| 2023
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| Shrivastav, Gourav and Borkotoy, Subhomoi and Dey, Debajit and Singh, Bhumika and Katyal, Nidhi and Azad, Kimi and Jayaram, B and Agarwal, Manish and Banerjee, Manidipa, Structure and Energetics Guide Dynamic Behaviour in a T=3 Icosahedral Virus Capsid. 2023. DOI: https://doi.org/10.1016/j.bpc.2023.107152 |
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Jayaram, B., and Devendra Prajapat. "Molecular dynamics in predicting the stability of drug-receptor interactions." Cheminformatics, QSAR and Machine Learning Applications for Novel Drug Development. Academic Press, 2023. 393-437. DOI:10.1016/B978-0-443-18638-7.00012-8. |
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Shashank Shekhar, Sanjay Dhir, James Gomes, B. Jayaram; "Academic Bioinformatics activities joining hands with Entrepreneurial Ventures: A way to go in Life Science Research (Case Studies from Indian academia, start-ups, and the life science sector)", Int. J. of Research, Innovation and Commercialisation, 2023. (Accepted) Read Abstract |
Surbhi Sharma, Pradeep Pant, Ranjana Arya, Bhyravabhotla Jayaram, Hirendra Kumar Das; "Bases immediate upstream of the TATAAT box of the sigma 70 promoter of Escherichia coli significantly influence the activity of a model promoter by altering the bending angle of DNA", Gene, 2023. |
Dinesh Sharma, Kopal Sharma, Akhilesh Mishra, Priyanka Siwach, Aditya Mittal, B. Jayaram; "Molecular Dynamics simulation based trinucleotide and tetranucleotide level structural and energy characterization of functional units of genomic DNA", Physical Chemistry Chemical Physics (PCCP), 2023. | 2022
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Pradeep Pant , Amita Pathak , B Jayaram;"Bicyclo-DNA mimics with enhanced protein binding affinities: insights from molecular dynamics simulations", Journal of Biomolecular Structure and Dynamics, 2022. |
Sahar Qazi, Bimal Prasad Jit, Abhishek Das, Muthukumarasamy Karthikeyan, Amit Saxena, M.D. Ray, Angel Rajan Singh, Khalid Raza, B. Jayaram, Ashok Sharma;"BESFA: bioinformatics based evolutionary, structural & functional analysis of prostate, Placenta, Ovary, Testis, and Embryo (POTE) paralogs",Heliyon, 2022. |
Kiruthika, S.; Bhat, Ruchika; Jayaram, B.; Vivekanandan,Perumal, "A small molecule targeting Hepatitis B surface antigen inhibits clinically relevant drug-resistant hepatitis B virus", Journal of Antimicrobial Chemotherapy, 2022. Manuscript ID: JAC-2021-1583.R2 | 2021
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Amita Pathak, B.Jayaram, "Seq2Enz: An application of mask BLAST methodology with a new chemical logic of amino acids for improved enzyme function prediction", Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 2021. |
S. Kiruthika, Bhat Ruchika, Rozaleen Dash, A. S. Rathore, Perumal Vivekanandan, B. Jayaram, "A Novel Piperazine derivative that targets Hepatitis B Surface Antigen effectively inhibits Tenofovir Resistant Hepatitis B Virus", Scientific Reports, 2021. |
Pradeep Pant and B. Jayaram, "A rapid computational screening of millions of molecules to identify sequence-specific DNA minor groove binders via physico-chemical descriptors", Biophysical and computational tools in drug discovery, Topics in Medicinal Chemistry, Springer Nature Switzerland AZ, Editor: Anil K Saxena, 2021, in press. |
| Ravi Jasuja, Daniel Spencer, Abhilash Jayaraj, Liming Peng, Meenakshi Krishna, Brian Lawney, Priyank Patel, B. Jayaram, Kelly M. Thayer, David L. Beveridge, Shalender Bhasin, "Estradiol induces Allosteric Coupling and Partitioning of Sex Hormone BindingGlobulin Monomers Among Conformational States", iScience, 102414, 2021. https://doi.org/10.1016/j.isci.2021.102414 |
| Pradeep Pant , Amita Pathak , B Jayaram; "Symmetric Nucleosides as Potent Purine Nucleoside Phosphorylase Inhibitors"
J. Phys. Chem., 2021. DOI: 10.1021/acs.jpcb.0c10553 |
| P. Amita; R. Toran; E. Avinash; B. Jayaram; "MASK BLAST WITH A NEW CHEMICAL LOGIC OF AMINO ACIDS FOR IMPROVED PROTEIN FUNCTION PREDICTION: Protein Function Prediction using New Chemical Logic", Proteins: Structure, Function, and Bioinformatics , 2021.https://doi.org/10.1002/prot.26069 |
| Akhilesh Mishra, Priyanka Siwach, Pallavi Misra, Simran Dhiman, Ashutosh Kumar Pandey, Parul Srivastava, B Jayaram, "Intron exon boundary junctions in human genome have in-built unique structural and energetic signals", Nucleic Acids Research, Oct. 2021. https://doi.org/10.1093/nar/gkab098 | 2020
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| Stefan Holderbach, Lukas Adam, B Jayaram, Rebecca C. Wade and Goutam Mukherjee, "RASPD+: Fast protein-ligand binding free energy prediction using simplified physicochemical features", Front. Mol. Biosci., 2020. https://doi: 10.3389/fmolb.2020.601065 |
| Ankita Singh, Shashank Shekhar, B. Jayaram,"CADD: Some success stories from Sanjeevini and the way forward", in Innovations and Implementations of Computer Aided Drug Discovery Strategies in Rational Drug Design", Springer Nature, Singapore Pte Ltd. S. K. Singh (ed.), 2020. https://doi.org/10.1007/978-981-15-8936-2_1 |
| Amita Pathak, Bhumika Singh, Dheeraj Kumar Chaurasia and B. Jayaram, "Molecular Simulation Driven Drug Repurposing for Identification of Inhibitors Against Non-Structural Proteins of SARS-CoV-2", SpringerProtocols In Silico Modeling of Drugs Against Coronaviruses - Computational Tools and Protocols, Editor: Prof. Kunal Roy, 2020. https://doi.org/10.1007/7653_2020_61 |
| Abhilash Jayaraj, B. Jayaram, Ravi Jasuja et al., "Allosterically coupled multi-site binding of testosterone to human serum albumin", Endocrinology, accepted for publication, Volume 162, Oct. 2020.https://doi.org/10.1210/endocr/bqaa199 |
| Fereshteh Mataeimoghadam, M. A. Hakim Newton, Abdollah Dehzangi, Abdul Karim, B. Jayaram, Shoba Ranganathan and Abdul Sattar, "Enhancing Protein Backbone Angle Prediction by Using Simpler Models of Deep Neural Networks", Scientific Reports, accepted for publication, volume 10, Oct. 2020. https://doi.org/10.1038/s41598-020-76317-6 |
| Praveen Kumar Tripathi, Anjali Soni, Shiv Pratap Singh Yadavd, Ankit Kumar,Nitika Gaurav, SivaRB, Pradeep Sharma, Sujatha Sunil, Ashish, Bhyravabhotla Jayaram, Ashok Kumar Patel "Evaluation of novobiocin and telmisartan for anti-CHIKV activity", Virology, available online 18 June 2020. https://doi.org/10.1016/j.virol.2020.05.010 |
| Ankita Singh, Rahul Kaushik, Dheeraj Kumar Chaurasia, Manpreet Singh, B Jayaram "PvP01-DB: computational structural and functional characterization of soluble proteome of PvP01 strain of Plasmodium vivax", Database , Volume 2020, 2020. https://doi.org/10.1093/database/baaa036 |
| Ruchika Bhat, Rahul Kaushik, Ankita Singh, Debarati DasGupta, Abhilash Jayaraj, Anjali Soni, Ashutosh Shandilya, Vandana Shekhar, Shashank Shekhar, B. Jayaram, " A comprehensive automated computer-aided discovery pipeline from genomes to hit molecules" Chemical Engineering Science, 2020. https://doi.org/10.1016/j.ces.2020.115711 | .
| Anjali Soni, Ruchika Bhat, B. Jayaram, "Improving the binding affinity estimations of protein-ligand complexes using machine-learning facilitated force field method" J Comput Aided Mol Des, 2020. https://doi.org/10.1007/s10822-020-00305-1 |
| 2019
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| Akhilesh Mishra, Sahil Dhanda, Priyanka Siwach, Shruti Aggarwal, B. Jayaram, "A novel method SEProm for prokaryotic promoter prediction based on DNA structure and energetics", Bioinformatics, 2019. doi/10.1093/bioinformatics/btz941/5697916 |
| Ruchika Bhat, Abhilash Jayaraj, Anjali Soni and B. Jayaram, An overview of protein-ligand docking and scoring algorithms, (Accepted for Publication), 2019, pg: 371-389, World Scientific Publishing Singapore, Editor: Michael Gromiha M. https://doi.org/10.1142/11596 |
| 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, 2019, Humana Press 1962, eBook ISBN 978-1-4939-9173-0, Pages 121-138. https://www.springer.com/gp/book/9781493991723 | 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, accepted for publication. https://doi.org/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 | 2018
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| Kamalika Banerjee, Ruchika Bhat, V. U. Bhaskara Rao, Anshu Nain, Kartik Lakshmi Rallapalli, Sohona Gangopadhyay, R. P. Singh, Manidipa Banerjee, B. Jayaram, "Towards development of generic inhibitors against the 3C proteases of picornaviruses", The FEBS Journal, 2018, Volume 286 (2019), pg. 765-787. DOI:https://doi.org/10.1111/febs.14707 |
| A. Mishra, P. Siwach, P. Misra, B. Jayaram, M. Bansal, W.K. Olson, K.M. Thayer, D.L.Beveridge,"Towards a universal structural and energetic
model for prokaryotic promoters", Biophysical Journal, 2018,115(7): 1180-1189. DOI:10.1016/j.bpj.2018.08.002 |
| Avinash Mishra, Shoba Ranganathan, B. Jayaram, and Abdul Sattar, "Role of solvent accessibility for aggregation-prone patches in protein folding",Scientific Reports, volume 8, Article number: 12896, 2018. doi.org/10.1038/s41598-018-31289-6 |
| Akhilesh Mishra, Pradeep Pant, B. Jayaram, "Onco-Plus: an integrated database and computational protocol for discovery of lead molecules targeting unique DNA", J Mol Genet Med, 2018,12:92. DOI: 10.4172/1747-0862-C2-028 |
| Akhilesh Mishra, Pradeep Pant, B. Jayaram, "Generating hit molecules against pathogenic DNA motifs in silico",Atlas of Science, 2018. http://atlasofscience.org/generating-hit-molecules-against-pathogenic-dna-motifs-in-silico |
| Jayaraj A., Bhat R., Pathak A., Singh M., Jayaram B. "Development of a Web-Server for Identification of Common Lead Molecules for Multiple Protein Targets". In: Methods in Pharmacology and Toxicology. Humana Press, 2018: 1-18. DOI: 10.1007/7653_2018_9 |
| Singh,A., Kaushik,R., Kuntal,H. et al. "PvaxDB: a comprehensive structural repository of Plasmodium vivax proteome". Database, 2018. Vol.2018: doi:10.1093/database/bay021. |
| Rahul Kaushik, Ankita Singh and B. Jayaram. "Where informatics lags chemistry leads".Biochemistry, 2018, 55(5): 503-505. DOI: 10.1021/acs.biochem.7b01073 |
| Ankita Singh, Rahul Kaushik, B. Jayaram. "Quality Assessment of Protein Tertiary Structures: Past, Present and Future". Bioinformatics: Sequences, Structures, Phylogeny. Springer Publishers, 2018. ISBN: 978-981-13-1561-9. https://doi.org/10.1007/978-981-13-1562-6_12 |
| Rahul Kaushik, Ankita Singh and B. Jayaram. Ab initio "Protein Structure Prediction. Reference Module in Life Sciences", 2018. Elsevier, ISBN: 978-012-80-9633-8. DOI: 10.1016/B978-0-12-809633-8.20321-X |
2017
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| Pawan Kumar, Ashutosh Shandilya, B. Jayaram and Indira Ghosh, "Integrative Method for Finding Antimalarials Using In Silico Approach", Computer Design for New Drugs and Materials: Molecular Dynamics of Nanoscale Phenomena,pp. 21-58, Ch-2 Editor: Kholmirzo T. Kholmurodov, Nova Science Publishers, 2017. ISBN:978-153612101-8, 978-153612082-0. |
| Rahul Kaushik, Ankita Singh and B Jayaram, "A new chemical logic of amino acids for improved protein tertiary structure prediction", Biochemistry and Analytical Biochemistry, 2017, 6:3 (Suppl) DOI: 10.4172/2161-1009-C1-014 |
| Ankita Singh, Rahul Kaushik and B. Jayaram, "ProTSAV+: A meta-server for identification and scoring of protein tertiary structures", Biochemistry and Analytical Biochemistry, 2017, 6:3 (Suppl) DOI: 10.4172/2161-1009-C1-014 |
| Jitendra Kumar,Asim Gill,Marziya Shaikh,Anju Singh, Ashutosh Shandilya, Ehtesham Jameel, Nitin Sharma, Nirotpal Mrinal, Nasimul Hoda, B. Jayaram, "Pyrimidine-Triazolopyrimidine and Pyrimidine-Pyridine Hybrids as Potential Acetylcholinesterase Inhibitors for Alzheimer's Disease", Chemistry Select: Medicinal Chemistry & Drug Discovery, 2017. https://doi.org/10.1002/slct.201702599 |
| Debarati DasGupta, B.Jayaram,"Molecular Origins of convergence and uniqueness of protein structures" Atlas of Science, 2017. https://atlasofscience.org/molecular-origins-of-convergence-and-uniqueness-of-protein-structures |
| Rahul Kaushik, Ankita Singh and B. Jayaram, "Algorithms for structure comparison and analysis: ab initio protein structure prediction", Elsevier Reference Module: Encyclopedia of Bioinformatics and Computational Biology, 2017. |
| B. Jayaram, "Breaking Barriers through Bioinformatics & Computational Biology", Guest Editorial, J. Proteins & Proteomics, 2017, 8(3). |
| Seema Bhatnagar, Anjali Soni, Swati Kaushik, Megha Rikhi, T R Santhosh Kumar, B. Jayaram, "Non-steroidal estrogen receptor iso form selective biphenyls", Chemical Biology & Drug Design, 2017. DOI: 10.1111/cbdd.13126 |
| Debarati DasGupta, Mandalaparthy Varun, B. Jayaram, "A component analysis of the free energies of folding of 35 proteins: A consensus view on the thermodynamics of folding at the molecular level",J. Computational Chemistry, 2017, 38(32), 2791-2801. DOI:10.1002/jcc.25072 |
| Akhilesh Mishra, Pradeep Pant, Nirotpal Mrinal and B. Jayaram, .A Computational protocol for the discovery of lead molecules targeting DNA unique to pathogens, Methods , 2017,131: 4-9. https://doi.org/10.1016/j.ymeth.2017.07.017 |
| 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
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| Ankita Singh, Akhilesh Mishra, Ali Khosravi, Garima Khandelwal, B. Jayaram, "Physico-chemical fingerprinting of RNA Genes", Nucleic Acids Research, 2016, 45 (7), e47. 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. doi: 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. doi: 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, baw116. doi:10.1093/database/baw116 |
| Rahul Kaushik, 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. |
| 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 doi:10.1038/nature16963 | 2015
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| 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
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| 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
. |
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 |
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. |
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. |
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.
|
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. |
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. |
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, |
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 |
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. |
| 2012
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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. |
B. Jayaram and Priyanka Dhingra, "Towards creating complete proteomic structural databases of whole organisms", Current Bioinformatics, 2012, 7, 424-435. |
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. |
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. |
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. |
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. |
Aditya Mittal, and B. Jayaram, "A possible molecular metric for biological evolvability", J. Bio Sc., 2012, 37, 573-577. |
Garima Khandelwal, Jalaj Gupta and B. Jayaram, "DNA energetics based analyses suggest additional genes in prokaryotes" J. Bio Sc., 2012, 37, 433-444. |
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. |
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. |
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. |
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. |
| 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
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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. |
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. |
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. |
A. Mittal and B. Jayaram, "Backbones of folded proteins reveal novel invariant amino-acid neighborhoods", J. Biomol. Struc. Dyn., 2011, 28, 443-454. |
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. |
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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Achintya Das & B.Jayaram,, "Brownian dynamics simulations of DNA-ligand interactions: a
theoretical study on the kinetics of DAPI-DNA complexation", Journal of Molecular Liquids 1998, Volume 77, Issues 1-3,, 157-163.
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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.