MOLDA for Protein Modeling: A Molecular Modeling Program for Biological Molecules

Hiroshi YOSHIDA

Center for Quantum Life Sciences and
Department of Chemistry, Graduate School of Science
Hiroshima University, Kagamiyama 1-chome, Higashi-Hiroshima 739-8526, Japan

(Received: July 22, 2003; Accepted for publication: August 28, 2003; Published on Web: November 27, 2003)

A molecular modeling program for biological molecules has been developed as a 3D data-interaction tool for computational chemistry and structural bioinformatics. This program named MOLDA for Protein Modeling is written in the Java language and works multiplatform environment. MOLDA for Protein Modeling has been implemented with various functions useful for studying biological molecules by structural bioinformatics. The functions are as follows: (1) the importing function of the PDB file is implemented, (2) 3D structure of polypeptides can be generated by inputting the sequences, (3) the conformation of the polypeptide can be changed by reading the dihedral angle matrix, and (4) an amino acid residue can be changed by the point mutation operation. MOLDA for Protein Modeling is expected to be a useful tool for drug design.

Keywords: Molecular modeling, Protein modeling, Protein Data Bank, Point mutation, Bioinformatics


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