S
Shibasish Chowdhury
Researcher at Birla Institute of Technology and Science
Publications - 42
Citations - 4813
Shibasish Chowdhury is an academic researcher from Birla Institute of Technology and Science. The author has contributed to research in topics: Medicine & Biology. The author has an hindex of 12, co-authored 32 publications receiving 4403 citations. Previous affiliations of Shibasish Chowdhury include University of California, Davis & Indian Institute of Science.
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A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.
Yong Duan,Chun Wu,Shibasish Chowdhury,Mathew C. Lee,Guoming Xiong,Wei Zhang,Rong Yang,Piotr Cieplak,Piotr Cieplak,Ray Luo,Tai-Sung Lee,Tai-Sung Lee,James W. Caldwell,Junmei Wang,Peter A. Kollman +14 more
TL;DR: A third‐generation point‐charge all‐atom force field for proteins is developed and initial tests on peptides demonstrated a high‐degree of similarity between the calculated and the statistically measured Ramanchandran maps for both Ace‐Gly‐nme and Ace‐Ala‐Nme di‐peptides.
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Ab initio Folding Simulation of the Trp-cage Mini-protein Approaches NMR Resolution
TL;DR: Analysis of the trajectory suggests that the rate-limiting step of folding of this mini-protein is the packing of the Trp side-chain, and the simulation has not only reached the correct main-chain conformation, but also a very high degree of accuracy in side- Chain packing conformation.
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Breaking non-native hydrophobic clusters is the rate-limiting step in the folding of an alanine-based peptide.
TL;DR: The formation mechanism of an alanine-based peptide has been studied by all- atom molecular dynamics simulations with a recently developed all-atom point-charge force field and the Generalize Born continuum solvent model and an extrapolated folding time of 16-20 ns is obtained in qualitative agreement with experiments.
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Characterizing the rate-limiting step of Trp-cage folding by all-atom molecular dynamics simulations
TL;DR: Detailed analysis suggests that packing of the structurally important Trp25 side chain is involved in the rate-limiting step and unfolding of the misfolded states and overcoming the additional entropic barrier also contribut...
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G-Quadruplex Structure Can Be Stable with Only Some Coordination Sites Being Occupied by Cations: A Six-Nanosecond Molecular Dynamics Study
Shibasish Chowdhury,Manju Bansal +1 more
TL;DR: A 6 ns molecular dynamics simulation on a 7-mer G-quadruplex, surrounded by Na+ counterions and explicit water molecules, but without any ions in the initial structure, leads to a quadruplex structure with more favorable free energy of hydration, which is comparable to that of a fully coordinated quadruplex.