| Research Abstract |
1. Development of FEDER/2, a program for conformational analysis of proteins.
(1) Improvement of algorithm and data structures of FEDER to treat any molecules in a tree structure,
(2) addition of the function to calculate hydration energy with hydration-shell model to simulate a protein molecule in solution, besides in vacuo,
(3) improvement of the methods to escape from local minimam with larger values ; e. g., variable objective function method, simulated annealing method, Monte Carlo method and linearized embedding method, and
(4) improvement of the program to simulate a multi-chain system.
2. Analysis of protein conformation.
(1) Study on dynamical domain structures by the normal mode analysis,
(2) comparative study on the simulations in vacuo and in solution,
(3) study on multi-conformation by using NMR data for oxytocin in solution,
(4) study on higher-order structures of proteins predicted by the empirically determined distances between amino acid residues, and
(5) study on minimizing method, with respect to reasonable initial conformation and efficiency of conformational energy calculation.
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