AWSEM-MD Publications


 

2018

[32] H.Wu, P.G. Wolynes, and G.A. Papoian (2018) AWSEM-IDP: A Coarse-Grained Force Field for Intrinsically Disordered Proteins. J. Phys. Chem. B, (available online). doi: 10.1021/acs.jpcb.8b05791


[31] X. Lin, S. Roy, M.K. Jolly, F. Bocci, N.P. Schafer, M.Y. Tsai, Y. Chen, Y. He, A. Grishaev, K. Weninger, J. Orban, P. Kulkarni, G. Rangarajan, H. Levine, and J.N. Onuchic (2018) PAGE4 and Conformational Switching: Insights from Molecular Dynamics Simulations and Implications for Prostate Cancer. J. Mol. Biol., 430(16), 2422-2438. doi: 10.1016/j.jmb.2018.05.011


[30] M. Chen, N.P. Schafer, W. Zheng, and P.G. Wolynes (2018) The Associative Memory, Water Mediated, Structure and Energy Model (AWSEM)-Amylometer: Predicting Amyloid Propensity and Fibril Topology Using an Optimized Folding Landscape Model. ACS Chem. Neurosci., 9(5), 1027-1039. doi: 10.1021/acschemneuro.7b00436



2017

[29] W. Zheng, M.Y. Tsai, and P.G. Wolynes (2017) Comparing the Aggregation Free Energy Landscapes of Amyloid Beta(1–42) and Amyloid Beta(1–40). J. Am. Chem. Soc., 139(46), 16666-16676. doi: 10.1021/jacs.7b08089


[28] B.J. Sirovetz, N.P. Schafer, and P.G. Wolynes (2017) Protein structure prediction: making AWSEM AWSEM-ER by adding evolutionary restraints. Proteins, 85, 2127–2142. doi: 10.1002/prot.25367


[27] M. Chen and P.G. Wolynes (2017) Aggregation landscapes of Huntington’s disease. PNAS, 114(17), 4406-4411. doi: 10.1073/pnas.1702237114


[26] D.A. Potoyan, C. Bueno, W. Zheng, E.A. Komives, and P.G. Wolynes (2017) Resolving the NFκB Heterodimer Binding Paradox: Strain and Frustration Guide the Binding of Dimeric Transcription Factors. J. Am. Chem. Soc., 139(51), 18558-18566. doi: 10.1021/jacs.7b08741


[25] M. Chen, X. Lin, W. Lu, J.N. Onuchic, and P.G. Wolynes (2017) Protein Folding and Structure Prediction from the Ground Up II: AAWSEM for α/β Proteins. J. Phys. Chem. B, 121(15), 3473-3482. doi: 10.1021/acs.jpcb.6b09347



2016

[24] M. Chen, M.Y. Tsai, W. Zheng, and P.G. Wolynes (2016) The Aggregation Free Energy Landscapes of Polyglutamine Repeats. J. Am. Chem. Soc., 138(46), 15197-15203. doi: 10.1021/jacs.6b08665


[23] R.G. Parra, N.P. Schafer, L.G. Radusky, M.Y. Tsai, A.B. Guzovsky, P.G. Wolynes, and D.U. Ferreiro (2016) Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics. Nucleic Acids Res., 44(W1), W356-W360. doi: 10.1093/nar/gkw304


[22] W. Zheng, M.Y. Tsai, M. Chen, and P.G. Wolynes (2016) Aggregation landscape of amyloid-β (1–40). PNAS, 113(42), 11835-11840. doi: 10.1073/pnas.1612362113


[21] M.Y. Tsai, B. Zhang, W. Zheng, and P.G. Wolynes (2016) Molecular Mechanism of Facilitated Dissociation of Fis Protein from DNA. J. Am. Chem. Soc., 138(41), 13497-13500. doi: 10.1021/jacs.6b08416


[20] H. Zhao, D. Winogradoff, M. Bui, Y. Dalal, and G.A. Papoian (2016) Promiscuous Histone Mis-Assembly Is Actively Prevented by Chaperones. J. Am. Chem. Soc., 138(40) 13207-13218. doi: 10.1021/jacs.6b05355


[19] B. Zhang, W. Zheng, G.A. Papoian, and P.G. Wolynes (2016) Exploring the Free Energy Landscape of Nucleosomes. J. Am. Chem. Soc., 138(26) 8126-8133. doi: 10.1021/jacs.6b02893


[18] 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, 120(33) 8557-8565. doi: 10.1021/acs.jpcb.6b02451


[17] 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, 120(33). 8532-8538. doi: 10.1021/acs.jpcb.6b02359


[16] 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


[15] 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


[14] 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


[13] 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


[12] 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



2015

[11] 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


[10] 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

[9] B.L. Kim, N.P. Schafer, and P.G. Wolynes (2014) Energy landscapes of α-helical membrane proteins. PNAS, 111(90), 11031-11036. doi: 10.1073/pnas.1410529111

[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