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Athi N. Naganathan · SciRah

Researcher profile · Semantic Scholar

Athi N. Naganathan

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Athi N. Naganathan — researcher profile on SciRah

h-index: 28
Works: 116
Citations: 2,320

Most-cited papers

Modulation of allosteric coupling by mutations: from protein dynamics and packing to altered native ensembles and function
Athi N. Naganathan
2018Current Opinion in Structural Biology103 citations Open access
Semantic Scholar
The need to implement FAIR principles in biomolecular simulations
R. Amaro, J. Åqvist, Ivet Bahar, F. Battistini +125 more
2024Nature Methods80 citations Open access
Semantic Scholar
The native ensemble and folding of a protein molten-globule: functional consequence of downhill folding.
Athi N. Naganathan, M. Orozco
2011Journal of the American Chemical Society59 citations
Semantic Scholar
A General Mechanism for the Propagation of Mutational Effects in Proteins.
Nandakumar Rajasekaran, S. Suresh, Soundhararajan Gopi, Karthik Raman +1 more
2017Biochemistry58 citations
Semantic Scholar
Modern Analysis of Protein Folding by Differential Scanning Calorimetry.
B. Ibarra-Molero, Athi N. Naganathan, J. Sanchez-Ruiz, V. Muñoz
2016Methods in Enzymology55 citations
Semantic Scholar
Predictions from an Ising-like Statistical Mechanical Model on the Dynamic and Thermodynamic Effects of Protein Surface Electrostatics.
Athi N. Naganathan
2012Journal of Chemical Theory and Computation49 citations Open access
Semantic Scholar
A Universal Pattern in the Percolation and Dissipation of Protein Structural Perturbations.
Nandakumar Rajasekaran, A. Sekhar, Athi N. Naganathan
2017Journal of Physical Chemistry Letters48 citations Open access
Semantic Scholar
Thermally versus Chemically Denatured Protein States
Abhishek Narayan, K. Bhattacharjee, Athi N. Naganathan
2019Biochemistry42 citations Open access
Semantic Scholar
Insight into the specificity and severity of pathogenic mechanisms associated with missense mutations through experimental and structural perturbation analyses
Encarnación Medina-Carmona, I. Betancor-Fernández, Jaime Santos, Noel Mesa-Torres +8 more
2018Human Molecular Genetics41 citations Open access
Semantic Scholar
Coarse-grained representation of protein flexibility. Foundations, successes, and shortcomings.
M. Orozco, Laura Orellana, Adam Hospital, Athi N. Naganathan +3 more
2011Advances in Protein Chemistry and Structural Biology40 citations Open access
Semantic Scholar
Quantitative prediction of protein folding behaviors from a simple statistical model.
P. Bruscolini, Athi N. Naganathan
2011Journal of the American Chemical Society38 citations
Semantic Scholar
Thermodynamics of downhill folding: multi-probe analysis of PDD, a protein that folds over a marginal free energy barrier.
Athi N. Naganathan, V. Muñoz
2014Journal of Physical Chemistry B37 citations
Semantic Scholar
Functional regulation of an intrinsically disordered protein via a conformationally excited state
Kulkarni Madhurima, Bodhisatwa Nandi, Sneha Munshi, Athi N. Naganathan +1 more
2022bioRxiv35 citations Open access
Semantic Scholar
Quantifying Protein Disorder through Measures of Excess Conformational Entropy.
Nandakumar Rajasekaran, Soundhararajan Gopi, Abhishek Narayan, Athi N. Naganathan
2016Journal of Physical Chemistry B32 citations
Semantic Scholar
The metal cofactor zinc and interacting membranes modulate SOD1 conformation-aggregation landscape in an in vitro ALS model
Achinta Sannigrahi, Sourav Chowdhury, Bidisha Das, A. Banerjee +6 more
2020bioRxiv29 citations Open access
Semantic Scholar
A rapid, ensemble and free energy based method for engineering protein stabilities.
Athi N. Naganathan
2013Journal of Physical Chemistry B29 citations
Semantic Scholar
Thermodynamic architecture and conformational plasticity of GPCRs
Sathvik Anantakrishnan, Athi N. Naganathan
2022bioRxiv28 citations Open access
Semantic Scholar
Folding RaCe: a robust method for predicting changes in protein folding rates upon point mutations
Priyashree Chaudhary, Athi N. Naganathan, M. Gromiha
2015Bioinform.28 citations Open access
Semantic Scholar
Tunable order–disorder continuum in protein–DNA interactions
Sneha Munshi, Soundhararajan Gopi, Gitanjali Asampille, Sandhyaa Subramanian +3 more
2018Nucleic Acids Research27 citations Open access
Semantic Scholar
Structural basis of the pleiotropic and specific phenotypic consequences of missense mutations in the multifunctional NAD(P)H:quinone oxidoreductase 1 and their pharmacological rescue
Juan Luis Pacheco-García, Ernesto Anoz-Carbonell, P. Vaňková, Adithi Kannan +7 more
2021Redox Biology26 citations Open access
Semantic Scholar
A self-consistent structural perturbation approach for determining the magnitude and extent of allosteric coupling in proteins.
Nandakumar Rajasekaran, Athi N. Naganathan
2017Biochemical Journal26 citations Open access
Semantic Scholar
The conformational landscape of an intrinsically disordered DNA-binding domain of a transcription regulator.
Athi N. Naganathan, M. Orozco
2013Journal of Physical Chemistry B26 citations
Semantic Scholar
Graded Structural Polymorphism in a Bacterial Thermosensor Protein.
Abhishek Narayan, L. A. Campos, Sandhya Bhatia, D. Fushman +1 more
2017Journal of the American Chemical Society25 citations
Semantic Scholar
A Disorder-Induced Domino-Like Destabilization Mechanism Governs the Folding and Functional Dynamics of the Repeat Protein IκBα
Srinivasan Sivanandan, Athi N. Naganathan
2013PLoS Comput. Biol.25 citations Open access
Semantic Scholar
Thermodynamics and folding landscapes of large proteins from a statistical mechanical model
Soundhararajan Gopi, Akashnathan Aranganathan, Athi N. Naganathan
2019Current Research in Structural Biology24 citations Open access
Semantic Scholar
A hierarchy of coupling free energies underlie the thermodynamic and functional architecture of protein structures
Athi N. Naganathan, Adithi Kannan
2021Current Research in Structural Biology20 citations Open access
Semantic Scholar
Switching Protein Conformational Substates by Protonation and Mutation
Abhishek Narayan, Athi N. Naganathan
2018Journal of Physical Chemistry B20 citations Open access
Semantic Scholar
Protein plasticity driven by disorder and collapse governs the heterogeneous binding of CytR to DNA
Sneha Munshi, Soundhararajan Gopi, Sandhyaa Subramanian, L. A. Campos +1 more
2018Nucleic Acids Research20 citations Open access
Semantic Scholar
Are protein folding intermediates the evolutionary consequence of functional constraints?
Athi N. Naganathan, J. Sanchez-Ruiz, Sneha Munshi, S. Suresh
2015Journal of Physical Chemistry B18 citations
Semantic Scholar
Entropic Control of an Excited Folded-Like Conformation in a Disordered Protein Ensemble
Sneha Munshi, Divya Rajendran, Athi N. Naganathan
2018Journal of Molecular Biology16 citations Open access
Semantic Scholar
Imprints of function on the folding landscape: functional role for an intermediate in a conserved eukaryotic binding protein.
Sneha Munshi, Athi N. Naganathan
2015Physical Chemistry, Chemical Physics - PCCP15 citations
Semantic Scholar
Molecular and thermodynamic determinants of self-assembly and hetero-oligomerization in the enterobacterial thermo-osmo-regulatory protein H-NS
Bincy Lukose, T. Maruno, Mohammed A. Faidh, Susumu Uchiyama +1 more
2024Nucleic Acids Research14 citations Open access
Semantic Scholar
Allosteric Communication in the Multifunctional and Redox NQO1 Protein Studied by Cavity-Making Mutations
Juan Luis Pacheco-García, Dmitry S. Loginov, Ernesto Anoz-Carbonell, P. Vaňková +6 more
2022Antioxidants14 citations Open access
Semantic Scholar
Electrostatic Frustration Shapes Folding Mechanistic Differences in Paralogous Bacterial Stress Response Proteins.
Abhishek Narayan, Soundhararajan Gopi, Bincy Lukose, Athi N. Naganathan
2020Journal of Molecular Biology14 citations
Semantic Scholar
pStab: prediction of stable mutants, unfolding curves, stability maps and protein electrostatic frustration
Soundhararajan Gopi, Devanshu Devanshu, Praveen Krishna, Athi N. Naganathan
2018Bioinform.14 citations Open access
Semantic Scholar
Evidence for the sequential folding mechanism in RNase H from an ensemble-based model.
Abhishek Narayan, Athi N. Naganathan
2014Journal of Physical Chemistry B14 citations
Semantic Scholar
A binding cooperativity switch driven by synergistic structural swelling of an osmo-regulatory protein pair
Abhishek Narayan, Soundhararajan Gopi, D. Fushman, Athi N. Naganathan
2019Nature Communications13 citations Open access
Semantic Scholar
Structural–Energetic Basis for Coupling between Equilibrium Fluctuations and Phosphorylation in a Protein Native Ensemble
Hemashree Golla, Adithi Kannan, Soundhararajan Gopi, Sowmiya Murugan +2 more
2022ACS Central Science12 citations Open access
Semantic Scholar
pPerturb: A Server for Predicting Long-Distance Energetic Couplings and Mutation-Induced Stability Changes in Proteins via Perturbations
Soundhararajan Gopi, Devanshu Devanshu, Nandakumar Rajasekaran, Sathvik Anantakrishnan +1 more
2020ACS Omega12 citations Open access
Semantic Scholar
Engineering Order and Cooperativity in a Disordered Protein
Sneha Munshi, Sandhyaa Subramanian, Samyuktha Ramesh, Hemashree Golla +5 more
2019Biochemistry11 citations Open access
Semantic Scholar
Energetic and topological determinants of a phosphorylation-induced disorder-to-order protein conformational switch.
Soundhararajan Gopi, Nandakumar Rajasekaran, A. Singh, Sayan Ranu +1 more
2015Physical Chemistry, Chemical Physics - PCCP11 citations
Semantic Scholar
The protein folding transition-state ensemble from a Gō-like model.
Athi N. Naganathan, M. Orozco
2011Physical Chemistry, Chemical Physics - PCCP11 citations
Semantic Scholar
Quantification of Entropic Excluded Volume Effects Driving Crowding-Induced Collapse and Folding of a Disordered Protein
Divya Rajendran, S. Mitra, Hiroyuki Oikawa, Kulkarni Madhurima +3 more
2022Journal of Physical Chemistry Letters10 citations Open access
Semantic Scholar
Ensemble origins and distance-dependence of long-range mutational effects in proteins
Adithi Kannan, Athi N. Naganathan
2022iScience10 citations Open access
Semantic Scholar
Folding Intermediates, Heterogeneous Native Ensembles and Protein Function.
Athi N. Naganathan, Rahul Dani, Soundhararajan Gopi, Akashnathan Aranganathan +1 more
2021Journal of Molecular Biology10 citations
Semantic Scholar
Toward a quantitative description of microscopic pathway heterogeneity in protein folding.
Soundhararajan Gopi, A. Singh, S. Suresh, S. Paul +2 more
2017Physical Chemistry, Chemical Physics - PCCP10 citations
Semantic Scholar
Loss of stability and unfolding cooperativity in hPGK1 upon gradual structural perturbation of its N-terminal domain hydrophobic core
Juan Luis Pacheco-García, Dmitry S. Loginov, Athi N. Naganathan, P. Vaňková +3 more
2022Scientific Reports9 citations Open access
Semantic Scholar
Controlling Structure and Dimensions of a Disordered Protein via Mutations
Sneha Munshi, Divya Rajendran, Samyuktha Ramesh, Sandhyaa Subramanian +3 more
2019Biochemistry9 citations Open access
Semantic Scholar
Tuning the Continuum of Structural States in the Native Ensemble of a Regulatory Protein
Abhishek Narayan, Athi N. Naganathan
2017Journal of Physical Chemistry Letters9 citations Open access
Semantic Scholar
Coarse‐grained models of protein folding as detailed tools to connect with experiments
Athi N. Naganathan
20139 citations
Semantic Scholar

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Abhishek Narayan×9
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Sneha Munshi×8
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Nandakumar Rajasekaran×6
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M. Orozco — researcher profile on SciRah

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L. A. Campos×4

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