AWSEM-MD Publications

[65] H. Wu, Y. Dalal, and G.A. Papoian (2021) Binding dynamics of disordered linker histone H1 with a nucleosomal particle. J. Mol. Biol., 433(6), 166881. doi: 10.1016/j.jmb.2021.166881

[64] D.S. Yang, A. Saeedi, A. Davtyan, M. Fathi, M.B. Sherman, M.S. Safari, A. Klindziuk, M.C. Barton, N. Varadarajan, A.B. Kolomeisky, and P.G. Vekilov (2021) Mesoscopic protein-rich clusters host the nucleation of mutant p53 amyloid fibrils. PNAS, 118(10), e2015618118. doi: 10.1073/pnas.2015618118

[63] J. Nde, P. Zhang, J.C. Ezerski, W. Lu, K. Knapp, P.G. Wolynes, and M.S. Cheung (2021) Coarse-Grained Modeling and Molecular Dynamics Simulations of Ca2+-Calmodulin. Front. Mol. Biosci., 8, 661322. doi: 10.3389/fmolb.2021.661322

[62] Y. Xu, K. Knapp, K.N. Le, N.P. Schafer, M.S. Safari, A. Davtyan, P.G. Wolynes, and P.G. Vekilov (2021) Frustrated peptide chains at the fibril tip control the kinetics of growth of amyloid-β fibrils. PNAS, 118(38), e2110995118. doi: 10.1073/pnas.2110995118

[61] Y.W. Ma, T.Y. Lin, and M.Y. Tsai. (2021) Fibril Surface-Dependent Amyloid Precursors Revealed by Coarse-Grained Molecular Dynamics Simulation. Front. Mol. Biosci., 8, 719320. doi: 10.3389/fmolb.2021.719320

[60] X. Lin, J.T. George, N.P. Schafer, K.N. Chau, M.E. Birnbaum, C. Clementi, J.N. Onuchic, and H. Levine (2021) Rapid assessment of T-cell receptor specificity of the immune repertoire. Nat. Comput. Sci., 1(5), 362-373. doi: 10.1038/s43588-021-00076-1

[59] F.C. Freitas, P.H.B. Ferreira, D.C. Favaro, and R.J.D. Oliveira (2021) Shedding Light on the Inhibitory Mechanisms of SARS-CoV-1/CoV-2 Spike Proteins by ACE2-Designed Peptides. J. Chem. Inf. Model., 61(3), 1226-1243. doi: 10.1021/acs.jcim.0c01320

[58] N.N. Thadani, Q. Zhou, K.R. Gamas, S. Butler, C. Bueno, N.P. Schafer, F. Morcos, P.G. Wolynes, and J. Suh (2021) Frustration and Direct-Coupling Analyses to Predict Formation and Function of Adeno-Associated Virus. Biophys. J., 120(3), 489-503. doi: 10.1016/j.bpj.2020.12.018

[57] V. Kumar (2021) Molecular interactions between C9ORF72 and SMCR8: A local energetic frustration perspective. Biochem. Biophys. Res. Commun., 570, 1-7. doi: 10.1016/j.bbrc.2021.07.016

[56] A.B. Junior, X. Lin, P. Kulkarni, J.N. Onuchic, S. Roy, and V.B. Leite (2021) Exploring Energy Landscapes of Intrinsically Disordered Proteins: Insights into Functional Mechanisms. J. Chem. Theory Comput., 17(5), 3178-3187. doi: 10.1021/acs.jctc.1c00027

[55] J. Procyk, E. Poppleton, and P. Šulc (2021) Coarse-grained nucleic acid–protein model for hybrid nanotechnology. Soft Matter, 17(13), 3586-3593. doi: 10.1039/D0SM01639J

[54] A. Ravikumar, A.G. Brevern, and N. Srinivasan (2021) Conformational Strain Indicated by Ramachandran Angles for the Protein Backbone Is Only Weakly Related to the Flexibility. J. Phys. Chem. B, 125(10), 2597-2606. doi: 10.1021/acs.jpcb.1c00168

[53] X. Lin, Y. Qi, A.P. Latham, and B. Zhang (2021) Multiscale modeling of genome organization with maximum entropy optimization. J. Chem. Phys., 155(1), 010901. doi: 10.1063/5.0044150

[52] AW. Lu, C. Bueno, N.P. Schafer, J. Moller, S. Jin, X. Chen, M. Chen, X. Gu, A. Davtyan, J.J. Pablo, and P.G. Wolynes (2021) OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations. PLoS Comput. Biol., 17(2), e1008308. doi: 10.1371/journal.pcbi.1008308

[51] K.J. Bari, and D.D. Prakashchand (2021) Fundamental Challenges and Outlook in Simulating Liquid–Liquid Phase Separation of Intrinsically Disordered Proteins. J. Phys. Chem. Lett., 12(6), 1644-1656. doi: 10.1021/acs.jpclett.0c03404

[50] S. Jin, M.D. Miller, M. Chen, N.P. Schafer, X. Lin, X. Chen, G.N. Phillips, P.G. Wolynes (2020) Molecular-replacement phasing using predicted protein structures from AWSEM-Suite. IUCrJ, 7(6), 1168-1178. doi: 10.1107/S2052252520013494

[49] P.H.B. Ferreira, F.C. Freitas, M.E. McCully, G.G. Slade, and R.J. Oliveira (2020) The role of electrostatics and folding kinetics on the thermostability of homologous cold shock proteins. J. Chem. Inf. Model., 60(2), 546-561. doi: 10.1021/acs.jcim.9b00797

[48] M. Chen, X. Chen, S. Jin, W. Lu, X. Lin, and P.G. Wolynes (2020) Protein Structure Refinement Guided by Atomic Packing Frustration Analysis. J. Phys. Chem. B, 124(48), 10889-10898. doi: 10.1021/acs.jpcb.0c06719

[47] X. Gu, N.P. Schafer, Q. Wang, S.S. Song, M. Chen, M.N. Waxham, and P.G. Wolynes (2020) Exploring the F-actin/CPEB3 interaction and its possible role in the molecular mechanism of long-term memory. PNAS, 117(36), 22128-22134. doi: 10.1073/pnas.2012964117

[46] M. Chen, X. Chen, N.P. Schafer, C. Clementi, E.A. Komives, D.U. Ferreiro, and P.G. Wolynes (2020) Surveying biomolecular frustration at atomic resolution. Nat. Commun., 11(1), 5944. doi: 10.1038/s41467-020-19560-9

[45] S. Jin, M. Chen, X. Chen, C. Bueno, W. Lu, N.P. Schaefer, X. Lin, J.N. Onuchic, and P.G. Wolynes (2020) Protein Structure Prediction in CASP13 Using AWSEM-Suite. J Chem Theory Comput, 16(6), 3977-3988. doi:10.1021/acs.jctc.0c00188

[44] S. Jin, V.G. Contessoto, M. Chen, N.P. Schaefer, W. Lu, X. Chen, C. Bueno, A. Hajitaheri, B.J. Sirovetz, A. Davtyan, G.A. Papoian, M.-Y. Tsai, and P.G. Wolynes (2020) AWSEM-Suite: a protein structure prediction server based on template-guided, coevolutionary-enhanced optimized folding landscapes. Nucleic Acids Res, 48(W1), W25-W30. doi: 10.1093/nar/gkaa356

[43] X. Chen, M. Chen, N.P. Schafer and P.G. Wolynes (2020) Exploring the interplay between fibrillization and amorphous aggregation channels on the energy landscapes of tau repeat isoforms. PNAS, 117(8), 4125-4130. doi: 10.1073/pnas.1921702117

[42] D. Krepela, A. Davtyan, N.P. Schafer, P.G. Wolynes, and J.N. Onuchic (2019) Braiding topology and the energy landscape of chromosome organization proteins. PNAS, 117(3), 1468-1477. doi: 10.1073/pnas.1917750117

[41] X. Lin, N.P. Schafer, W. Lu, S. Jin, X. Chen, M. Chen, J.N. Onuchic, P.G. Wolynes (2019) Forging tools for refining predicted protein structures. PNAS, 116(19), 9400-9409. doi: 10.1073/pnas.1900778116

[40] X. Lin, P. Kulkarni, F. Bocci, N.P. Schafer, S. Roy, M.Y. Tsai, Y. He et al. (2019) Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level. Biomolecules, 9(2), 77. doi: 10.3390/biom9020077

[39] A.P. Latham, B. Zhang (2019) Improving Coarse-Grained Protein Force Fields with Small-Angle X-ray Scattering Data. J. Phys. Chem. B, 123(5), 1026-1034. doi: 10.1021/acs.jpcb.8b10336

[38] W. Lu, N.P. Schafer, P.G. Wolynes (2018) Energy landscape underlying spontaneous insertion and folding of an alpha-helical transmembrane protein into a bilayer. Nature Communications, 9(1), 4949. doi: 10.1038/s41467-018-07320-9

[37] M. Chen, X. Lin, W. Lu, N.P. Schafer, J.N. Onuchic, P.G. Wolynes (2018) Template-Guided Protein Structure Prediction and Refinement Using Optimized Folding Landscape Force Fields. J. Chem. Theory Comput., 14(11), 6102-6116. doi: 10.1021/acs.jctc.8b00683

[36] M. Chen, N.P. Schafer, P.G. Wolynes (2018) Surveying the Energy Landscapes of Aβ Fibril Polymorphism. J. Phys. Chem. B, 122(49), 11414-11430. doi: 10.1021/acs.jpcb.8b07364

[35] 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, 122(49), 11115–11125. doi: 10.1021/acs.jpcb.8b05791

[34] J. Chen, J. Chen, G. Pinamonti, C. Clementi (2018) Learning effective molecular models from experimental observables. J. Chem. Theory Comput., 14(7), 3849-3858. doi: 10.1021/acs.jctc.8b00187

[33] S. Husain, V. Kumar, Md. I. Hassan (2018) Phosphorylation-induced changes in the energetic frustration in human Tank binding kinase 1. J. Theor. Biol., 449, 14-22. doi: 10.1016/j.jtbi.2018.04.016

[32] 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

[31] 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

[30] 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

[29] 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

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

[27] 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

[26] 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

[25] P.G. Wolynes, G.A. Papoian (2017) AWSEM-MD: From Neural Networks to Protein Structure Prediction and Functional Dynamics of Complex Biomolecular Assemblies. Coarse-Grained Modeling of Biomolecules, CRC Press, 121-190. doi: 10.1201/9781315374284

[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

[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

[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

[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. Schafer, 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

[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. 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