Sizes, conformational fluctuations, and SAXS profiles for intrinsically disordered proteins.
M. L. Mugnai, D. Chakraborty, A. Kumar, H. T. Nguyen, F. Maksudov, W. Zeno, J. C. Stachowiak, J. E. Straub and D. Thirumalai, Prot. Sci., 34, e70067, 2025.
Competition between stacking and divalent cation mediated electrostatic interactions determines the conformations of short DNA sequences.
B. Mondal, D. Chakraborty, N. Hori, H. T. Nguyen and D. Thirumalai, J. Chem. Theory Comput., 20, 2934, 2024.
Brewing COFFEE: a coarse-grained energy function for simulation of DNA-protein complexes.
D. Chakraborty, B. Mondal and D. Thirumalai, J. Chem. Theory Comput., 20, 1398, 2024.
Conformational fluctuations and phases in fused in sarcoma (FUS) low complexity protein.
D. Thirumalai, A. Kumar, D. Chakraborty, J. E. Straub and M. L. Mugnai, Biopolymers, 115, e23558, 2023.
Energy landscapes of Ab monomers are sculpted in accordance with Ostwald’s rule of stages.
D. Chakraborty, J. E. Straub and D. Thirumalai, Sci. Adv., 9, eadd6921, 2023.
Energy landscapes for base-flipping in a model DNA duplex.
N. Yadav, D. Chakraborty, and D. J. Wales, J. Phys. Chem. B, 126, 3012, 2022.
Sequence determines the switch in the fibril forming regions in the low-complexity FUS protein and its variants.
A. Kumar, D. Chakraborty, M. L. Mugnai J. E. Straub and D. Thirumalai, J. Phys. Chem. Lett., 12, 9026, 2021.
Side-chain polarity modulates the conformational landscape of model dipeptides.
D. Chakraborty, A. Banerjee, and D. J. Wales, J. Phys. Chem. B, 125, 5809, 2021.
On the emergence of orientational order in folded proteins with implications for allostery.
D. Chakraborty, M. L. Mugnai and D. Thirumalai, Symmetry, 13, 770, 2021. (Selected as Journal Cover)
Differences in the free energies between the excited states of Ab40 and Ab42 encode their aggregation propensities.
D. Chakraborty, J. E. Straub and D. Thirumalai, Proc. Natl. Acad. Sci. USA, 117, 19926, 2020.
A multifunnel energy landscape encodes the competing a-helix and b-hairpin conformations for a designed pepide.
D. Chakraborty, Y. Chebaro and D. J. Wales, Phys. Chem. Chem. Phys. 22, 1359, 2020.
Energy landscapes and hybridization pathways for DNA hexamer duplexes.
S. Xiao, D. J. Sharpe, D. Chakraborty and D. J. Wales, J. Phys. Chem. Lett., 10, 6771, 2019.
Sequence effects on size, shape, and structural heterogeneity in intrinsically disordered proteins.
U. Baul, D. Chakraborty, M. L. Mugnai, J. E. Straub and D. Thirumalai, J. Phys. Chem B, 123, 3462, 2019.
Dynamics of an Adenine-Adenine RNA conformational switch from discrete path sampling.
D. Chakraborty and D. J. Wales, J. Chem. Phys., 150, 125101, 2019.
Energy landscape for fold-switching in regulatory protein RfaH.
J. A. Joseph, D. Chakraborty and D. J. Wales, J. Chem. Theory Comput., 15, 731, 2019.
Charge fluctuation effects on the shape of flexible polyampholytes with applications to intrinsically disordered proteins.
H. S. Samanta, D. Chakraborty and D. Thirumalai, J. Chem. Phys., 149, 163323, 2018.
Sequence-dependent three interaction site (TIS) model for single and double-stranded DNA.
D. Chakraborty, N. Hori, and D. Thirumalai, J. Chem. Theory. Comput., 14, 3763, 2018.
Energy landscape and pathways for transitions between Watson-Crick and Hoogsteen base pairing in DNA.
D. Chakraborty and D. J. Wales, J. Phys. Chem. Lett., 9, 229, 2018.
Multifunctional energy landscape for a DNA G-Quadruplex: An evolved molecular switch.
T. Cragnolini, D. Chakraborty, J. Sponer, P. Derreumaux, S. Pasquali and D. J. Wales, J. Chem. Phys., 147, 152715, 2017.
Exploring biomolecular energy landscapes.
J. A. Joseph, K. Roder, D. Chakraborty, R. G. Mantell and D. J. Wales, Chem. Commun., 53, 6974, 2017.
Probing helical transitions in a DNA duplex.
D. Chakraborty and D. J. Wales, Phys. Chem. Chem. Phys., 19, 878, 2017.
Conformational energy landscape of the ritonavir molecule.
D. Chakraborty, N. Sengupta and D. J. Wales, J. Phys. Chem. B, 120, 4331, 2016.
Computational investigation of RNA CUG repeats responsible for myotonic dystrophy 1.
I. Yildirim, D. Chakraborty, M. Disney, D. J. Wales and G. C. Schatz, J. Chem. Theory Comput., 11, 4943, 2015.
Intrinsically disordered energy landscapes.
Y. Chebaro, A. Ballard, D. Chakraborty and D. J. Wales, Sci. Rep., 5, 10386, 2015.
Energy landscapes, folding mechanisms, and kinetics of RNA tetraloop hairpins.
D. Chakraborty, R. Collepardo-Guevara and D. J. Wales, J. Am. Chem. Soc., 136, 18052, 2014.
Structure and properties of DNA in apolar solvents.
A. Arcella, G. Portella, R. Collepardo-Guevara, D. Chakraborty, D. J. Wales and M. Orozco, J. Phys. Chem. B, 118, 8540, 2014.
Photoinduced charge transfer in solvated anthraquinones is facilitated by low frequency ring deformations.
A. Jha, D. Chakraborty, V. Srinivasan and J. Dasgupta, J. Phys. Chem. B, 117, 12276, 2013.
Coarse-grained simulations of DNA overstretching.
F. Romano, D. Chakraborty, J. P. K. Doye, T. E. Ouldridge and A. A. Louis, J. Chem. Phys., 138, 085101, 2013.