DNA, RNA, proteins, and small molecules. As most genetic regulatory networks of interest involve many components connected through interlocking positive and negative feedback loops, an intuitive understanding of their dynamics is hard to obtain. As a consequence, formal methods and computer tools

their interaction with multiple target proteins, they ensure coordinated control of other cellular activities such as gene transcription and adhesion. The story begins back in the early 1990s with the analysis of Rho, then a newly described member of the Ras superfamily of small guanosine triphosphatases (GTPases

annealing procedure rapidly and frequently generates native-like structures for small helical proteins and better than random structures for small b sheet containing proteins. Most of the simulated structures have native-like solvent accessibility and secondary structure patterns, and thus ensembles

Understanding how a protein folds is a long-standing challenge in modern science. We have used an optimized atomistic model (unitedresidue force field) to simulate folding of small proteins of various structures: HP-36 (a protein), protein A (h), 1fsd (a+h), and betanova (h). Extensive Monte Carlo

A key step in RNA interference (RNAi) is assembly of the RISC, the protein-siRNA complex that mediates target RNA cleavage. Here, we show that the two strands of an siRNA duplex are not equally eligible for assembly into RISC. Rather, both the absolute and relative stabilities of the base pairs

embryonic stem cells and fetal fibroblasts, along with comparative analysis of messenger RNA and small RNA components of the transcriptome, several histone modifications, and sites of DNA-protein interaction for several key regulatory factors. Widespread differences were identified in the composition

We have developed a fully flexible docking method that uses a reduced lattice representation of protein molecules, adapted for modeling peptide ligand — protein complexes. The CABS model (Carbon Alpha, Carbon Beta, Side Group) employed here was initially designed for single-chain protein folding

Identification of components present in biological complexes requires their purification to near homogeneity. Methods of purification vary from protein to protein, making it impossible to design a general purification strategy valid for all cases. We have devel-oped the tandem affinity purification

, proteins with their native fold can be distinguished by their Z-score. Second and somewhat surprising, all small proteins up to 100 residues in length have significant structure alignments to other proteins in a different secondary structure and fold class; i.e. 24.0 % of them have 60% coverage by a

which may be important, for example, for their binding properties or for their enzymatic activity are conserved in both structure and sequence. These structural requirements impose very tight constraints on the evolution of these small but important portion(s) of a protein sequence. The use of protein