ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures.

ProBiS-Database is a searchable repository of precalculated local structural alignments in proteins detected by the ProBiS algorithm in the Protein Data Bank. Identification of functionally important binding regions of the protein is facilitated by structural similarity scores mapped to the query protein structure. PDB structures that have been aligned with a query protein may be rapidly retrieved from the ProBiS-Database, which is thus able to generate hypotheses concerning the roles of uncharacterized proteins.

Binding-sites Prediction Assisting Protein-protein Docking.

Most biological actions of proteins, including their ability to interact with one another, involve some specific parts of their three-dimensional structure, called binding sites. These have evolved for their ability to bind other molecules effectively and are often conserved in different proteins. Identifying protein-protein binding sites in a protein that is known to interact with other proteins can provide important clues to the function of the protein and can also be used in protein-protein docking studies to reduce the search space explored by docking algorithms.

ENZO: a web tool for derivation and evaluation of kinetic models of enzyme catalyzed reactions.

We describe a web tool ENZO (Enzyme Kinetics), a graphical interface for building kinetic models of enzyme catalyzed reactions. ENZO automatically generates the corresponding differential equations from a stipulated enzyme reaction scheme. These differential equations are processed by a numerical solver and a regression algorithm which fits the coefficients of differential equations to experimentally observed time course curves.

New all-atom force field for molecular dynamics simulation of an AlPO(4)-34 molecular sieve.

A force field of the triclinic framework of AlPO(4)-34, important in methanol-hydrocarbon conversion reactions, was developed using an empirical potential function. Molecular dynamics simulation of an AlPO(4)-34 triclinic framework segment of 1216 atoms, containing the template molecules isopropylamine and water, was performed with explicit consideration of atomic charges. The average RMS difference between instantaneous positions of the framework atoms during 1 ns simulation and their positions in the structure determined from single crystal X-ray diffraction was calculated, and the average structure of the flexible framework was determined.