonideally in electrolyte and polyelectrolyte solutions", J. Phys. Chem.,
1991, 95, 2506-2516.
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B. Jayaram, F. M. DiCapua, and D. L. Beveridge, "A theoretical study of polyelectrolyte effects in protein-DNA interactions:Monte Carlo free energy simulations on the ion atmosphere contribution to the thermodynamics of .lambda. repressor-operator complex formation", J. Am. Chem. Soc., 1991, 113, 5211-5215.
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B. Jayaram, and D. L. Beveridge, "A simple method to estimate free energy from a molecular simulation: renormalization on the unit interval", J. Phys. Chem., 1990, 94, 7288-7293.
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B. Jayaram, and D. L. Beveridge "Free energy of an arbitrary charge distribution imbedded in coaxial cylindrical dielectric continua: application to conformational preferences of DNA in aqueous solutions", J. Phys. Chem., 1990, 94, 4666-4671.
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B. Jayaram, S. Swaminathan, D. L. Beveridge, K. Sharp and B. Honig, "Monte Carlo simulation studies on the structure of the counterion atmosphere of B-DNA. variations on the primitive dielectric model", Macromolecules, 1990, 23, 3156-3165.
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B. Jayaram , K. A. Sharp, and B. Honig,
"The electrostatic potential of B-DNA,
Biopolymers", 1989, 28, 975-993.
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B. Jayaram, R. Fine, K. Sharp, and B. Honig,
"Free-energy calculations Of ion hydration - an analysis of the born model
in terms of microscopic simulations,
J. Phys. Chem., 1989, 93, 4320-4327.
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B. Jayaram, M. Mezei, and D. L. Beveridge, "Conformational stability of dimethyl phosphate anion in water: liquid-state free energy simulations", J. Am. Chem. Soc., 1988, 110, 1691-1694.
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B. Jayaram, and D. L. Beveridge, "Tanford-Kirkwood theory for concentric dielectric continua: application to dimethylphosphate", Biopolymers, 1988, 27, 617-627.
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B. Jayaram, G. Ravishanker, and D. L. Beveridge, "Conformational preferences of phosphodiester torsion angles in dimethylphosphate anion In free space and water: Quasi-harmonic monte carlo and hydration shell calculations", J. Phys. Chem., 1988, 92, 1032-1034.
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B. Jayaram, M. Mezei, and D. L. Beveridge, "Monte carlo study of the aqueous hydration of dimethylphosphate conformations", J. Comp. Chem., 1987, 8, 917-942.
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D. L. Beveridge, P. V. Maye, B. Jayaram, G. Ravishanker, M. Mezei, "Aqueous hydration of nucliec acid constituents: Monte carlo computer simulation studies", J. Biomolec. Struc. & Dyn., 1984, 2, 261-270.
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* Publications in red color have more than 50 citations.
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