Protein integration level
Proteins are key elements of gene networks. Due to their unique 3-dimensional structure they maintain gene expression regulation, biosynthesis, degradation of molecular components of organisms etc. Possessing information on 3-dimensional structure of proteins and on machinery of their interaction with DNA and RNA is necessary for solving a wide range of tasks in pharmacology, gene and protein engineering, biotechnology, artificial synthesis of molecular-genetic systems. For solving the tasks connected with the protein level of organization and functioning of gene networks the module "Protein Integration Level" is developed within the system GeneNetWorks.
The present version of "Protein Integration Level" comprises:
- search system for query implementation to the PDB (Protein Data Bank).
- a database on protein active sites and their spatial environment.
(Artificial Selected Peptides/Proteins Database) - a curated database on proteins and peptides selected by in vitro directed evolution methods (phage display, ribosome display, SIP etc.) from randomized pools.
- program package for revealing and analysis of co-adaptive amino acid substitutions in pairs of positions based on multiple sequence alignment in families of related proteins.
- a Tool for Search for Functional Sites in Protein Tertiary Structures.
- system generating C-codes for recognition of a given pattern in amino acid sequence.
- database on local conformations of protein chains ("conformons").
- database on structural and physico-chemical information on amino acid residue coordination spheres in protein 3D structures.