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Mobley Lab, UCI

Free energy methods for pharmaceutical drug discovery

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Sukanya Sasmal

Biography

Sukanya obtained her undergraduate degree in Chemical Engineering from Indian Institute of Technology, Kharagpur in India where she worked on developing droplet-based microfluidic devices for studying protein aggregation. She did her PhD from University of California, Berkeley. Her dissertation research was on understanding intrinsically disordered proteins, in particular the Alzheimer’s amyloid-beta peptide and  amyloid fibril aggregation using all-atom and coarse-grained molecular dynamic simulations. In the Mobley lab, she is focusing on using molecular simulations and modeling to better understand protein-ligand interactions. Her projects are listed below-
1) Predicting the probability of different binding modes for flexible ligands using an non-equilibrium candidate Monte Carlo method (BLUES)
2) Structure based drug design using a combination of docking and binding free energy methods for protein targets. This work is in collaboration with Prof. Jefferson Perry at UC Riverside.
3) Predicting protein-ligand binding poses and binding affinities  for the 2018 D3R grand challenge .
4) Calculatingwater/1-octanol and water/hexadecane partition coefficients for small molecules using alchemical free energy calculations. Anh Nguyen, an undergraduate in UC Irvine is working on this project.
5) Predicting free energy differences between different loop conformations.

Contact

sasmals@uci.edu

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Categories

  • Papers (12)
  • News (29)
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People

  • Dr. David L. Mobley
  • PostDoc
    • Lea El Khoury
    • Sukanya Sasmal
  • Graduate
    • Sam Gill
    • Victoria Lim
    • Kalistyn Burley
    • David Wych
    • Jessica Maat
    • Danielle (Teresa) Bergazin
    • Hannah Baumann
    • Oanh Tran
  • Undergraduate
    • Meghan Osato
    • Jordan Ehrman

Recent Papers

Escaping Atom Types in Force Fields Using Direct Chemical Perception

David L. Mobley , Caitlin C. Bannan , Andrea … [Read More...]

Challenges in the use of atomistic simulations to predict solubilities of drug-like molecules

Guilherme Duarte Ramos Matos, David L. … [Read More...]

SAMPL6 challenge results from pKa predictions based on a general Gaussian process model

Caitlin C. Bannan, David L. Mobley, A. Geoffrey … [Read More...]

Open Force Field Consortium: Escaping atom types using direct chemical perception with SMIRNOFF v0.1

David Mobley, Caitlin C. Bannan, Andrea Rizzi, … [Read More...]

Binding modes of ligands using enhanced sampling (BLUES)

Samuel C. Gill, Nathan M. Lim, Patrick B. … [Read More...]

RSS What we’re reading:

  • A reoptimization of the five-site water potential (TIP5P) for use with Ewald sums November 25, 2020
  • Characterization of the TIP4P-Ew water model: Vapor pressure and boiling point November 25, 2020
  • Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew November 25, 2020
  • A computational investigation of thermodynamics, structure, dynamics and solvation behavior in modif November 25, 2020
  • The missing term in effective pair potentials November 25, 2020

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Contact

David L. Mobley
dmobley@mobleylab.org
phone: 949.385.2436
office: 3134B Nat. Sci. I

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