SAAP Force Field Technology Project

Overview of the project


In the post genomic research, such as peptide drug discovery, it is important to understand the structures, interactions, and dynamic motions of a polypeptide molecule at the atomic resolution. However, the conventional technologies used in this field are suffering a claim like, expertise knowledge on computer manipulation is required to start the molecular simulation. In addition, the speed of the simulation significantly relies on the performance of the hardware and the algorithm of the software. gIt would be fascinating if a new high-speed simulation methodology is devised for a use of experimental researchers who may not always be familiar with computer manipulation.h According to this motivation, we are developing a simulation program with high accuracy and high speed based on the single amino acid potential (SAAP) force field.


Although various programs have been developed for molecular simulation of peptide structures, there are still many points to be improved in this field. For example, thousands of explicit water molecules need to be placed around a peptide molecule in the molecular simulation in water. Handling of the program packages is not easy when the user does not have enough knowledge as to computer manipulation.

The SAAP force field is different from conventional ones in several points. The total energy is defined by using single amino acid units, not by using atom units. Solvent effects are implicitly included in the parameters (applying the polarized continuum model), rendering high-speed simulation feasible in water. The SAAP simulation program can be run on a personal computer. Simplicity of the force field equation is another feature of the SAAP force field.


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