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3D structure prediction

The topology of transmembrane proteins can be predicted quite accurately from their amino acid sequences. Based on the results of the topology predictions we developed a method, called TMFoldWeb that aid the modeling of transmembrane domain structure. To achieve this, we used the predicted interactions between transmembrane helices and the differences in the folding of transmembrane regions of various transmembrane proteins (this is called „fold recognition”, or „threading”).

Related publications

  1. Dobson L, Szekeres LI, Gedán C, Langó T, Zeke A and Tusnády GE (2023) TmAlphaFold database: membrane localization and evaluation of AlphaFold2 predicted alpha-helical transmembrane protein structures Nucleic Acids Research , .
  2. Dobson L and Tusnády GE (2021) MemDis: Predicting Disordered Regions in Transmembrane Proteins Int. J. Mol. Sci. 22, 12270.
  3. Czimer D, Porok K, Csete D, Gyüre Zs, Lavró V, Fülöp K, Chen Z, Gyergyák H, Tusnády GE, Burgess SM, Mócsai A, Váradi A and Varga M (2021) A New Zebrafish Model for Pseudoxanthoma Elasticum Front Cell Dev Biol 9, 628699.
  4. Csizmadia, G, Farkas, B, Katona, E, Tusnády, GE and Hegedűs, T (2020) Using MemBlob to Analyze Transmembrane Regions Based on Cryo-EM Maps. Methods Mol Biol. 2112, 123-30.
  5. Farkas, B, Csizmadia, G, Katona, E, Tusnady, GE and Hegedűs, T (2020) MemBlob database and server for identifying transmembrane regions using cryo-EM maps Bioinformatics 36, 2595-98.
  6. Vargja, JK and Tusnady, GE (2019) The TMCrys server for supporting crystallization of transmembrane proteins. Bioinformatics 35, 4203-4.
  7. Varga J and Tusnady, GE (2018) TMCrys: predict propensity of success for transmembrane protein crystallization. Bioinformatics , .
  8. Varga J, Dobson L, Remenyi I and Tusnady GE (2017) TSTMP: target selection for structural genomics of human transmembrane proteins. Nucleic Acids Res 45, D325-330.
  9. Kozma D and Tusnady GE (2015) TMFoldWeb: a web server for predicting transmembrane protein fold class. Biol Direct 10, 54.
  10. Kozma D and Tusnady GE (2015) TMFoldRec: a statistical potential-based transmembrane protein fold recognition BMC Bioinformatics 16, 201.
  11. Kozma D, Simon I and Tusnady GE (2013) PDBTM: Protein Data Bank of transmembrane proteins after 8 years. Nucleic Acids Res 41, D524-9.
  12. Kozma D, Simon I and Tusnady GE (2012) CMWeb: an interactive on-line tool for analysing residue-residue contacts and Nucleic Acids Res 40, W329-33.
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