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Arvind Ramanathan - Publications

Affiliations: 
Oak Ridge National Laboratory, Oak Ridge, TN, United States 
Area:
Computational biology, biophysics, computer science
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17 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Demerdash O, Shrestha UR, Petridis L, Smith JC, Mitchell JC, Ramanathan A. Using Small-Angle Scattering Data and Parametric Machine Learning to Optimize Force Field Parameters for Intrinsically Disordered Proteins. Frontiers in Molecular Biosciences. 6: 64. PMID 31475155 DOI: 10.3389/Fmolb.2019.00064  0.306
2019 Romero R, Ramanathan A, Yuen T, Bhowmik D, Mathew M, Munshi LB, Javaid S, Bloch M, Lizneva D, Rahimova A, Khan A, Taneja C, Kim SM, Sun L, New MI, et al. Mechanism of glucocerebrosidase activation and dysfunction in Gaucher disease unraveled by molecular dynamics and deep learning. Proceedings of the National Academy of Sciences of the United States of America. PMID 30808805 DOI: 10.1073/Pnas.1818411116  0.319
2017 Ban D, Iconaru LI, Ramanathan A, Zuo J, Kriwacki RW. A small molecule causes a population shift in the conformational landscape of an intrinsically disordered protein. Journal of the American Chemical Society. PMID 28885015 DOI: 10.1021/Jacs.7B01380  0.312
2017 Treece BW, Loesche M, Heinrich F, Ramanathan A. Modeling Membrane Associated Proteins through Neutron Reflectivity Augmented Molecular Dynamics Biophysical Journal. 112. DOI: 10.1016/J.Bpj.2016.11.770  0.33
2016 Agarwal PK, Doucet N, Chennubhotla C, Ramanathan A, Narayanan C. Conformational Sub-states and Populations in Enzyme Catalysis. Methods in Enzymology. 578: 273-97. PMID 27497171 DOI: 10.1016/Bs.Mie.2016.05.023  0.312
2015 Chennubhotla CS, Ramanathan A, Stanley C. Enabling Biophysical Characterization of Intrinsically Disordered Protein Ensembles Biophysical Journal. 108: 227a. DOI: 10.1016/J.Bpj.2014.11.1254  0.342
2014 Ramanathan A, Savol A, Burger V, Chennubhotla CS, Agarwal PK. Protein conformational populations and functionally relevant substates. Accounts of Chemical Research. 47: 149-56. PMID 23988159 DOI: 10.1021/Ar400084S  0.344
2012 Ramanathan A, Savol AJ, Agarwal PK, Chennubhotla CS. Event detection and sub-state discovery from biomolecular simulations using higher-order statistics: application to enzyme adenylate kinase. Proteins. 80: 2536-51. PMID 22733562 DOI: 10.1002/Prot.24135  0.318
2011 Ramanathan A, Yoo JO, Langmead CJ. On-the-Fly Identification of Conformational Substates from Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. 7: 778-89. PMID 26596308 DOI: 10.1021/Ct100531J  0.321
2011 Ramanathan A, Agarwal PK. Evolutionarily conserved linkage between enzyme fold, flexibility, and catalysis. Plos Biology. 9: e1001193. PMID 22087074 DOI: 10.1371/Journal.Pbio.1001193  0.311
2011 Kamisetty H, Ramanathan A, Bailey-Kellogg C, Langmead CJ. Accounting for conformational entropy in predicting binding free energies of protein-protein interactions. Proteins. 79: 444-62. PMID 21120864 DOI: 10.1002/Prot.22894  0.3
2011 Savol A, Ramanathan A, Chennubhotla C. Generating Global Protein Dynamics with Structure-From-FRET Biophysical Journal. 100. DOI: 10.1016/J.Bpj.2010.12.2793  0.351
2011 Ramanathan A, Borreguero JM, Chennubhotla CS, Agarwal PK. Protein Flexibility and Energy Flow During Enzyme Catalysis Biophysical Journal. 100: 194a. DOI: 10.1016/J.Bpj.2010.12.1277  0.323
2010 Ramanathan A, Agarwal PK, Kurnikova M, Langmead CJ. An online approach for mining collective behaviors from molecular dynamics simulations. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 309-24. PMID 20377447 DOI: 10.1089/Cmb.2009.0167  0.313
2010 Ramanathan A, Savol A, Langmead C, Agarwal P, Chennubhotla SC. High-Order Correlations in Internal Protein Motions and Energetics Biophysical Journal. 98: 235a-236a. DOI: 10.1016/J.Bpj.2009.12.1276  0.349
2009 Ramanathan A, Agarwal PK. Computational identification of slow conformational fluctuations in proteins. The Journal of Physical Chemistry. B. 113: 16669-80. PMID 19908896 DOI: 10.1021/Jp9077213  0.317
2009 Ramanathan A, Borreguero J, Langmead CJ, Agarwal PK. Conserved Protein Flexibility And Pathways Of Energy Flow In Enzyme Catalysis Biophysical Journal. 96: 71a. DOI: 10.1016/J.Bpj.2008.12.265  0.314
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