List of publications:
- 39. S. Bazmi and S. Wallin S. Comparing effects of attractive interactions in crowded systems: nonspecific, hydrophobic, and hydrogen bond interactions. PeerJ Physical Chemistry 6 e31 (2024)
[Full text at journal website] - 38. S. Bazmi, B. Seifi, S. Wallin. Simulations of a protein fold switch reveal crowding-induced population shifts driven by disordered regions. Communications Chemistry 6 191 (2023).
[Full text at journal website ] - 37. V. T. Ranganathan, S. Bazmi, S. Wallin, Y. Liu, and A. Yethiraj. Is Ficoll a Colloid or Polymer? A Multitechnique Study of a Prototypical Excluded-Volume Macromolecular Crowder. Macromolecules 55 9103-9112 (2022).
[Full text at journal website ]. - 36. S. Bazmi and S. Wallin. Crowding-induced protein destabilization in the absence of soft attractions. Biophysical Journal 21 2503-2513 (2022).
[ Full text at journal website ]. - 35. B. Seifi and S. Wallin. The C-terminal domain of transcription factor RfaH: folding, fold switching and energy landscape. Biopolymers 112 e23420 (2021).
[ BioRxiv ] [Full text at journal website ] - 34. B. Seifi, A. Aina and S. Wallin. Structural fluctuations and mechanical stabilities of the metamorphic protein RfaH. Proteins 89 289-300 (2021).
[ Full text at journal website ]
The full peer review history is available for this paper. - 33. D. Trotter and S. Wallin. Effects of topology and sequence in protein folding linked via conformational fluctuations. Biophysical Journal 118 1370-1380 (2020).
[ Full text at journal website ] - 32. N. A. S. Robichaud, I. Saika-Voivod, S. Wallin. Phase behavior of blocky charge lattice polymers: Crystals, liquids, sheets, filaments, and clusters. Physical Review E 100 052404 (2019). Editor's Suggestion.
[ Full text at journal website ] - 31. B. M. Coady, J. D. Marshall, L. E. Hattie, A. E. Brannan, M. N. Fitzpatrick, K. E.Hickey, S. Wallin, V. Booth, and R. J. Brown. Characterization of a peptide containing the major heparin binding domain of human hepatic lipase. Journal of Peptide Science 24 e3123 (2018).
[ Full text at journal website ] - 30. A. Aina, S. Wallin. Multisequence algorithm for coarse-grained biomolecular simulations: exploring the sequence-structure relationship of proteins. Journal of Chemical Physics 147 095102 (2017).
[ Full text at journal website ] - 29. L. Zhu, J. Petrlova, P. Gysbers, H. Hebert, S. Wallin, C. Jegerschöld and J. O. Lagerstedt. Structures of Apolipoprotein A-I in High Density Lipoprotein generated by electron microscopy and biased simulations BBA General Subjects 1861 2726-2738 (2017).
[ Full text at journal website ] - 28. S. Wallin. Intrinsically disordered proteins: structural and functional dynamics. Research and Reports in Biology. 8 7--16 (2017).
[Full text at journal website ]
- 27. S. Wallin. Binding specificity profiles from computational peptide screening. In "Modeling of protein-peptide interactions: Methods and protocols", eds Ora Schueler-Furman and Nir London, Springer Press (2017).
[ Full text at journal website ] - 26. C. Holzgräfe and S. Wallin. Local vs global fold switching in
protein evolution: Insight from a 3-letter continuous model. Physical
Biology 12 026002 (2015).
[ Full text at journal website ] - 25. J. Petrolova, A. Bhattacherjee, W. Boomsma, S. Wallin, J. Lagerstedt,
and A. Irbäck. Conformational and aggregation properties of the 1-93
fragment of the apolipoprotein A-I.Protein Science 23
1559-1571 (2015).
[ Full text at journal website ] - 24. C. Holzgräfe and S. Wallin. Smooth functional transition across
a mutational pathway with an abrupt protein fold switch. Biophysical
Journal 107 1217-1225 (2014).
[ Full text at journal website ] [ New and notable ] - 23. A. Bhattacherjee and S. Wallin. Exploring protein-peptide binding
specificity through computational peptide screening. PLoS Computational
Biology 9 e1003277 (2013).
[ Full text at journal website ] - 22. H. Behringer, R. Eichhorn, and S. Wallin. Dynamics of biomolecular
processes Physica Scripta 87, 058501 (2013).
[ Full text at journal website ] - 21. E. Follin, M. Karlsson, C. Lundegaard, M. Nielsen, S. Wallin,
K. Paulsson, and H. Westerdahl. In silico peptide-binding predictions of
passerine MHC class I reveal similarities across distantly related species,
suggesting convergence on the level of protein
function. Immunogenetics 65, 299-311 (2013).
[ Full text at journal website ] - 20. A. Irbäck, S. Æ. Jónsson, N. Linnemann, B. Linse, and S. Wallin.
Aggregate geometry in amyloid fibril nucleation. Physical Review
Letters 110, 058101 (2013).
[ Full text at journal website ] - 19. N. Olsson, S. Wallin, P. James, C. A. K. Borrebaeck, and C. Wingren.
Epitope-specificity of recombinant antibodies reveals promiscuous
peptide-binding properties. Protein Science 21, 1897-1910 (2012).
[ Full text at journal website ] - 18. I. Staneva, Y. Huang, Z. Liu, and S. Wallin. Binding of two intrinsically
disordered peptides to a multi-specific protein: A combined Monte Carlo and
Molecular Dynamics study. PLoS Computational Biololy 8,
e1002682 (2012).
[ Full text at journal website ] - 17. A. Bhattacherjee and S. Wallin. Coupled folding-binding in a
hydrophobic/polar protein model: Impact of synergistic folding and
disordered flanks. Biophysical Journal 102, 569-578
(2012). Correction 103 846 (2012).
[ Full text at journal website ] [Correction ] - 16. I. Staneva and S. Wallin. Binding free energy landscape of domain-peptide
interactions. PLoS Computational Biology 7, e1002131 (2011).
[ Full text at journal website ] - 15. H. S. Chan, Z. Zhang, S. Wallin, and Z. Liu. Cooperativity, local-nonlocal
coupling, and nonnative interactions: Principles of protein folding from
coarse-grained models. Annual Review of Physical Chemistry 62 , 301-326 (2011).
[ Full text at journal website ] - 14. I. Staneva and S. Wallin. All-atom Monte Carlo approach to protein-peptide
binding. Journal of Molecular Biology 393, 1118-1128 (2009).
[ Full text at journal website ] - 13. A. Zarrine-Afsar, S. Wallin, A. M. Neculai, P. Neudecker, P. L. Howell,
A. R. Davidson, and H. S. Chan. Theoretical and experimental demonstration
of the importance of specific nonnative interactions in protein
folding.Proceedings of the National Academy of Sciences USA 105, 9999-10004 (2008).
[ Full text at journal website ] - 12. S. Wallin and E. I. Shakhnovich. Understanding ensemble protein
folding at atomic detail Journal of Physics: Condensed Matter
20, 283101 (2008).
[ Full text at journal website ] - 11. J. S. Yang, S. Wallin, and E. I. Shakhnovich. Universality and
diversity of folding mechanics for three-helix bundle proteins.
Proceedings of the National Academy of Sciences USA 105, 7113-7117 (2008).
[ Full text at journal website ] - 10. S. Wallin, K. B. Zeldovich, and E. I. Shakhnovich. Folding mechanics
of a knotted protein. Journal of Molecular Biology 368, 884-893 (2007).
[ Full text at journal website ] [ Movie ] - 9. S. Wallin and H. S. Chan. Conformational entropic barriers in
topology-dependent protein folding: Perspectives from a simple native-centric
polymer model.
Journal of Physics: Condensed Matter 18, S307-S328 (2006).
[ Full text at journal website ] - 8. S. Wallin and H. S. Chan. A critical assessment of the topomer
search model of protein folding using a continuum explicit-chain model
with extensive conformational sampling. Protein Science 14, 1643--1660 (2005).
[ Full text at journal website ] - 7. G. Favrin, A. Irbäck and S. Wallin. Sequence-based study of
two related proteins with different folding behaviors.
Proteins: Structure, Function, and Bioinformatics 54, 8--12 (2004).
[ Full text at journal website ] - 6. A. Irbäck, B. Samuelsson, F. Sjunnesson and S. Wallin.
Thermodynamics of alpha- and beta-structure formation in proteins.
Biophysical Journal 85, 1466--1473 (2003).
[ Full text at journal website ] - 5. S. Wallin, J. Farwer and U. Bastolla. Testing similarity measures
with continuous and discrete protein models.
Proteins: Structure, Function, and Genetics 50, 144--157 (2003).
[ Full text at journal website ] - 4. G. Favrin, A. Irbäck, B. Samuelsson and S. Wallin. Two-state
folding over a weak free-energy barrier.
Biophysical Journal 85, 1457--1465 (2003).
[ Full text at journal website ] - 3. G. Favrin, A. Irbäck and S. Wallin. Folding of a small helical
protein using hydrogen bonds and hydrophobicity forces.
Proteins: Structure, Function, and Genetics 47, 99--105 (2002).
[ Full text at journal website ] - 2. A. Irbäck, F. Sjunnesson and S. Wallin. Hydrogen bonds,
hydrophobicity forces and the character of the collapse
transition. Proceedings of the ISI Workshop "Protein Folding: Simple Models and
Experiments", eds. P. Bruscolini et al.
Journal of Biological Physics 27, 169--179 (2001).
[ Full text at journal website ] - 1. A. Irbäck, F. Sjunnesson and S. Wallin.
Three-helix-bundle protein in a Ramachandran model.
Proceedings of the National Academy of Sciences USA 97, 13614--13618 (2000).
[ Full text at journal website ]