Selected List of Publications



2017
Ehtesham Jameel, Poonam Meena, Mudasir Maqbool, Jitendra Kumar, Waqar Ahmed, Syed Mumtazuddin, Manisha Tiwari, Nasimul Hoda, B Jayaram "Rational design, synthesis and biological screening of triazine-triazolopyrimidine hybrids as multi target anti-Alzheimer agents", European Journal of Medicinal Chemistry, 2017, 136, 36-51.
https://www.ncbi.nlm.nih.gov/pubmed/28478343

Tanya Singh, B Jayaram, Olayiwola Adedotun Adekoya "Computational Approaches to Matrix Metalloprotease Drug Design", Matrix Metalloproteases: Methods and Protocols, 2017, 1579, 273-285.
https://link.springer.com/protocol/10.1007/978-1-4939-6863-3_15

Anjali Soni, Pooja Khurana, Tanya Singh, B. Jayaram, "A DNA Intercalation Methodology for an Efficient Prediction of Ligand Binding Pose and Energetics", Bioinformatics, 2017.
https://doi.org/10.1093/bioinformatics/btx006

2016
Ankita Singh, Akhilesh Mishra, Ali Khosravi, Garima Khandelwal, B. Jayaram, "Physico-chemical fingerprinting of RNA Genes", Nucleic Acids Research2016.
DOI: 10.1093/nar/gkw1236

Pradeep Pant, Saher Afshan Shaikh, B. Jayaram, "Design and Characterization of Symmetric Nucleic Acids via Molecular Dynamics Simulations", Biopolymers, 2016.
DOI: 10.1002/bip.23002

Debarati Das Gupta, Rahul Kaushik, B. Jayaram, "Protein folding is a convergent problem!", Biochemical and Biophysical Research Communications, 2016, 480 (4), 741-44.
http://dx.doi.org/10.1016/j.bbrc.2016.10.119.

Ashutosh Shandilya, Nasimul Hoda, Sameena Khan, Ehtesham Jameel, Jeetendra Kumar, B. Jayaram "De novo lead optimization of triazine derivatives identifies potent antimalarials" Journal of Molecular Graphic and Modelling,  2016, 71, 96-103.
10.1016/j.jmgm.2016.10.022

Navneet Tomar, Akhilesh Mishra, Nirotpal Mrinal and B. Jayaram, "Onco-Regulon: An Integrated database and software suite for site specific targeting of transcription factors of cancer genes", Database,  2016, 116.
DOI:10.1093/database/baw116

Rahul Kaushik and B. Jayaram "Structural difficulty index: A reliable measure for modelability of protein tertiary structures", Protein Engineering Design and Selection, 2016, 29(9), 391-97.
doi: 10.1093/protein/gzw025
DOI: 10.3410/f.726444057.793520369

Parvez Khan, Ashutosh Shandilya, B. Jayaram, Asimul Islam, Faizan Ahmad & Md.Imtaiyaz Hassan "Effect of pH on the Stability of Hemochromatosis Factor E: A Combined Spectroscopic and Molecular Dynamics Simulation Based Study", Journal of Biomolecular Structure and Dynamics, 2016.
doi: 10.1080/07391102.2016.1189359

Mudasir Maqbool, Apra Manral, Ehtesham Jameel, Vikas Saini, Ashutosh Shandilya, Manisha Tiwari, Nasimul Hoda, B Jayaram,"Development of cyanopyridine-triazine hybrids as lead multitarget anti-Alzheimer agents", Bioorganic and Medicinal Chemistry, 2016 24 (12), 2777-88.
doi:10.1016/j.bmc.2016.04.041

Jitendra Kumar, Poonam Meena, Anju Singh, Ehtesham Jameel, Mudasir Maqbool, Mohammad Mobashir, Ashutosh Shandilya, Manisha Tiwari, Nasimul Hoda, B Jayaram, "Synthesis and screening of triazolopyrimidine scaffold as multi-functional agents for Alzheimer's disease therapies" European Journal of Medicinal Chemistry, 2016, 119, 260-77.
doi: http://dx.doi.org/10.1016/j.ejmech.2016.04.053

Ashutosh Shandilya, M. Ganesan, F. Parveen, Namakkal G. Ramesh and B. Jayaram, "Molecular basis for the affinity and specificity in the binding of amino modified five-membered iminocyclitols with glycosidases: An experimental and theoretical synergy", Carbohydrate Research, 2016, 429, 87-97.
doi:10.1016/j.carres.2016.03.010

Anjeeta Rani, Abhilash Jayaraj, B. Jayaram, Pannuru Venkatesu, "Trimethylamine-*N*-oxide switches from stabilizing nature: A mechanistic outlook through experimental techniques and molecular dynamics simulation", Scientific Reports (NPG), 2016, 6, 23656.
doi:10.1038/srep23656

Joy L. Nishikawa, Andras Boeszoermenyi, Luis A. Vale-Silva, Riccardo Torelli, Brunella Posteraro, Yoo-Jin Sohn, Fei Ji, Vladimir Gelev, Dominique Sanglard, Maurizio Sanguinetti, Ruslan I. Sadreyev, Goutam Mukherjee, Jayaram Bhyravabhotla, Sara J. Buhrlage, Nathanael S. Gray, Gerhard Wagner, Anders M. Naar & Haribabu Arthanari "Inhibiting fungal multidrug resistance by disrupting an activator-Mediator interaction". Nature  2016, 530, 485- 489.
doi:10.1038/nature16963

2015
H Naz, E Jameel, N Hoda, A Shandilya P Khan, A Islam,F Ahmad, B. Jayaram, I Hassan "Structure guided design of potential inhibitors of human calcium-calmodulin dependent protein kinase IV containing pyrimidine scaffold". Bioorganic and medicinal chemistry letters 2015
doi:10.1016/j.bmcl.2015.12.098

Ankita Singh, Rahul Kaushik, Avinash Mishra, Asheesh Shanker and B. Jayaram "ProTSAV: A Protein Tertiary Structure Analysis and Validation Server", BBA - Proteins and Proteomics, 2015. Volume 1864, Issue 1, January 2016, Pages 11 - 19.
DOI: 10.1016/j.bbapap.2015.10.004

Debarati DasGupta, Rahul Kaushik, and B. Jayaram "From Ramachandran Maps to Tertiary Structures of Proteins",J. Phys. Chem. B , 2015 . 119 (34), pp 11136 - 11145.
DOI: 10.1021/acs.jpcb.5b02999

Nasimul Hodaa, Huma Nazb, Ehtesham Jameel, Ashutosh Shandilya, Sarmishtha Dey, Md. Imtaiyaz Hassan*, Faizan Ahmad & B. Jayaram, "Curcumin Specifically binds to the Human Calcium-calmodulin Dependent Protein Kinase IV: Fluorescence and Molecular Dynamics Simulation Studies", Journal of Biomolecular Structure and Dynamics, 2015.
DOI:10.1080/07391102.2015.1046934

G. Mukherjee, P. L. Gupta, B. Jayaram, "Predicting the binding modes and sites of metabolism of xenobiotics", *Molecular BioSystems*, 2015, 11, 1914 - 1924.
DOI:10.1039/C5MB00118H

Tanya Singh, Olayiwola Adedotun Adekoya, B. Jayaram, "Understanding the binding of inhibitors of Matrix Metalloproteinases by molecular docking, quantum mechanical calculations, molecular dynamics simulations, and a MMGBSA/MMBappl study", Mol. BioSyst., 2015, 11, 1041-1051. Advance Article
http://pubs.rsc.org/en/content/articlepdf/2015/mb/c5mb00003c

2014
B Jayaram, Priyanka Dhingra, Avinash Mishra, Rahul Kaushik, Goutam Mukherjee, Ankita Singh and Shashank Shekhar, "Bhageerath-H: A homology ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins", BMC Bioinformatics, 2014, 15(Suppl 16):S7 (8 December 2014).
http://www.biomedcentral.com/1471-2105/15/S16/S7

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 )

2013

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
http://www.nature.com/srep/2013/130206/srep01225/full/srep01225.html

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,
Read Article


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

2012

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.
Read Article
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.
Read Article
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.
Read Article
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.
Read Article
http://europepmc.org/abstract/MED/22545401

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, 13-35.
Read Article
2011

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.
Read Article
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.
Read Article

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.
Read Article
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.
Read Article
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.
Read Article
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


2010

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.
http://www.tandfonline.com/doi/abs/10.1080/07391102.2010.10507349
Download Supplementary files1  Supplementary files2   Primary Contact Data.xls

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. 
Read Article
http://www.cell.com/biophysj/retrieve/pii/S0006349510006016

G. Khandelwal, and B. Jayaram, "A Phenomenological model for predicting melting temperatures of DNA sequences", PLoS One , 20105, e12433.
http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012433

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.
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S. R. Shenoy and B. Jayaram, "Proteins: sequence to structure and function- current Status", Current Protein and Peptide Science2010, 11, 498-514.
Read Article
http://www.eurekaselect.com/87294/article

2009

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.
Read Article
http://nar.oxfordjournals.org/content/38/1/299.long

2008

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
Download Supplementary Pdf


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.
Read Article
http://www.cell.com/biophysj/retrieve/pii/S0006349508700754

 

2007

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. 
Read Article
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.
Read Article 


  2006

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.
Read Article 

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.
Read Article 
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.
Read Article 
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.

http://www.tandfonline.com/doi/abs/10.1080/07391102.2006.10531234

  2005

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.
Read Article
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.
Read Article
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.
Read Article

http://www.eurekaselect.com/90329/article/binding-affinity-based-computational-pathway-active-site-directed-lead-molecule-design
  2004

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.
Read Article
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.
Read Article
http://www.annualreviews.org/doi/abs/10.1146/annurev.biophys.33.110502.140414

 
2002 and before ( i.e. before inauguration of SCFBio on 31st July, 2002 )

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.
Read Full Text

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.
Read Full Text


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.
Read Full Text

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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* Publications in red color have more than 50 citations.


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