B. Jayaram
B. Jayaram
Supercomputing Facility for Bioinformatics & Computational Biology, IIT Delhi
Verified email at - Homepage
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Intrusion of counterions into the spine of hydration in the minor groove of B-DNA: fractional occupancy of electronegative pockets
MA Young, B Jayaram, DL Beveridge
Journal of the American Chemical Society 119 (1), 59-69, 1997
The electrostatic potential of B‐DNA
B Jayaram, KA Sharp, B Honig
Biopolymers: Original Research on Biomolecules 28 (5), 975-993, 1989
A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA
R Lavery, K Zakrzewska, D Beveridge, TC Bishop, DA Case, ...
Nucleic acids research 38 (1), 299-313, 2010
Solvation free energy of biomacromolecules: Parameters for a modified generalized Born model consistent with the AMBER force field
B Jayaram, D Sprous, DL Beveridge
The Journal of Physical Chemistry B 102 (47), 9571-9576, 1998
The role of water in protein-DNA recognition
B Jayaram, T Jain
Annu. Rev. Biophys. Biomol. Struct. 33 (1), 343-361, 2004
Free energy analysis of the conformational preferences of A and B forms of DNA in solution
B Jayaram, D Sprous, MA Young, DL Beveridge
Journal of the American Chemical Society 120 (41), 10629-10633, 1998
Sanjeevini: a freely accessible web-server for target directed lead molecule discovery
B Jayaram, T Singh, G Mukherjee, A Mathur, S Shekhar, V Shekhar
BMC bioinformatics 13, 1-13, 2012
μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA
M Pasi, JH Maddocks, D Beveridge, TC Bishop, DA Case, T Cheatham III, ...
Nucleic acids research 42 (19), 12272-12283, 2014
Free energy calculations of ion hydration: an analysis of the Born model in terms of microscopic simulations
B Jayaram, R Fine, K Sharp, B Honig
The Journal of Physical Chemistry 93 (10), 4320-4327, 1989
AADS - An Automated Active Site Identification, Docking, and Scoring Protocol for Protein Targets Based on Physicochemical Descriptors
T Singh, D Biswas, B Jayaram
Journal of chemical information and modeling 51 (10), 2515-2527, 2011
Do water molecules mediate protein-DNA recognition?
CK Reddy, A Das, B Jayaram
Journal of Molecular Biology 314 (3), 619-632, 2001
Modeling DNA in aqueous solutions: theoretical and computer simulation studies on the ion atmosphere of DNA
B Jayaram, DL Beveridge
Annual review of biophysics and biomolecular structure 25 (1), 367-394, 1996
Local dielectric environment of B-DNA in solution: results from a 14 ns molecular dynamics trajectory
MA Young, B Jayaram, DL Beveridge
The Journal of Physical Chemistry B 102 (39), 7666-7669, 1998
ParDOCK: an all atom energy based Monte Carlo docking protocol for protein-ligand complexes
A Gupta, A Gandhimathi, P Sharma, B Jayaram
Protein and peptide letters 14 (7), 632-646, 2007
Free energy analysis of protein–DNA binding: the EcoRI endonuclease–DNA complex
B Jayaram, KJ McConnell, SB Dixit, DL Beveridge
Journal of Computational Physics 151 (1), 333-357, 1999
A molecular thermodynamic view of DNA–drug interactions: a case study of 25 minor-groove binders
SA Shaikh, SR Ahmed, B Jayaram
Archives of biochemistry and biophysics 429 (1), 81-99, 2004
Inhibiting fungal multidrug resistance by disrupting an activator-Mediator interaction
JL Nishikawa, A Boeszoermenyi, LA Vale-Silva, R Torelli, B Posteraro, ...
Nature 530, 485-489, 2016
A modification of the generalized Born theory for improved estimates of solvation energies and pK shifts
B Jayaram, Y Liu, DL Beveridge
The Journal of chemical physics 109 (4), 1465-1471, 1998
Bhageerath: an energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins
B Jayaram, K Bhushan, SR Shenoy, P Narang, S Bose, P Agrawal, ...
Nucleic acids research 34 (21), 6195-6204, 2006
A stoichiometry driven universal spatial organization of backbones of folded proteins: are there Chargaff's rules for protein folding?
A Mittal, B Jayaram, S Shenoy, TS Bawa
Journal of Biomolecular Structure and Dynamics 28 (2), 133-142, 2010
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