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2019 |
Mahboubeh Mehmankhah, Ruchika Bhat, Mohammad Sabery Anvar, Shahnawaz Ali, Aftab Alam, Anam Farooqui, Fatima Amir, Ayesha Anwer,Saniya Khan, Iqbal Azmi, Rafat Ali, Romana Ishrat, Md. Imtaiyaz Hassan, Zarrin Minuchehr, and Syed Naqui Kazim, "Structure-Guided Approach to Identify Potential Inhibitors of Large Envelope Protein to Prevent Hepatitis B Virus Infection," Oxidative Medicine and Cellular Longevity, vol. 2019, Article ID 1297484, 14 pages, 2019. https://doi.org/10.1155/2019/1297484. |
Ali Khosravi, B. Jayaram, Bahram Goliaei and Ali Masoudi-Nejad, "Active repurposing of drug candidates for melanoma based on GWAS, PheWAS and a wide range of omics data", Molecular Medicine , 2019. DOI:10.1186/s10020-019-0098-x |
Pradeep Pant, B Jayaram, "C5' omitted DNA enhances bendability and protein binding", Biochemical and Biophysical Research Communications, 2019. DOI:10.1016/j.bbrc.2019.05.051 |
Ali Khosravi, Morteza Kouhsar, Bahram Goliaei, B. Jayaram, Ali Masoudi-Nejad, "Systematic analysis of genes and diseases using PheWAS-Associated networks", Computers in Biology and Medicine, 2019, DOI:10.1016/j.compbiomed.2019.04.037 |
Akhilesh Mishra, Priyanka Siwach, Poonam Singhal and B. Jayaram "ChemGenome2.1: An ab initio gene prediction software". Methods in Molecular Biology | Pradeep Pant, Amita Pathak and B. Jayaram* "Symmetrization of the backbone of nucleic acids: A molecular dynamics study",
J Biomol Struct Dyn. 2019, Accepted Manuscript. https://doi.org/10.1080/07391102.2019.1585292 |
Bhaskar Chatterjee, Abhilash Jayaraj, Vinay Kumar, Brian Blagg, Rachel Davis, B.Jayaram, Shashank Deep, and Tapan Chaudhuri "Stimulation of Heat Shock Protein90 chaperone function through binding of a Novobiocin analogue KU-32", J. Biological Chemistry, 2019. DOI: 10.1074/jbc.RA118.002502 |
Venkatesan Santhanam, Pradeep Pant, B. Jayaram and Namakkal G Ramesh*, "Design, Synthesis and Glycosidase Inhibition Studies of Novel Triazole Fused Iminocyclitol-delta-lactams" Org. Biomol. Chem., 2019, Accepted Manuscript http://dx.doi.org/10.1039/C8OB03084G |
Marco Passi, John H.Maddocks, David Beveridge, Thomas C. Bishop, David A. Case, Thomas Cheatham III, Pablo D. Dans, B. Jayaram, Filip Lankas, Charles Laughton, Jonathan Mitchell, Roman Osman, Modesto Orozco, Alberto Perez, DaivaPetkeciuvite, Nada Spackova, Jiri Sponer, KrystynaZakrzewska, Richard Lavery, "{mu}ABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA"., Nucl. Acids Res., 2014, 42, 12272-12283
.
http://nar.oxfordjournals.org/content/early/2014/09/26/nar.gku855.ful
Avinash Mishra, Prashant S. Rana, Aditya Mittal, B Jayaram, "D2N: Distance to the native", BBA - Proteins and Proteomics,2014, 1844 (10), 1798-1807. http://www.sciencedirect.com/science/article/pii/S1570963914001848
Suhas V. Vasaikar, Bhyravabhotla Jayaram and JamesGomes, "Rapid computation and interpretation of Boolean attractors in biological networks" Journal of Complex Networks, 2014 ,doi:10.1093/comnet/CNU011
http://comnet.oxfordjournals.org/content/early/2014/05/03/comnet.cnu011.abstract
Garima Khandelwal, Rebecca A. Lee, B. Jayaram and David L. Beveridge, "A Statistical Thermodynamic Model for Investigating the Stability of DNA Sequences from Oligonucleotides to Genomes", Biophys. J., 2014, 106 (11), 2465-73.
http://www.cell.com/biophysj/abstract/S0006-3495%2814%2900446-9
Padhi AK, Vasaikar SV, Jayaram B and Gomes J (2014) "ANGDelMut - a web-based tool for predicting and analyzing functional loss mechanisms of amyotrophic lateral sclerosis-associated angiogenin mutations" [v3; ref status: indexed, http://f1000r.es/2yt] F1000Research 2014, 2:227 (http://f1000research.com/articles/2-227/v1 )
B. Jayaram, "Some recent progresses and perspectives in predictions of
protein structure, dynamics and function", 2013, Journal of Proteins and
Proteomics, 4(2), 65-66.
http://jpp.org.in/index.php/jpp/article/view/78/69
Ashutosh Shandilya, B. Jayaram, Sajeev Chacko, Indira Ghosh, "A Plausible mechanism for the antimalarial activity of artemisinin", 2013, Scientific Reports 3, Article number: 2513 http://www.nature.com/srep/2013/130829/srep02513/full/srep02513.html .
M. Singh, S. Sur, G. K. Rastogi, B. Jayaram, V. Tandon, "Bi and tri-substituted phenyl rings containing bisbenzimidazoles bind differentially with DNA duplexes: a biophysical and molecular simulation study." Mol BioSyst., 2013, 9, 2541-2553. http://pubs.rsc.org/en/content/articlehtml/2013/mb/c3mb70169g
Aditya K. Padhi, S. V. Vasaikar, B. Jayaram, James Gomes, "Fast prediction
of Deleterious Angiogenin mutations causing amyotrophic lateral sclerosis",
FEBS Letts.,2013, 587, 1762-6. http://www.febsletters.org/article/S0014-5793%2813%2900317-7/abstract
Avinash Mishra; Satyanarayan Rao; Aditya Mittal; B Jayaram, "Capturing
Native/Native like Structures with a Physico-Chemical Metric (pcSM) in
Protein Folding" BBA - Proteins and Proteomics. 2013 1834, 1520-31.
http://www.sciencedirect.com/science/article/pii/S1570963913001775.
Priyanka Dhingra and B. Jayaram, "A homology/ab initio hybrid algorithm for sampling near-native protein conformations", J Comput.Chem., 2013 34, 1925-36, http://onlinelibrary.wiley.com/doi/10.1002/jcc.23339/abstract
Goutam Mukherjee and B. Jayaram, "A Rapid Identification of Hit Molecules
for Target Proteins via Physico-Chemical Descriptors", Phys. Chem. Chem. Phys., 2013 15, 9107-16.
http://pubs.rsc.org/en/Content/ArticleLanding/2013/CP/C3CP44697B
Aditya K. Padhi, B. Jayaram, and James Gomes, "Prediction of Functional Loss of Human Angiogenin Mutants Associated with ALS by Molecular Dynamics Simulations", Scientific Reports (NPG), 2013, 3, 1225
S. V. Vasaikar, A K. Padhi, B. Jayaram, and J. Gomes, "NeuroDnet - an open source platform for constructing and analyzing neurodegenerative disease networks", BMC Neurosci., 2013, 14, 3.
http://www.biomedcentral.com/1471-2202/14/3/abstract
B. Jayaram, Aditya Mittal, Avinash Mishra, Chanchal Acharya, and Garima Khandelwal, "Universalities in Protein Tertiary Structures: Some New Concepts", in Biomolecular Forms and Functions, 2013, 210-219. World Scientific Publishing Co. Pte. Ltd., Singapore, Eds: Manju Bansal & N. Srinivasan,
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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", Curr. Pharma. Des., 2013 , 19, 4687-4700
http://www.eurekaselect.com/111973/article
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”, Cancer Medicine, 2013, 2, 108-115.
http://onlinelibrary.wiley.com/doi/10.1002/cam4.42/full
B. Jayaram, Tanya Singh, Goutam Mukherjee, Abhinav Mathur, Shashank Shekhar, and Vandana Shekhar, "Sanjeevini: a freely accessible web-server for target directed lead molecule discovery", BMC Bioinformatics, 2012, 13, S7.
http://www.biomedcentral.com/1471-2105/13/S17/S7
B. Jayaram and Priyanka Dhingra, "Towards creating complete proteomic structural databases of whole organisms", Current Bioinformatics, 2012, 7, 424-435.
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http://benthamscience.com/UpcomingArticles.php?JCode=CBIO
M. Bansal, B. Jayaram, and 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://eprints.iisc.ernet.in/44979/
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., 2012, 3, 592-595.
http://pubs.acs.org/doi/abs/10.1021/ml3001006
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
G. Khandelwal, and B. Jayaram, "DNA-water interactions distinguish messenger RNA genes from transfer RNA genes", J. Am. Chem. Soc., 2012, 134, 8814-8816. DOI:10.1021/ja3020956.
http://pubs.acs.org/doi/abs/10.1021/ja3020956
Aditya Mittal, and B. Jayaram, "A possible molecular metric for biological evolvability", J. Bio Sc., 2012, 37, 573-577.
http://www.ncbi.nlm.nih.gov/pubmed/22750993
Garima Khandelwal, Jalaj Gupta and B. Jayaram, "DNA energetics based analyses suggest additional genes in prokaryotes" J. Bio Sc., 2012, 37, 433-444.
http://link.springer.com/article/10.1007%2Fs12038-012-9221-7
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, 2012, 124, 83-91.
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http://link.springer.com/article/10.1007%2Fs12039-011-0189-x
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, e32479.
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http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0032479
Shaikh SA, Jain T, Sandhu G, Soni, A, Jayaram B. From drug target to leads-sketching a physicochemical pathway for lead molecule design in Silico. Frontiers in Medicinal Chemistry, 2012, 6, 324-360. Eds: Atta ur Rahman, Allen B. Reitz and M. Iqbal Choudhary, Bentham Publishers.
doi:10.2174/97816080546401120601
http://www.benthamscience.com/ebooks/Sample/9781608054640-sample.pdf
Prateek Pandya, Surendra P. Gupta, Kumud Pandav, Ritu Barthwal, B. Jayaram and Surat Kumar, "DNA Binding Studies of Vinca Alkaloids: Experimental and Computational Evidence", Natural Product Communications, 2012, 7, 305-309.
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http://europepmc.org/abstract/MED/22545401
M. M. Gromiha, N. Saranya, S. Selvaraj, B. Jayaram and Kazuhiko Fukui, "Sequence and structural features of binding site residues in protein-protein complexes: comparison with protein-nucleic acid complexes", Proteome Science, 2011, 9, S13.
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http://www.proteomesci.com/content/9/S1/S13
B. Jayaram, Tanya Singh, and Marcia Fenley, "DNA-Drug Interactions: A Theoretical Perspective" in "Methods for Studying DNA/Drug Interactions", Eds, Dr. Meni Wanunu & Prof. Yitzhak Tor, 2011, Ch-14, 317-338, CRC Press.
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Tanya Singh, D. Biswas, and B. Jayaram, “AADS - An automated active site identification, docking and scoring protocol for protein targets based on physico-chemical descriptors”, J. Chem. Inf. Modeling, 2011, 51, 2515-2527.
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http://pubs.acs.org/doi/abs/10.1021/ci200193z
A. Mittal and B. Jayaram, "Backbones of folded proteins reveal novel invariant amino-acid neighborhoods", J. Biomol. Struc. Dyn., 2011, 28, 443-454.
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http://www.tandfonline.com/doi/abs/10.1080/073911011010524954
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, 28, 669-674.
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http://www.jbsdonline.com/The-Newest-View-on-Protein-Folding-Stoichiometric-and-Spatial-Unity-in-Structural-and-Functional-Diversity-p17965.html
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. Comput. Chem., 2011, 32, 893-907. http://onlinelibrary.wiley.com/doi/10.1002/jcc.21671/abstract
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, 28, 133-142. |
M. O. Fenley, R. Harris, B. Jayaram, and A. H. Boschitsch, "Revisiting the association of cationic groove-binding drugs to DNA using a poisson-boltzmann approach", Biophys J., 2010, 99, 879-886. |
G. Khandelwal, and B. Jayaram, "A Phenomenological model for predicting melting temperatures of DNA sequences", PLoS One , 2010, 5, e12433. |
P. Pandya, Md. M. Islam, G. S. Kumar, B. Jayaram, and S. Kumar, "DNA minor groove binding of small molecules: experimental and computational evidence", J. Chemical Sciences, 2010, 122, 247-257. |
S. R. Shenoy and B. Jayaram, "Proteins: sequence to structure and function- current Status", Current Protein and Peptide Science, 2010, 11, 498-514. |
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, 38, 299-313.
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http://nar.oxfordjournals.org/content/38/1/299.long
B. Jayaram, "Decoding the design principles of amino acids and the chemical logic of protein sequences", Nature Precedings, 2008.
http://precedings.nature.com/documents/2135/version/1
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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, 4173-4183.
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http://www.cell.com/biophysj/retrieve/pii/S0006349508700754
Gupta, A. Gandhimathi, P. Sharma, and B. Jayaram, "ParDOCK: An all atom energy based monte carlo docking protocol for protein-ligand complexes", Protein and Peptide Letters, 2007, 14, 632-646.
http://www.eurekaselect.com/78655/article
S. A. Shaikh, T. Jain, G. Sandhu, N. Latha, and B. Jayaram, "From drug target to leads- sketching, A physicochemical pathway for lead molecule design in silico", Curr. Pharma. Des., 2007, 13, 3454-3470.
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http://www.eurekaselect.com/66010/article
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.
http://pubs.acs.org/doi/abs/10.1021/jm060542c
T. Jain, and B. Jayaram, "A computational protocol for predicting the binding affinities of zinc containing metalloprotein-ligand complexes", PROTEINS: Struct. Funct. Bioinfo., 2007, 67, 1167-1178.
http://onlinelibrary.wiley.com/doi/10.1002/prot.21332/abstract
L. Thukral, S. R. Shenoy, K. Bhusan and B.Jayaram, "ProRegIn: A regularity index for the selection of native-like tertiary structures of proteins", J. Biosci., 2007, 32, 71-81.
http://www.ncbi.nlm.nih.gov/pubmed/17426381
M. Vidyasagar, et al. BioSuite: A comprehensive bioinfromatics software package (a unique industry -academia collaboration), Current Science, 2007, 92, 29-38.
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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, 1147-1152.
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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.
http://nar.oxfordjournals.org/content/34/21/6195.long
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, 78-85.
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http://pubs.acs.org/doi/abs/10.1021/ci050119x
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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http://www.niscair.res.in/sciencecommunication/researchjournals/rejour/ijca/ijca2k6/ijca_jan06.asp#p21
P. Narang, K. Bhushan, S. Bose, and B. Jayaram, "Protein structure evaluation using an all-atom energy based empirical scoring function", J. Biomol. Str. Dyn., 2006, 23,385-406.
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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http://www.febsletters.org/article/S0014-5793%2805%2901291-3/abstract
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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http://pubs.rsc.org/en/content/articlelanding/2005/CP/b502226f
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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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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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.
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http://www.tandfonline.com/doi/abs/10.1080/07391102.2004.10506969
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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http://www.annualreviews.org/doi/abs/10.1146/annurev.biophys.33.110502.140414
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.
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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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