Publiction

2024

Publication (Preprint): B. Jayaram, Dinesh Sharma, Danish Aslam et al. Exon-Intron Boundary Detection Made Easy by Physicochemical Properties of DNA, 26 May 2024, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.rs-4359229/v1]
The tool is available publicly on GitHub (along with Readme) and is freely accessible at: https://github.com/rnsharma478/ChemEXIN

2023

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

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.

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.
DOI: https://doi.org/10.1016/j.gene.2022.146968

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.
DOI: https://doi.org/10.1039/D2CP04820E

2022

Devendra Prajapat and B. Jayaram, "Molecular Dynamics in Predicting Stability of Drug-Receptor Interactions", European Journal of Medicinal Chemistry, 2022. Editor: Kunal Roy,Enterprise Product Manager: Tim Eslava.
Book Chapter
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.
https://doi.org/10.1080/07391102.2022.2061594
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.
https://doi.org/10.1016/j.heliyon.2022.e10476
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

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.
https://doi.org/10.1016/j.bbapap.2021.140721
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.
https://doi.org/10.1038/s41598-021-91196-1
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.
Read Abstract
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

Devendra Prajapat and B. Jayaram, "Molecular Dynamics in Predicting Stability of Drug-Receptor Interactions", European Journal of Medicinal Chemistry, 2022. Editor: Kunal Roy,Enterprise Product Manager: Tim Eslava.
Book Chapter
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.
https://doi.org/10.1080/07391102.2022.2061594
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, .
https://doi.org/10.1016/j.heliyon.2022.e10476

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

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 2019, Humana Press 1962, eBook ISBN 978-1-4939-9173-0.

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. doi: 10.1074/jbc.RA118.002502jbc.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

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.
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, accepted, 2018.
Read Abstract

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.
http://www.scfbio-iitd.res.in/publication/Abstract_Bio_Seq_Str.pdf

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

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.

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.
DOI: 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

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

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.
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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

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.
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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.
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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

 

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 , 2010, 5, 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. Read Article

S. R. Shenoy and B. Jayaram, "Proteins: sequence to structure and function- current Status", Current Protein and Peptide Science, 2010, 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.
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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.
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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. 
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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.
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.
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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.

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.
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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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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.
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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