AWSEM-MD Publications


 

2016

[17] M. Chen, X. Lin, W. Zheng, J.N. Onuchic, and P.G. Wolynes (2016) Protein Folding and Structure Prediction from the Ground Up: The Atomistic Associative Memory, Water Mediated, Structure and Energy Model. J. Phys. Chem. B, Article ASAP. doi:10.1021/acs.jpcb.6b02451


[16] D.A. Potoyan, W. Zheng, D.U. Ferreiro, P.G. Wolynes, and E.A. Komives (2016) PEST Control of Molecular Stripping of NFκB from DNA Transcription Sites. J. Phys. Chem. B, Article ASAP. doi:10.1021/acs.jpcb.6b02359


[15] D.A. Potoyan, W. Zheng, E.A. Komives, and P.G. Wolynes (2016) Molecular stripping in the NF-κB/IκB/DNA genetic regulatory network. PNAS 113(1) 110-115. doi:10.1073/pnas.1520483112


[14] M. Chen, W. Zheng, and P.G. Wolynes (2016) Energy landscapes of a mechanical prion and their implications for the molecular mechanism of long-term memory. PNAS, 113 (18) 5006-5011. doi:10.1073/pnas.1602702113


[13] M.Y. Tsai, W. Zheng, D. Balamurugan, N.P. Schafer, B.L. Kim, M.S. Cheung, and P.G. Wolynes (2016) Electrostatics, structure prediction, and the energy landscapes for protein folding and binding. Protein Science, 25, 255–269. doi:10.1002/pro.2751


[12] M.B. Trelle, K.M. Ramsey, T.C. Lee, W. Zheng, J. Lamboy, and P.G. Wolynes, A. Deniz, E.A. Komives (2016) Binding of NFκB Appears to Twist the Ankyrin Repeat Domain of IκBα, Biophys. J., 110(4), 887-895. doi: 10.1016/j.bpj.2016.01.001


[11] N.P. Schafer, H.H. Truong, D.E. Otzen, K. Lindorff-Larsen, and P.G. Wolynes (2016) Topological constraints and modular structure in the folding and functional motions of GlpG, an intramembrane protease. PNAS, 113 (8) 2098-2103. doi:10.1073/pnas.1524027113

doi:10.1073/pnas.1524027113


2015

[10] H.H. Truong, B.L. Kim, N.P. Schafer, and P.G. Wolynes (2015) Predictive energy landscapes for folding membrane protein assemblies. J. Chem. Phys., 143, 243101. doi: 10.1063/1.4929598


[9] B.J. Sirovetz, N.P. Schafer, and P.G. Wolynes (2015) Water Mediated Interactions and the Protein Folding Phase Diagram in the Temperature–Pressure Plane. J. Phys. Chem. B, 119 (34), 11416-11427. doi: 10.1021/acs.jpcb.5b03828



2014

[8] N.P. Schafer, B.L. Kim, W. Zheng, and P.G. Wolynes (2014) Learning To Fold Proteins Using Energy Landscape Theory. Isr. J. Chem., 54(8-9), 1869-5868. doi: 10.1002/ijch.201300145


[7] F. Morcos, N.P. Schafer, R.R Cheng, J.N. Onuchic, and P.G. Wolynes (2014) Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection. PNAS, 111(34), 12408-12413. doi: 10.1073/pnas.1413575111


2013

[6] W. Zheng, N.P. Schafer, and P.G. Wolynes (2013) Free energy landscapes for initiation and branching of protein aggregation. PNAS 110(51) 20515-20520. doi: 10.1073/pnas.1320483110


[5] H.H. Truong, B.L. Kim, N.P. Nicholas, and P.G. Wolynes (2013) Funneling and frustration in the energy landscapes of some designed and simplified proteins. J. Chem. Phys., 139, 121908. doi: 10.1063/1.4813504


[4] W. Zheng, N.P. Schafer, and P.G. Wolynes (2013) Frustration in the energy landscapes of multidomain protein misfolding. PNAS, 110(5) 1680-1685. doi: 10.1073/pnas.1222130110


2012

[3] N.P. Schafer, R.M.B. Hoffman, A. Burger, P.O. Craig, E.A. Komives, and P.G. Wolynes (2012) Discrete Kinetic Models from Funneled Energy Landscape Simulations. PLoS ONE, 7(12) e50635. doi: 10.1073/pnas.1216215109


[2] W. Zheng, N.P. Schafer, A. Davtyan, G.A. Papoian, and P.G. Wolynes (2012) Predictive energy landscapes for protein–protein association. PNAS, 109 (47) 19244-19249; published ahead of print November 5, 2012, doi:10.1073/pnas.1216215109. doi:10.1073/pnas.1216215109


[1] A. Davtyan, N.P. Schafer, W. Zheng, C. Clementi, P.G. Wolynes, and G.A. Papoian (2012) AWSEM-MD: Protein Structure Prediction Using Coarse-Grained Physical Potentials and Bioinformatically Based Local Structure Biasing. J. Phys. Chem. B, 116 (29), 8494–8503. doi: 10.1021/jp212541y