Multiscale models

Multiscale models

Fully atomistic models are the gold standard for simulations of biological macromolecules but their cost limits the system size and time scales that can be studied. We are pursuing multiscale approaches that reduce degrees of freedoms that are not essential via coarse-graining while still maintaining coupling to atomistic representations. We have developed the PRIMO coarse-grained model that is closely coupled to the CHARMM all-atom force field and demonstrated its transferablity to membrane environments in PRIMO-M. Current efforts are focused on coupling PRIMO directly with CHARMM in AA/CG models and resolution exchange formalisms.

 

Related Publications:

2017
  7. Parimal Kar, Michael Feig: Hybrid All-Atom/Coarse-Grained Simulations of Proteins by Direct Coupling of CHARMM and PRIMO force Fields Journal of Chemical Theory and Computation (2017) in press, Abstract PDF
2014
  6. Parimal Kar, Michael Feig: Recent Advances in Transferable Coarse-Grained Modeling of Proteins Advances in Protein Chemistry & Structural Biology: Biomolecular Modelling and Simulations (2014) 10, 3459-3472 Abstract PDF
  5. Parimal Kar, Srinivasa Murthy Gopal, Yi-Ming Cheng, Afra Panahi, Michael Feig: Transferring the PRIMO Coarse-Grained Force Field to the Membrane Environment: Simulation of Proteins and Helix-Helix Association Journal of Chemical Theory and Computation (2014) 10, 3459-3472 Abstract PDF
2013
  4. Parimal Kar, Srinivasa Murthy Gopal, Yi-Ming Cheng, Alexander Predeus, Michael Feig: PRIMO: A transferable coarse-grained force field for proteins Journal of Chemical Theory and Computation (2013) 9, 3769-3788 Abstract PDF
2012
  3. Yiming Cheng, Srinivasa Gopal, Sean Law, Michael Feig: Molecular dynamics trajectory compression with a coarse-grained model IEEE/ACM Transactions in Computational Biology and Bioinformatics (2012) 6, 476-486 Abstract PDF
2010
  2. Srinivasa M. Gopal, Shayantani Mukherjee, Yi-Ming Cheng, Michael Feig: PRIMO/PRIMONA: A coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy Proteins (2010) 78, 1266-1281 Abstract PDF
2008
  1. Mark A. Olson, Michael Feig, Charles L. Brooks III: Prediction of Protein Loop Conformations Using Multiscale Modeling Methods with Physical Energy Scoring Functions Journal of Computational Chemistry (2008) 29, 820-831 Abstract PDF