Computational lab.

Facility manager: Dr. Imre Jákli

Members: Dr. Imre Jákli, Dr. Dóra K. Menyhárd , Dr. Gábor Náray-Szabó, Ádám Kelemen

From bioinformatics to database mining and form molecular modelling to applied quantum chemistry our techniques in use cover a wide range of methodology. We are conducting conformational analysis, spectral property calculations (e.g. IR, NMR), energy distribution and potential energy calculations of alpha- and beta-amino acid residues, peptides and proteins. Depending on their size ab initio or MM and MD methods are routinely used. In addition, we parameterize force fields, design new algorithms or even make a standalone software (e.g. CCA+) depending on the scientific topic to be solved.

Laboratory News

  • Long, longer, perhaps the longest helix and sheet by QM

    We are pleased to inform you that our most recent manuscript entitled “Helix compactness and stability: electron structure calculations of conformer dependent thermodynamic functions” Jákli et al. is now accepted for publication in Chemical Physics Letters. Congratulations to all contributors!


  • Pohl G , Jákli I , Csizmadia IG , Papp D , Matías GF , Perczel A
    The role of entropy in initializing the aggregation of peptides: A first principle study on oligopeptide oligomerization
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS 14:(4) pp. 1507-1516. (2012) Kivonat
  • Pohl G , Beke-Somfai T , Csizmadia IG , Perczel A
    Exploiting diverse stereochemistry of b-amino acids: Toward a rational design of sheet-forming b-peptide systems
    AMINO ACIDS 43:(2) pp. 735-749. (2012) Kivonat
  • Dániel Süveges , Zoltán Gáspári , Gábor Tóth , László Nyitray
    Charged single α-helix: a versatile protein structural motif
    Proteins 74:905-916. (2009) Kivonat
  • Jákli I , Knak Jensen SJ , Csizmadia IG , Perczel A
    Variation of conformational properties at a glance. True graphical visualization of the Ramachandran surface topology as a periodic potential energy surface
    CHEMICAL PHYSICS LETTERS 547: pp. 82-88. (2012) Kivonat
  • Westler WM , Lin IJ , Perczel A , Weinhold F , Markley JL
    Hyperfine-Shifted (13)C Resonance Assignments in an Iron-Sulfur Protein with Quantum Chemical Verification: Aliphatic C-H center dot center dot center dot S 3-Center-4-Electron Interactions
    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 133:(5) pp. 1310-1316. (2011)