Publications

326 entries « 3 of 7 »

2016

101.

Effects of point mutations on the thermostability of B. subtilis lipase: investigating nonadditivity Journal Article

Abhijit Mitra

Bipin Singh, Gopalakrishnan Bulusu, Abhijit Mitra

Journal of computer-aided molecular design, 30 , 899–916 (2016)

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102.

Regulatory checkpoint remodeling during experimental evolution of flagellar motility Journal Article

Bhaswar Ghosh

Bin Ni, Bhaswar Ghosh, Ferencz S. Pop, Remy Colin, Thomas Heimerl, Victor Sourjik

Cell Report, 18 , 1–12 (2016)

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103.

Sugar Influx Sensing by the Phosphotransferase System of Escherichia coli. Journal Article

Bhaswar Ghosh

Somavanshi R, Bhaswar Ghosh, Sourjik V

PLoS Biol, 14 (8), e2000074. (2016)

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104.

Structure, interaction, and dynamics of Au/Pd bimetallic nanoalloys dispersed in aqueous ethylpyrrolidone, a monomeric moiety of polyvinylpyrrolidone Journal Article

U. Deva Priyakumar

Aditi Gupta, Bundet Boekfa, Hidehiro Sakurai, Masahiro Ehara, U. Deva Priyakumar

The Journal of Physical Chemistry C, 120 , 17454–17464 (2016)

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105.

Observing Ultra‐Small Gold Cluster to Plasmonic Nanoparticle Evolution in a One‐Pot Aqueous Synthesis Journal Article

Tapan kumar Sau

Shweta Bhardwaj, Ramakrishna Itteboina, Tapan kumar Sau

ChemistrySelect, 1 , 3091-3096 (2016)

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106.

Probing compositeness with the CMS eejj & eej data Journal Article

Subhadip Mitra

Tanumoy Mandal, Subhadip Mitra, Satyajit Seth

Physics Letters B, 758 , 219-225 (2016)

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107.

NAPS: Network analysis of protein structures Journal Article

Nita Parekh

Broto Chakrabarty, Nita Parekh

Nucleic acids research, 44 , W375–W382 (2016)

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108.

Ligand-induced stabilization of a duplex-like architecture is crucial for the switching mechanism of the SAM-III riboswitch Journal Article

U. Deva Priyakumar

Gorle Suresh, Harini Srinivasan, Shivani Nanda, U. Deva Priyakumar

Biochemistry, 55 , 3349–3360 (2016)

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109.

Cooperation of hydrophobic gating, knock-on effect, and ion binding determines ion selectivity in the p7 channel Journal Article

U. Deva Priyakumar

Siladitya Padhi, U. Deva Priyakumar

The Journal of Physical Chemistry B, 120 , 4351–4356 (2016)

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110.

Dynamic ligand-based pharmacophore modeling and virtual screening to identify mycobacterial cyclopropane synthase inhibitors Journal Article

U. Deva Priyakumar

Chinmayee Choudhury, U. Deva Priyakumar, G Narahari Sastry

Journal of Chemical Sciences, 128 , 719–732 (2016)

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111.

Structural and Functional Diversities of the Hexadecahydro‐1H‐cyclopenta [a] phenanthrene Framework, a Ubiquitous Scaffold in Steroidal Hormones Journal Article

U. Deva Priyakumar

Chinmayee Choudhury, U. Deva Priyakumar, G Narahari Sastry

Molecular Informatics, 35 , 145-157 (2016)

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112.

Ability of density functional theory methods to accurately model the reaction energy pathways of the oxidation of CO on gold cluster: A benchmark study Journal Article

U. Deva Priyakumar

Saumya Gurtu, Sandhya Rai, Masahiro Ehara, U. Deva Priyakumar

Theoretical Chemistry Accounts, 135 , 6693-7512 (2016)

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113.

Copy number variation detection workflow using next generation sequencing data Journal Article

Nita Parekh

Prashanthi Dharanipragada, Nita Parekh

BMC Bioinformatics, 15 , 55-60 (2016)

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114.

Pair production of scalar leptoquarks at the LHC to NLO parton shower accuracy Journal Article

Subhadip Mitra

Tanumoy Mandal, Subhadip Mitra, Satyajit Seth

Physical Review D, 93 , 035018 (2016)

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115.

Non-relativistic matter and dark energy in a quantum conformal model Journal Article

Subhadip Mitra

Gopal Kashyap, Pankaj Jain, Subhadip Mitra

Astroparticle Physics, 75 , 64-71 (2016)

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116.

Molecular Origins of Polymer-Coupled Helical Motion of Ions in a Crystalline Polymer Electrolyte Journal Article

Marimuthu Krishnan

Ramesh Cheerla, Marimuthu Krishnan

Macromolecules, 49 , 700–707 (2016)

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2015

117.

Sumoylation of Sir2 differentially regulates transcriptional silencing in yeast Journal Article

U. Deva Priyakumar

Abdul Hannan, Neethu Maria Abraham, Siddharth Goyal, Imlitoshi Jamir, U. Deva Priyakumar, Krishnaveni Mishra

Nucleic acids research, 43 , 10213–10226 (2015)

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118.

Modeling the structure of SARS 3a transmembrane protein using a minimum unfavorable contact approach Journal Article

U. Deva Priyakumar

S Ramakrishna, Siladitya Padhi, U. Deva Priyakumar

Journal of Chemical Sciences, 127 , 2159-2169 (2015)

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119.

The fine tuning of the cosmological constant in a conformal model Journal Article

Subhadip Mitra

Pankaj Jain, Gopal Kashyap, Subhadip Mitra

International Journal of Modern Physics A, 30 , 1550171 (2015)

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120.

On a boundary-localized Higgs boson in 5D theories Journal Article

Subhadip Mitra

Roberto Barceló, Subhadip Mitra, Grégory Moreau

The European Physical Journal C, 75 , 527 (2015)

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121.

ELKO fermions as dark matter candidates Journal Article

Subhadip Mitra

Bakul Agarwal, Pankaj Jain, Subhadip Mitra, Alekha C Nayak, Ravindra K Verma

Physical Review D, 92 , 075027 (2015)

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122.

Molecular dynamics study of the structure, flexibility, and hydrophilicity of PETIM dendrimers: a comparison with PAMAM dendrimers Journal Article

U. Deva Priyakumar

Subbarao Kanchi, Gorle Suresh, U. Deva Priyakumar, KG Ayappa, Prabal K Maiti

The Journal of Physical Chemistry B, 119 , 12990–13001 (2015)

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123.

Atomistic details of the molecular recognition of DNA-RNA hybrid duplex by ribonuclease H enzyme Journal Article

U. Deva Priyakumar

Gorle Suresh, U. Deva Priyakumar

Journal of Chemical Sciences, 127 , 1701-1713 (2015)

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124.

Supercritical Carbon Dioxide at Smectite Mineral-Water Interfaces: Molecular Dynamics and Adaptive Biasing Force Investigation of CO2/H2O Mixtures Nanoconfined in Na … Journal Article

Marimuthu Krishnan

Mohan Maruthi Sena, Christin P. Morrow, R. James James Kirkpatrick, Marimuthu Krishnan

Chemistry of Materials, 27 , 6946–6959 (2015)

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125.

Robustness of Chimera States in Non-locally Coupled Logistic Maps Journal Article

Nita Parekh

B Pranneetha, Nita Parekh

The Chaotic Modeling and Simulation Journal, 2 , 012217 (2015)

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126.

The role of N7 protonation of guanine in determining the structure, stability and function of RNA base pairs Journal Article

Abhijit Mitra

Antarip Halder, Sohini Bhattacharya, Ayan Datta, Dhananjay Bhattacharyya, Abhijit Mitra

Physical Chemistry Chemical Physics, 17 , 26249-26263 (2015)

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127.

Inclusion of methoxy groups inverts the thermodynamic stabilities of DNA–RNA hybrid duplexes: A molecular dynamics simulation study Journal Article

U. Deva Priyakumar

Gorle Suresh, U. Deva Priyakumar

Journal of Molecular Graphics and Modelling, 61 , 150-159 (2015)

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128.

Nucleobases tagged to gold nanoclusters cause a mechanistic crossover in the oxidation of CO Journal Article

U. Deva Priyakumar

Sandhya Rai, Masahiro Ehara, U. Deva Priyakumar

Physical Chemistry Chemical Physics, 17 , 24275-24281 (2015)

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129.

Double zipper helical assembly of deoxyoligonucleotides: mutual templating and chiral imprinting to form hybrid DNA ensembles Journal Article

U. Deva Priyakumar

Nagarjun Narayanaswamy, Gorle Suresh, U. Deva Priyakumar, T Govindaraju

Chemical Communications, 51 , 5493-5496 (2015)

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130.

Functional characterization of drought-responsive modules and genes in Oryza sativa: a network-based approach Journal Article

Nita Parekh

Sanchari Sircar, Nita Parekh

Frontiers in genetics, 6 , 3389 (2015)

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131.

Structure, Energetics, and Dynamics of Supercritical Carbon Dioxide at Smectite Mineral-Water Interfaces: Molecular Dynamics Modeling and Adaptive Force Investigation of CO2 … Journal Article

Marimuthu Krishnan

MM Sena, CP Morrow, RJ Kirkpatrick, Marimuthu Krishnan

Chem. Mater, 27 , 2256-3100 (2015)

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132.

NMR and computational molecular modeling studies of mineral surfaces and interlayer galleries: A review Journal Article

Marimuthu Krishnan

R James Kirkpatrick, Andrey G Kalinichev, Geoffrey M Bowers, A Özgür Yazaydin, Marimuthu Krishnan, Moumita Saharay, Christin P Morrow

American Mineralogist, 100 , 1341–1354 (2015)

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133.

Single productions of colored particles at the LHC: an example with scalar leptoquarks Journal Article

Subhadip Mitra

Tanumoy Mandal, Subhadip Mitra, Satyajit Seth

Journal of High Energy Physics, 28 , 2256-2262 (2015)

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134.

BREATH ACETONE-BASED NON-INVASIVE DETECTION OF BLOOD GLUCOSE LEVELS Journal Article

Tapan Kumar Sau

Anand Thati, Arunangshu Biswas, Shubhajit Roy Chowdhury, Tapan Kumar Sau

INTERNATIONAL JOURNAL ON SMART SENSING AND INTELLIGENT SYSTEMS, 8 , 665-721 (2015)

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135.

Ion hydration dynamics in conjunction with a hydrophobic gating mechanism regulates ion permeation in p7 viroporin from hepatitis C virus Journal Article

U. Deva Priyakumar

Siladitya Padhi, U. Deva Priyakumar

The Journal of Physical Chemistry B, 119 , 6204–6210 (2015)

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136.

Binding to gold nanoclusters alters the hydrogen bonding interactions and electronic properties of canonical and size-expanded DNA base pairs Journal Article

U. Deva Priyakumar

Sandhya Rai, Harjinder Singh, U. Deva Priyakumar

RSC Advances, 5 , 49408-49419 (2015)

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137.

Small-molecule inhibitors of ERK-mediated immediate early gene expression and proliferation of melanoma cells expressing mutated BRaf Journal Article

U. Deva Priyakumar

Ramin Samadani, Jun Zhang, Amanda Brophy, Taiji Oashi, U. Deva Priyakumar, E Prabhu Raman, Franz J St John, Kwan-Young Jung, Steven Fletcher, Edwin Pozharski, Alexander D MacKerell Jr, Paul Shapiro

Biochemical Journal, 467 , 425–438 (2015)

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138.

Dynamics based pharmacophore models for screening potential inhibitors of mycobacterial cyclopropane synthase Journal Article

U. Deva Priyakumar

Chinmayee Choudhury, U. Deva Priyakumar, G Narahari Sastry

Journal of chemical information and modeling, 55 , 848–860 (2015)

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139.

Prediction of the structures of helical membrane proteins based on a minimum unfavorable contacts approach Journal Article

U. Deva Priyakumar

Siladitya Padhi, Siddabattula Ramakrishna, U. Deva Priyakumar

Journal of computational chemistry, 36 , 539-552 (2015)

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140.

Model scenarios for switch-like mitotic transitions Journal Article

Vinod PK

Vinod PK , Bela Novak

FEBS letters, 589 , 667-671 (2015)

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141.

Dispersion interactions between urea and nucleobases contribute to the destabilization of RNA by urea in aqueous solution Journal Article

U. Deva Priyakumar

Koushik Kasavajhala, Swetha Bikkina, Indrajit Patil, Alexander D MacKerell Jr, U. Deva Priyakumar

The Journal of Physical Chemistry B, 119 , 3755–3761 (2015)

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142.

Theoretical studies of Raman scattering properties of methylphosphine and methylamine adsorbed on gold clusters Journal Article

Tapan Kumar Sau

Shweta Bhardwaj,Sandhya Rai,Tapan Kumar Sau,Harjinder Singh

Vibrational Spectroscopy, 76 , 38-47 (2015)

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143.

Understanding the Thermostability and Activity of Bacillus subtilis Lipase Mutants: Insights from Molecular Dynamics Simulations Journal Article

Abhijit Mitra

Bipin Singh, Gopalakrishnan Bulusu, Abhijit Mitra

The Journal of Physical Chemistry B, 119 , 392–409 (2015)

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144.

RNABP COGEST: a resource for investigating functional RNAs Journal Article

Abhijit Mitra

Sohini Bhattacharya, Shriyaa Mittal, Swati Panigrahi, Purshotam Sharma, Preethi SP, Rahul Paul, Sukanya Halder, Antarip Halder, Dhananjay Bhattacharyya, Abhijit Mitra

Database, 2015 , 2566-2599 (2015)

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145.

Theoretical studies of Raman scattering properties of methylphosphine and methylamine adsorbed on gold clusters Journal Article

Harjinder Singh

Shweta Bhardwaj, Sandhya Rai, Tapan Kumar Sau, Harjinder Singh

Vibrational Spectroscopy, 76 , 38-47 (2015)

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2014

146.

Identifying tandem Ankyrin repeats in protein structures Journal Article

Nita Parekh

Broto Chakrabarty, Nita Parekh

BMC bioinformatics, 15 , 6599 (2014)

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147.

Relaxed neighbor based graph transformations for effective preprocessing: A function prediction case study Journal Article

Nita Parekh

D Satheesh Kumar, Polepalli Krishna Reddy, Nita Parekh

International Conference on Big Data Analytics, 8883 , 114-128 (2014)

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148.

Exploring the Catalytic Potential of DNA/x-DNA Base−Gold Nanocluster Complex Journal Article

U. Deva Priyakumar

Sandhya Rai,Harjinder Singh,U. Deva Priyakumar

Theoretical Chemistry Symposium, 11 , 112-119 (2014)

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149.

Graph centrality analysis of structural ankyrin repeats Journal Article

Nita Parekh

Broto Chakrabarty, Nita Parekh

International Journal of Computer Information Systems and Industrial Management Applications. , 6 , 55-62 (2014)

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150.

Atomistic detailed mechanism and weak cation-conducting activity of HIV-1 Vpu revealed by free energy calculations Journal Article

U. Deva Priyakumar

Siladitya Padhi, Raghunadha Reddy Burri, Shahid Jameel, U. Deva Priyakumar

PloS one, 9 , e112983 (2014)

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326 entries « 3 of 7 »