Identification of transcription factor binding sites (regulatory motifs) is a major interest in contemporary biology. We propose a new likelihood based method, COMODE, for identifying structural motifs in DNA sequences. Commonly used methods (e.g. MEME, Gibbs motif sampler) model binding sites as families of sequences described by a position weight matrix (PWM) and identify PWMs that maximize t...

Transcriptional networks are central to any biological process and changes affecting transcription factors or their binding sites in the genome are a key factor driving evolution. As more organisms are being sequenced, tools are needed to easily predict transcription factor binding sites (TFBS) presence and affinity from mere inspection of genomic sequences. Although many TFBS discovery algorit...

A sex steroid-binding protein (SBP) that binds to 17 b-estradiol with high affinity and moderate capacity was identified in the plasma of female and juvenile of kutum (Rutilus frisii kutum) sampled during the early stage of gonadal maturation in October and prior to spawning in March. Mean maximum specific binding (Bmax) and equilibrium dissociation constant (Kd) of the fish were as follows: In...

most of the biological phenomena are influenced by intermolecular recognition and interaction. thus, understanding the thermodynamics of biomacromolecule ligand interaction is a very interesting area in biochemistry and biotechnology. one of the most powerful techniques to obtain precise information about the energetics of (bio) molecules binding to other biological macromolecules is isothermal...

G protein-coupled receptors (GPCRs) are essential cell membrane signaling molecules and represent the most important class of drug targets. Some pathways downstream a GPCR may be responsible for adverse effects, while others mediate therapeutic efficacy. Biased ligands preferentially activate only subset all pathways. They hold great potential to become next-generation drugs with less side effe...

objective(s): as t-cell immunoglobulin and mucin domain 3 (tim-3) is an immune regulatory molecule; its blocking or stimulating could alter the pattern of immune response towards a desired condition. based on the unique features of nanobodies, we aimed to construct an anti-tim-3 nanobody as an appropriate tool for manipulating immune responses for future therapeutic purposes. materials and meth...

Calcium-binding proteins play essential roles in the cell. One important class of calcium-binding proteins is the annexin family. This is a family of 13 proteins, which binds to phospholipids in a calcium-dependent manner. Osteosarcoma cell line (MG-63) is a transformed cell that has many characteristics of the differentiated cell, such as a considerable serum dependency in its growth rate. Usi...