Center of Excellence of the European Union
 
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Recent publications

Articles

1.   Szilágyi A, Nussinov R and Csermely P (2013) [23409766]
  Allo-Network Drugs: Extension of the Allosteric Drug Concept to Protein-Protein Interaction and Signaling Networks.
  Curr Top Med Chem notSet,
2.   Abrusán G, Szilágyi A, Zhang Y and Papp B (2013) [23341038]
  Turning gold into \'junk\': transposable elements utilize central proteins of cellular networks.
  Nucleic Acids Res 41, 3190-3200
3.   Szilágyi A, Zhang Y and Závodszky P (2012) [22079367]
  Intra-chain 3D segment swapping spawns the evolution of new multidomain protein architectures.
  J Mol Biol 415, 221-35
4.   Györffy D, Závodszky P and Szilágyi A (2012) [23221093]
  Pull moves for rectangular lattice polymer models are not fully reversible.
  Ieee Acm T Comput Bi 9, 1847-9
5.   Wu S, Szilagyi A and Zhang Y (2011) [21827953]
  Improving protein structure prediction using multiple sequence-based contact predictions.
  Structure 19, 1182-91
6.   Than NG, Romero R, Meiri H, Erez O, Xu Y, Tarquini F, Barna L, Szilagyi A, Ackerman R, Sammar M, Fule T, Karaszi K, Kovalszky I, Dong Z, Kim CJ, Zavodszky P, Papp Z and Gonen R (2011) [21799738]
  PP13, Maternal ABO Blood Groups and the Risk Assessment of Pregnancy Complications.
  PLoS ONE 6, e21564
7.   Nimrod G, Schushan M, Szilágyi A, Leslie C and Ben-Tal N (2010) [20089514]
  iDBPs: a web server for the identification of DNA binding proteins.
  Bioinformatics 26, 692-3
8.   Hajdú I, Szilágyi A, Kardos J and Závodszky P (2009) [19527660]
  A link between hinge-bending domain motions and the temperature dependence of catalysis in 3-isopropylmalate dehydrogenase.
  Biophys J 96, 5003-12
9.   Than NG, Romero R, Goodman M, Weckle A, Xing J, Dong Z, Xu Y, Tarquini F, Szilagyi A, Gal P, Hou Z, Tarca AL, Kim CJ, Kim JS, Haidarian S, Uddin M, Bohn H, Benirschke K, Santolaya-Forgas J, Grossman LI, Erez O, Hassan SS, Zavodszky P, Papp Z and Wildman DE (2009) [19497882]
  A primate subfamily of galectins expressed at the maternal-fetal interface that promote immune cell death.
  P Natl Acad Sci Usa 106, 9731-6
10.   Nimrod G, Szilágyi A, Leslie C and Ben-Tal N (2009) [19233205]
  Identification of DNA-binding proteins using structural, electrostatic and evolutionary features.
  J Mol Biol 387, 1040-53
11.   Szilágyi A (2008) [18338387]
  A mathematically related singularity and the maximum size of protein domains.
  Proteins 71, 2086-8; discussion 2
12.   Hajdú I, Bőthe C, Szilágyi A, Kardos J, Gál P and Závodszky P (2008) [18449535]
  Adjustment of conformational flexibility of glyceraldehyde-3-phosphate dehydrogenase as a means of thermal adaptation and allosteric regulation.
  Eur Biophys J Biophy 37, 1139-44
13.   Kamondi S, Szilágyi A, Barna L and Závodszky P (2008) [18667161]
  Engineering the thermostability of a TIM-barrel enzyme by rational family shuffling.
  Biochem Bioph Res Co 374, 725-30
14.   Szilágyi A, Györffy D and Závodszky P (2008) [18441033]
  The twilight zone between protein order and disorder.
  Biophys J 95, 1612-26
15.   Gráczer É, Varga A, Hajdú I, Melnik B, Szilágyi A, Semisotnov G, Závodszky P and Vas M (2007) [17887729]
  Rates of unfolding, rather than refolding, determine thermal stabilities of thermophilic, mesophilic, and psychrotrophic 3-isopropylmalate dehydrogenases.
  Biochemistry-us 46, 11536-49
16.   Szilágyi A and Skolnick J (2006) [16551468]
  Efficient prediction of nucleic acid binding function from low-resolution protein structures.
  J Mol Biol 358, 922-33
17.   Szilágyi A, Grimm V, Arakaki AK and Skolnick J (2005) [16204844]
  Prediction of physical protein-protein interactions.
  Phys Biol 2, S1-16
18.   Tompa P, Buzder-Lantos P, Tantos A, Farkas A, Szilágyi A, Bánóczi Z, Hudecz F and Friedrich P (2004) [14988399]
  On the sequential determinants of calpain cleavage.
  J Biol Chem 279, 20775-85
19.   Barna L, Bellyei S, Szigeti A, Boronkai Á, Szabó Z, Ohmacht R, Janáky T, Than NG, Szilágyi A, Závodszky P and Sümegi B (2003) [-100002802]
  Humán placenta protein: szerkezettől a funkcióig.
  Biokémia 27, 88-96
20.   Skolnick J, Zhang Y, Arakaki AK, Kolinski A, Boniecki M, Szilágyi A and Kihara D (2003) [14579335]
  TOUCHSTONE: a unified approach to protein structure prediction.
  Proteins 53 Suppl 6, 469-79
21.   Szilágyi A, Kovács KL, Rákhely G and Závodszky P (2002) [12032599]
  Homology modeling reveals the structural background of the striking difference in thermal stability between two related [NiFe]hydrogenases.
  J Mol Model 8, 58-64
22.   Németh A, Kamondi S, Szilágyi A, Magyar C, Kovári Z and Závodszky P (2002) [12034443]
  Increasing the thermal stability of cellulase C using rules learned from thermophilic proteins: a pilot study.
  Biophys Chem 96, 229-41
23.   Németh A, Svingor A, Pócsik M, Dobó J, Magyar C, Szilágyi A, Gál P and Závodszky P (2000) [10683439]
  Mirror image mutations reveal the significance of an intersubunit ion cluster in the stability of 3-isopropylmalate dehydrogenase.
  FEBS Lett 468, 48-52
24.   Szilágyi A and Závodszky P (2000) [10801491]
  Structural differences between mesophilic, moderately thermophilic and extremely thermophilic protein subunits: results of a comprehensive survey.
  Structure 8, 493-504
25.   Wallon G, Lovett ST, Magyar C, Svingor A, Szilagyi A, Závodszky P, Ringe D and Petsko GA (1997) [9278279]
  Sequence and homology model of 3-isopropylmalate dehydrogenase from the psychrotrophic bacterium Vibrio sp. I5 suggest reasons for thermal instability.
  Protein Eng 10, 665-72
26.   Magyar C, Szilágyi A and Závodszky P (1996) [8875643]
  Relationship between thermal stability and 3-D structure in a homology model of 3-isopropylmalate dehydrogenase from Escherichia coli.
  Protein Eng 9, 663-70
27.   Szilágyi A and Závodszky P (1995) [8637847]
  Structural basis for the extreme thermostability of D-glyceraldehyde-3-phosphate dehydrogenase from Thermotoga maritima: analysis based on homology modelling.
  Protein Eng 8, 779-89

Books or book chapters

1.   Kucukural A, Szilágyi A, Sezerman O and Zhang Y (2010)
  Protein homology analysis for function prediction with parallel sub-graph isomorphism
  Chemoinformatics and Advanced Machine Learning Perspectives: Complex Computational Methods and Collaborative Techniques , 129-144
2.   Mukherjee S, Szilágyi A, Roy A and Zhang Y (2010)
  Genome-wide protein structure prediction
  Multiscale approaches to protein modeling: structure prediction, dynamics, thermodynamics and macromolecular assemblies , 255-280
3.   Szilagyi A, Kardos J, Osvath Sz, Barna L and Zavodszky P (2007)
  Protein folding
  Handbook of Neurochemistry and Molecular Neurobiology 7, Chapter 10