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Can correct protein models be identified?
Wallner B, Elofsson A. Wallner B, et al. Among authors: elofsson a. Protein Sci. 2003 May;12(5):1073-86. doi: 10.1110/ps.0236803. Protein Sci. 2003. PMID: 12717029 Free PMC article.
These correct models are defined by the existence of a fragment that shows significant similarity between this model and the native structure. ...We have developed ProQ, a neural-network-based method to predict the quality of a protein model that extracts str …
These correct models are defined by the existence of a fragment that shows significant similarity between this model and the native s …
An intrinsically disordered proteins community for ELIXIR.
Davey NE, Babu MM, Blackledge M, Bridge A, Capella-Gutierrez S, Dosztanyi Z, Drysdale R, Edwards RJ, Elofsson A, Felli IC, Gibson TJ, Gutmanas A, Hancock JM, Harrow J, Higgins D, Jeffries CM, Le Mercier P, Mészáros B, Necci M, Notredame C, Orchard S, Ouzounis CA, Pancsa R, Papaleo E, Pierattelli R, Piovesan D, Promponas VJ, Ruch P, Rustici G, Romero P, Sarntivijai S, Saunders G, Schuler B, Sharan M, Shields DC, Sussman JL, Tedds JA, Tompa P, Turewicz M, Vondrasek J, Vranken WF, Wallace BA, Wichapong K, Tosatto SCE. Davey NE, et al. Among authors: elofsson a. F1000Res. 2019 Oct 15;8:ELIXIR-1753. doi: 10.12688/f1000research.20136.1. eCollection 2019. F1000Res. 2019. PMID: 31824649 Free PMC article.
A New Census of Protein Tandem Repeats and Their Relationship with Intrinsic Disorder.
Delucchi M, Schaper E, Sachenkova O, Elofsson A, Anisimova M. Delucchi M, et al. Among authors: elofsson a. Genes (Basel). 2020 Apr 9;11(4):407. doi: 10.3390/genes11040407. Genes (Basel). 2020. PMID: 32283633 Free PMC article.
How consistent are molecular dynamics simulations? Comparing structure and dynamics in reduced and oxidized Escherichia coli thioredoxin.
Elofsson A, Nilsson L. Elofsson A, et al. J Mol Biol. 1993 Oct 20;233(4):766-80. doi: 10.1006/jmbi.1993.1551. J Mol Biol. 1993. PMID: 8411178
It is shown that although vacuum simulations may reproduce some parameters, all the features of a water simulation cannot be reproduced in any of these simulations. ...It is also shown that 100 ps is too short a time to obtain statistically certain temperature facto …
It is shown that although vacuum simulations may reproduce some parameters, all the features of a water simulation cannot be reproduc …
Architecture of helix bundle membrane proteins: an analysis of cytochrome c oxidase from bovine mitochondria.
Wallin E, Tsukihara T, Yoshikawa S, von Heijne G, Elofsson A. Wallin E, et al. Among authors: elofsson a. Protein Sci. 1997 Apr;6(4):808-15. doi: 10.1002/pro.5560060407. Protein Sci. 1997. PMID: 9098890 Free PMC article.
Our results lead to a considerably more precise general picture of membrane protein architecture than has hitherto been possible to obtain....
Our results lead to a considerably more precise general picture of membrane protein architecture than has hitherto been possible to o …
Helix-helix packing in a membrane-like environment.
Mingarro I, Elofsson A, von Heijne G. Mingarro I, et al. Among authors: elofsson a. J Mol Biol. 1997 Oct 3;272(4):633-41. doi: 10.1006/jmbi.1997.1276. J Mol Biol. 1997. PMID: 9325117
The unique ability of the glycophorin A transmembrane helix to dimerize in SDS has previously been exploited in studies of the sequence specificity of helix-helix packing in a micellar environment. Here, we have made different insertion mutants in the critical helix …
The unique ability of the glycophorin A transmembrane helix to dimerize in SDS has previously been exploited in studies of the sequen …
Architecture of beta-barrel membrane proteins: analysis of trimeric porins.
Seshadri K, Garemyr R, Wallin E, von Heijne G, Elofsson A. Seshadri K, et al. Among authors: elofsson a. Protein Sci. 1998 Sep;7(9):2026-32. doi: 10.1002/pro.5560070919. Protein Sci. 1998. PMID: 9761484 Free PMC article.
The distribution of surface-exposed residues in a direction perpendicular to the membrane is similar to that in helical membrane proteins, with aliphatic residues concentrated in the central 20 A of the bilayer. ...By comparing the interface and noninterface residue …
The distribution of surface-exposed residues in a direction perpendicular to the membrane is similar to that in helical membrane prot …
Interaction of mitochondrial presequences with DnaK and mitochondrial hsp70.
Zhang XP, Elofsson A, Andreu D, Glaser E. Zhang XP, et al. Among authors: elofsson a. J Mol Biol. 1999 Apr 23;288(1):177-90. doi: 10.1006/jmbi.1999.2669. J Mol Biol. 1999. PMID: 10329135
Mitochondrial heat shock protein 70 (mt-hsp70) functions as a molecular chaperone in mitochondrial biogenesis. The chaperone in co-operation with its co-proteins acts as a translocation motor pulling the mitochondrial precursor into the matrix. ...Here we have used …
Mitochondrial heat shock protein 70 (mt-hsp70) functions as a molecular chaperone in mitochondrial biogenesis. The chaperone in co-op …
Hidden Markov models that use predicted secondary structures for fold recognition.
Hargbo J, Elofsson A. Hargbo J, et al. Among authors: elofsson a. Proteins. 1999 Jul 1;36(1):68-76. Proteins. 1999. PMID: 10373007
To test the performance of different fold recognition methods, we have developed a rigorous benchmark where representatives for all proteins of known structure are matched against each other. ...Further, we combine the use of predicted secondary structures and multiple seq …
To test the performance of different fold recognition methods, we have developed a rigorous benchmark where representatives for all p …
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