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The interacting residues of protein and nucleic acid sequences are close to each other – they are co-located. Structure databases (like Protein Data Bank, PDB and Nucleic Acid Data Bank, NDB) contain all information about these co-locations; however it is not an easy task to penetrate this complex information. We developed a JAVA tool, called SeqX for this(More)
  • JC Biro
  • Theoretical Biology and Medical Modelling
  • 2005
Prediction of protein folding and specific interactions from only the sequence (ab initio) is a major challenge in bioinformatics. It is believed that such prediction will prove possible if Anfinsen's thermodynamic principle is correct for all kinds of proteins, and all the information necessary to form a concrete 3D structure is indeed present in the(More)
  • Jan C Biro
  • Theoretical Biology and Medical Modelling
  • 2007
The Proteomic Code is a set of rules by which information in genetic material is transferred into the physico-chemical properties of amino acids. It determines how individual amino acids interact with each other during folding and in specific protein-protein interactions. The Proteomic Code is part of the redundant Genetic Code. The 25-year-old history of(More)
A periodic table of codons has been designed where the codons are in regular locations. The table has four fields (16 places in each) one with each of the four nucleotides (A, U, G, C) in the central codon position. Thus, AAA (lysine), UUU (phenylalanine), GGG (glycine), and CCC (proline) were placed into the corners of the fields as the main codons (and(More)
  • Jan C Biro
  • Theoretical Biology and Medical Modelling
  • 2008
There is a 3-fold redundancy in the Genetic Code; most amino acids are encoded by more than one codon. These synonymous codons are not used equally; there is a Codon Usage Bias (CUB). This article will provide novel information about the origin and evolution of this bias. Codon Usage Bias (CUB, defined here as deviation from equal usage of synonymous(More)
The previous observation that hysterectomy of rats results in increased pituitary nucleic acid turnover was followed up by studies on pituitary function in hysterectomized adult female rats with or without treatment with charcoal-treated crude uterine aqueous extracts. Hysterectomy had no effect on the pituitary or plasma LH and FSH concentrations.(More)
  • Jan C Biro
  • Theoretical Biology and Medical Modelling
  • 2008
The secondary structure and complexity of mRNA influences its accessibility to regulatory molecules (proteins, micro-RNAs), its stability and its level of expression. The mobile elements of the RNA sequence, the wobble bases, are expected to regulate the formation of structures encompassing coding sequences. The sequence/folding energy (FE) relationship was(More)
  • Jan C Biro
  • Annals of the New York Academy of Sciences
  • 2006
Nucleic acid subsequences comprising the 1st and/or 3rd codon residues in mRNAs express significantly higher free folding energy (FFE) than the subsequence containing only the 2nd residues (P < 0.0001, n = 81). This periodic FFE difference is not present in introns. The FFE in the 1st and 3rd residues is additive, which suggests that these residues contain(More)
Plasma concentrations and anterior pituitary content of growth hormone (rGH), thyroid stimulating hormone (rTSH), and rat prolactin (rPrl) as well as the plasma concentrations of triiodothyronine (T3), thyroxine (T4) and somatomedin A (SM-A) have been determined in intact, castrated or hysterectomized adult rats with and without treatment with steroid-free,(More)
Plasma concentrations of GH, TSH, tri-iodothyronine (T3) and thyroxine (T4) were measured in adult rats 2 and 4 weeks after ovariectomy and and ovariohysterectomy. Two weeks after ovariohysterectomy, the concentration of GH was significantly higher, but TSH and T3 concentrations were significantly lower than in rats which had been ovariectomized only.(More)