Biopolymer Object Oriented Library (Biopool)
The Biopool class implementation follows the composite design pattern and for a complete description of the class hierarchy we recommend to see the [Doxygen documentation]. Without going into implementation details a Protein object is just a container for vectors representing chains. Each vector has 2 elements: the Spacer and the Ligand Set. The Spacer is the container for AminoAcid objects whereas the LigandSet is a container for all other molecules and ions, including DNA/RNA chains. Ultimately all molecules, both in the Spacer and in the LigandSet are collections of Atom objects. The main feature in Biopool is that each AminoAcid object in the Spacer is connected to its neighbours by means of one rotational vector plus one translational vector.
This implementation make easy the modification of the protein structure and lot of functions were implemented to modify/perturbate/transformate the residue relative position in an efficient way, rotation and Translation vectors.
LOop Build-up and Optimization (Lobo)
Energy functions implementation
Energy functions are used in a variety of roles in protein modeling. An energy function precise enough to always discriminate the native protein structure from all possible decoys would not only simplify the protein structure prediction problem considerably. It would also increase our understanding of the protein folding process itself. If feasible, one would like to use quantum mechanical models, being the most detailed representation, to calculate the energy of a protein. It can theoretically be done by solving the Schrödinger equation. This equation can be solved exactly for the hydrogen atom, but is no longer trivial for three or more particles. In recent years it has become possible to approximately solve the Schrödinger equation for systems up to hundred atoms with the Hartree-Fock or self-consistent field approximations. Their main idea is that the many-body interactions are reduced to several two-body interactions.
Energy functions are important to all aspects of protein structure prediction, as they give a measure of confidence for optimization. An ideal energy function would also explain the process of protein folding. The most detailed way to calculate energies are quantum mechanical methods. These are, to date, still overly time consuming and impractical. Two alternative classes of functions have been developed: force fields and knowledge-based potentials.
Force fields (e.g. AMBER ) are empirical models approximating the energy of a protein with bonded and non-bonded interactions, attempting to describe all contributions to the total energy. They tend to be very detailed and are prone to yield many erroneous local minima. An alternative are knowledge-based potentials (e.g. ), where the “energy” is derived from the probability of a structure being similar to interaction patterns found in the database of known structures. This approach is very popular for fold recognition, as it produces a smoother “global” energy surface, allowing the detection of a general trend. Abstraction levels for knowledge-based potentials vary greatly, and several functional forms have been proposed.
iNDLUDE PAGE 102
The energy functions presented in the package allows us to optimize procedures. The main feature is its applicability in the context of the protein classes implemented in the package. It should be possible to invoke the energy calculation with any structure from all programs. At the same time the parameters of the energy models had to be stored externally to allow their rapid modification. With this considerations in mind, the package Energy was designed to collect the classes and programs dealing with energy calculation. The main design decision was to use the “strategy” design pattern from Gamma et al. The abstract class Potential was defined to provide a common interface for energy calculation. It contains the necessary methods to load the energy parameters during initialization of an object. Computing the energy value for objects of the Atom and Spacer classes as well as a combination of both is allowed.